UpdateSNPPositionQualityPlugin error
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Debora Santo
Dec 14, 2015, 9:29:31 AM12/14/15
to TASSEL - Trait Analysis by Association, Evolution and Linkage
Hello!
I am getting an error when running the UpdateSNPPositionQualityPlugin. I am using TASSEL V5.2.17 on a cluster, so I am getting two resulting log files, one with errors and other with the plugin output. The error only appears in the error file, the output file doesn't show that anything has went wrong, although it usually does. I have also run this with -debug on. Below is what is contained in all three log/output files. If further information is needed, I can provide it in response. Also, is this step necessary for the proper use of the later plugins? Because I have tried to skip updating the SNP quality and have ended up having a non-functional h5 file in the end, although all the log files show no problems, as much as I've seen.
Thank you for your help in advance!
The text of the error is this (it is repeated over a thousand times, so I will not copy the whole error log file):
Error in SNP Position QualityScore file format:/home/facon/GBS_PVd_unified_analysis/SNPqualityStatsUniAn.txt
Expecting tab-delimited file with 2 integer and 1 float value per row with header values CHROM POS QUALITYSCORE
The plugin output log file is the following:
/home/bin/Tassel/5.2.14/x64/lib/cisd-jhdf5-batteries_included_lin_win_mac.jar:/home/bin/Tassel/5.2.14/x64/lib/jcommon-1.0.6.jar:/home/bin/Tassel/5.2.14/x64/lib/itextpdf-5.1.0.jar:/home/bin/Tassel/5.2.14/x64/lib/batik-xml.jar:/home/bin/Tassel/5.2.14/x64/lib/batik-awt-util.jar:/home/bin/Tassel/5.2.14/x64/lib/trove-3.0.3.jar:/home/bin/Tassel/5.2.14/x64/lib/batik-dom.jar:/home/bin/Tassel/5.2.14/x64/lib/biojava-core-4.0.0.jar:/home/bin/Tassel/5.2.14/x64/lib/batik-gui-util.jar:/home/bin/Tassel/5.2.14/x64/lib/biojava-phylo-4.0.0.jar:/home/bin/Tassel/5.2.14/x64/lib/javax.json-1.0.4.jar:/home/bin/Tassel/5.2.14/x64/lib/postgresql-9.4-1201.jdbc41.jar:/home/bin/Tassel/5.2.14/x64/lib/batik-css.jar:/home/bin/Tassel/5.2.14/x64/lib/jfreechart-1.0.3.jar:/home/bin/Tassel/5.2.14/x64/lib/log4j-1.2.13.jar:/home/bin/Tassel/5.2.14/x64/lib/sqlite-jdbc-3.8.5-pre1.jar:/home/bin/Tassel/5.2.14/x64/lib/commons-math3-3.4.1.jar:/home/bin/Tassel/5.2.14/x64/lib/colt.jar:/home/bin/Tassel/5.2.14/x64/lib/poi-3.0.1-FINAL-20070705.jar:/home/bin/Tassel/5.2.14/x64/lib/biojava-alignment-4.0.0.jar:/home/bin/Tassel/5.2.14/x64/lib/json-simple-1.1.1.jar:/home/bin/Tassel/5.2.14/x64/lib/batik-ext.jar:/home/bin/Tassel/5.2.14/x64/lib/forester.jar:/home/bin/Tassel/5.2.14/x64/lib/slf4j-simple-1.7.10.jar:/home/bin/Tassel/5.2.14/x64/lib/commons-codec-1.10.jar:/home/bin/Tassel/5.2.14/x64/lib/xmlParserAPIs.jar:/home/bin/Tassel/5.2.14/x64/lib/batik-parser.jar:/home/bin/Tassel/5.2.14/x64/lib/batik-svg-dom.jar:/home/bin/Tassel/5.2.14/x64/lib/slf4j-api-1.7.10.jar:/home/bin/Tassel/5.2.14/x64/lib/batik-util.jar:/home/bin/Tassel/5.2.14/x64/lib/snappy-java-1.1.1.6.jar:/home/bin/Tassel/5.2.14/x64/lib/geronimo-spec-activation-1.0.2-rc4.jar:/home/bin/Tassel/5.2.14/x64/lib/batik-gvt.jar:/home/bin/Tassel/5.2.14/x64/lib/ejml-0.23.jar:/home/bin/Tassel/5.2.14/x64/lib/mail-1.4.jar:/home/bin/Tassel/5.2.14/x64/lib/xml.jar:/home/bin/Tassel/5.2.14/x64/lib/guava-14.0.1.jar:/home/bin/Tassel/5.2.14/x64/lib/junit-4.10.jar:/home/bin/Tassel/5.2.14/x64/lib/xercesImpl.jar:/home/bin/Tassel/5.2.14/x64/lib/batik-svggen.jar:/home/bin/Tassel/5.2.14/x64/sTASSEL.jar
Memory Settings: -Xms512m -Xmx15G
Tassel Pipeline Arguments: -fork1 -UpdateSNPPositionQualityPlugin -db ./GBSPVDunified.db -qsFile SNPqualityStatsUniAn.txt -endplugin -runfork1
[main] INFO net.maizegenetics.tassel.TasselLogging - Tassel Version: 5.2.14 Date: August 27, 2015
[main] INFO net.maizegenetics.tassel.TasselLogging - Max Available Memory Reported by JVM: 13653 MB
[main] INFO net.maizegenetics.tassel.TasselLogging - Java Version: 1.8.0_45
[main] INFO net.maizegenetics.tassel.TasselLogging - OS: Linux
[main] INFO net.maizegenetics.pipeline.TasselPipeline - Tassel Pipeline Arguments: [-fork1, -UpdateSNPPositionQualityPlugin, -db, ./GBSPVDunified.db, -qsFile, SNPqualityStatsUniAn.txt, -endplugin, -runfork1]
net.maizegenetics.analysis.gbs.v2.UpdateSNPPositionQualityPlugin
[pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin - Starting net.maizegenetics.analysis.gbs.v2.UpdateSNPPositionQualityPlugin: time: Dec 14, 2015 13:55:31
[pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin -
UpdateSNPPositionQualityPlugin Parameters
db: ./GBSPVDunified.db
qsFile: SNPqualityStatsUniAn.txt
size of all tags in tag table=561393
size of all tags in mappingApproach table=2
size of all taxa in taxa table=297
updateSNPPosition next 100001
updateSNPPosition next 100001
size of all positions in snpPosition table=283515
Closing SQLDB
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.UpdateSNPPositionQualityPlugin - UupdateSNPPositionQualityPlugin: Finished writing quality scores file to snpposition table.
[pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin - Finished net.maizegenetics.analysis.gbs.v2.UpdateSNPPositionQualityPlugin: time: Dec 14, 2015 13:55:55
[pool-1-thread-1] INFO net.maizegenetics.pipeline.TasselPipeline - net.maizegenetics.analysis.gbs.v2.UpdateSNPPositionQualityPlugin: time: Dec 14, 2015 13:55:55: progress: 100%
[pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin - net.maizegenetics.analysis.gbs.v2.UpdateSNPPositionQualityPlugin Citation: Bradbury PJ, Zhang Z, Kroon DE, Casstevens TM, Ramdoss Y, Buckler ES. (2007) TASSEL: Software for association mapping of complex traits in diverse samples. Bioinformatics 23:2633-2635.
(END)
The debug file contains the following:
[main] INFO net.maizegenetics.tassel.TasselLogging - Tassel Version: 5.2.14 Date: August 27, 2015
[main] INFO net.maizegenetics.tassel.TasselLogging - Max Available Memory Reported by JVM: 13653 MB
[main] INFO net.maizegenetics.tassel.TasselLogging - Java Version: 1.8.0_45
[main] INFO net.maizegenetics.tassel.TasselLogging - OS: Linux
[main] INFO net.maizegenetics.pipeline.TasselPipeline - Tassel Pipeline Arguments: [-fork1, -UpdateSNPPositionQualityPlugin, -db, ./GBSPVDunified.db, -q
sFile, SNPqualityStatsUniAn.txt, -endplugin, -runfork1]
net.maizegenetics.analysis.gbs.v2.UpdateSNPPositionQualityPlugin
[pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin - Starting net.maizegenetics.analysis.gbs.v2.UpdateSNPPositionQualityPlugin: time: Dec
9, 2015 10:35:36
[pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin -
UpdateSNPPositionQualityPlugin Parameters
db: ./GBSPVDunified.db
qsFile: SNPqualityStatsUniAn.txt
Error in SNP Position QualityScore file format:/home/facon/GBS_PVd_unified_analysis/SNPqualityStatsUniAn.txt
Expecting tab-delimited file with 2 integer and 1 float value per row with header values CHROM POS QUALITYSCORE
(THE LAST TWO LINES ARE THEN JUST REPEATED MANY TIMES)
Debora Santo
Dec 17, 2015, 5:17:52 PM12/17/15
to TASSEL - Trait Analysis by Association, Evolution and Linkage
Hi!
I run the same sequence reads using TASSEL v5.2.18 and got the same error again (no errors before, everything looks fine, but then the SNP quality cannot be updated, and it looks like the stat file from the previous step is not ok). Did anyone else have the same problem or can solve it?
Thank you!
Debora
Lynn Carol Johnson
Dec 18, 2015, 7:06:20 AM12/18/15
to tas...@googlegroups.com
Hi Debora -
The software that reads the quality score file parses each input line, expecting there to be exactly 3 values that are tab-delimited (not comma or space delimited). If extraneous tabs are found the error below is printed. Can you verify there are exactly
3 values on each line of the file, that they are tab-delimited and that there are no extra tabs at the end of each line?
Thanks - Lynn
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Debora Santo
Dec 18, 2015, 1:04:19 PM12/18/15
to TASSEL - Trait Analysis by Association, Evolution and Linkage
Dear Lynn,
I see that the file I used was inadequate. Is there a standard procedure for acquiring/calculating the quality scores of SNP positions based on the stat file from the SNPQualityProfilerPlugin that the other users are applying?
Sincerely,
Debora
Lynn Carol Johnson
Dec 18, 2015, 1:24:21 PM12/18/15
to tas...@googlegroups.com
HI Debora -
I don’t know how other users calculate their quality scores. I presume each user has specifications unique to their own research. I am a computer programmer, not a biologist, so am afraid I can’t provide much guidance.
Perhaps some of the tassel users will respond with suggestions.
Thanks - Lynn
To view this discussion on the web visit
https://groups.google.com/d/msgid/tassel/69a70c29-2a73-487b-9a50-b0954bbcf41d%40googlegroups.com.
Debora Santo
Dec 18, 2015, 3:02:20 PM12/18/15
to TASSEL - Trait Analysis by Association, Evolution and Linkage
Dear Lynn,
Thanks for the feedback in any case. If I understood right, the step of importing the SNP position quality information into the database can be skipped in case no filtering based upon it is needed while running the ProductionSNPCallerPluginV2. That is what I did and proceeded to the Production Pipeline.
When running the ProductionSNPCallerPluginV2 I set the -ko to true, since in previous analyses the run would be terminated before the end if the -ko option was set to false (I am still not sure why). However, when running the BuildUnfinishedHDF5GenotypesPlugin to close the h5 file, I got an error. The debug files for those two plugins I attached below. Could you (or anyone else) help me understand what is the cause for the error?
BuildUnfinishedHDF5GenotypesPlugin DEBUG FILE
[main] INFO net.maizegenetics.tassel.TasselLogging - Tassel Version: 5.2.18 Date: December 10, 2015
[main] INFO net.maizegenetics.tassel.TasselLogging - Max Available Memory Reported by JVM: 9102 MB
[main] INFO net.maizegenetics.tassel.TasselLogging - Java Version: 1.8.0_45
[main] INFO net.maizegenetics.tassel.TasselLogging - OS: Linux
[main] INFO net.maizegenetics.tassel.TasselLogging - Number of Processors: 16
[main] INFO net.maizegenetics.pipeline.TasselPipeline - Tassel Pipeline Arguments: [-fork1, -BuildUnfinishedHDF5GenotypesPlugin, -i, ./GBSPVdUnifiedResultsOpen.h5, -o, ./GBSPVdUnifiedResultsClosed.h5, -endplugin, -runfork1]
net.maizegenetics.analysis.data.BuildUnfinishedHDF5GenotypesPlugin
[pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin - Starting net.maizegenetics.analysis.data.BuildUnfinishedHDF5GenotypesPlugin: time: Dec 18, 2015 20:35:30
[pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin -
BuildUnfinishedHDF5GenotypesPlugin Parameters
i: ./GBSPVdUnifiedResultsOpen.h5
o: ./GBSPVdUnifiedResultsClosed.h5
name: null
desc: null
[pool-1-thread-1] INFO net.maizegenetics.analysis.data.BuildUnfinishedHDF5GenotypesPlugin -
BuildUnfinishedHDF5GenotypesPlugin: Copying the HDF5 genotypes from the file:
./GBSPVdUnifiedResultsOpen.h5
and finalizing them in this output file:
./GBSPVdUnifiedResultsClosed.h5
Number of taxa in HDF5 file:106
[pool-1-thread-1] ERROR net.maizegenetics.plugindef.AbstractPlugin - null
[pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin -
Usage:
BuildUnfinishedHDF5GenotypesPlugin <options>
-i <Input file> : Input, unfinished HDF5 genotype (*.h5) file to be fininalized (required)
-o <Output file> : Output, finished HDF5 genotype (*.h5) file which can be opened with the TASSEL5 GUI. __DATE__ is replaced with a _yyyyMMdd date stamp.
-name <Data set name> : (Optional) Short data set name to be added as an root level annotation under "dataSetName"
-desc <Data set description> : (Optional) Short data set description to be added as an root level annotation under "dataSetDescription"
[pool-1-thread-1] DEBUG net.maizegenetics.plugindef.AbstractPlugin - null
java.lang.NullPointerException
at net.maizegenetics.taxa.TaxaArrayList.<init>(TaxaArrayList.java:33)
at net.maizegenetics.taxa.TaxaListBuilder.build(TaxaListBuilder.java:116)
at net.maizegenetics.taxa.TaxaListBuilder.buildFromHDF5(TaxaListBuilder.java:149)
at net.maizegenetics.dna.snp.depth.HDF5AlleleDepth.<init>(HDF5AlleleDepth.java:39)
at net.maizegenetics.dna.snp.depth.AlleleDepthBuilder.getExistingHDF5Instance(AlleleDepthBuilder.java:90)
at net.maizegenetics.dna.snp.GenotypeTableBuilder.getInstance(GenotypeTableBuilder.java:449)
at net.maizegenetics.dna.snp.GenotypeTableBuilder.build(GenotypeTableBuilder.java:661)
at net.maizegenetics.analysis.data.BuildUnfinishedHDF5GenotypesPlugin.buildUnfinishedHDF5Genotypes(BuildUnfinishedHDF5GenotypesPlugin.java:119)
at net.maizegenetics.analysis.data.BuildUnfinishedHDF5GenotypesPlugin.processData(BuildUnfinishedHDF5GenotypesPlugin.java:80)
at net.maizegenetics.plugindef.AbstractPlugin.performFunction(AbstractPlugin.java:110)
at net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:1631)
at net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
**********************************
ProductionSNPCallerPluginV2 DEBUG FILE
[main] INFO net.maizegenetics.tassel.TasselLogging - Tassel Version: 5.2.18 Date: December 10, 2015
[main] INFO net.maizegenetics.tassel.TasselLogging - Max Available Memory Reported by JVM: 13653 MB
[main] INFO net.maizegenetics.tassel.TasselLogging - Java Version: 1.8.0_45
[main] INFO net.maizegenetics.tassel.TasselLogging - OS: Linux
[main] INFO net.maizegenetics.tassel.TasselLogging - Number of Processors: 16
[main] INFO net.maizegenetics.pipeline.TasselPipeline - Tassel Pipeline Arguments: [-fork1, -ProductionSNPCallerPluginV2, -batchSize, 8, -d, 0, -db, ./GBSPVDunified.db, -e, ApeKI, -eR, 0.01, -i, ./AllFastqFiles/, -k, ./GBS_PVd_unified_keyfile.txt, -ko, true, -kmerLength, 126, -minPosQS, 0, -mnQS, 20, -do, true, -o, GBSPVdUnifiedResultsOpen.h5, -endplugin, -runfork1]
net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2
[pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin - Starting net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2: time: Dec 18, 2015 19:31:45
Enzyme: ApeKI
[pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin -
ProductionSNPCallerPluginV2 Parameters
i: ./AllFastqFiles/
k: ./GBS_PVd_unified_keyfile.txt
e: ApeKI
db: ./GBSPVDunified.db
o: GBSPVdUnifiedResultsOpen.h5
eR: 0.01
d: 0
ko: true
do: true
kmerLength: 126
minPosQS: 0.0
batchSize: 8
mnQS: 20
size of all tags in tag table=600431
size of all tissues in tissue table=0
size of all tags in mappingApproach table=2
size of all taxa in taxa table=297
ProductionSNPCallerPluginV2: Total batches to process: 4
size of all positions in snpPosition table=207913
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 -
The target HDF5 file:
GBSPVdUnifiedResultsOpen.h5
does not exist. A new HDF5 file of that name will be created
to hold the genotypes from this run.
size of all positions in snpPosition table=207913
size of all alleles in allele table=448635
Start processing batch 1
Enzyme: ApeKI
Enzyme: ApeKI
Enzyme: ApeKI
Enzyme: ApeKI
Enzyme: ApeKI
Enzyme: ApeKI
Enzyme: ApeKI
Enzyme: ApeKI
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.GBSUtils - /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol007-1-CAGATC_L008-R1_fastq.fastq: Quality score base:33
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.GBSUtils - /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol2-1-CGATGT_L008-R1_fastq.fastq: Quality score base:33
[ForkJoinPool.commonPool-worker-4] INFO net.maizegenetics.analysis.gbs.v2.GBSUtils - /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol013-1-AGTCAA_L008-R1_fastq.fastq: Quality score base:33
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.GBSUtils - /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol6-1-GCCAAT_L008-R2_fastq.fastq: Quality score base:33
[ForkJoinPool.commonPool-worker-2] INFO net.maizegenetics.analysis.gbs.v2.GBSUtils - /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol1-1-ATCACG_L008-R1_fastq.fastq: Quality score base:33
[ForkJoinPool.commonPool-worker-13] INFO net.maizegenetics.analysis.gbs.v2.GBSUtils - /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol011-1-GGCTAC_L008-R1_fastq.fastq: Quality score base:33
[ForkJoinPool.commonPool-worker-6] INFO net.maizegenetics.analysis.gbs.v2.GBSUtils - /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol008-1-ACTTGA_L008-R1_fastq.fastq: Quality score base:33
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.GBSUtils - /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol5-1-ACAGTG_L008-R2_fastq.fastq: Quality score base:33
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:1000000 Reads with barcode and cut site overhang:457862 rate:24251 ns/read
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:1000000 Reads with barcode and cut site overhang:355967 rate:25569 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:3000000 Reads with barcode and cut site overhang:1344680 rate:23773 ns/read
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:3000000 Reads with barcode and cut site overhang:972443 rate:24187 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:4000000 Reads with barcode and cut site overhang:1778118 rate:23815 ns/read
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:4000000 Reads with barcode and cut site overhang:1563205 rate:23919 ns/read
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:6000000 Reads with barcode and cut site overhang:2200560 rate:23740 ns/read
[ForkJoinPool.commonPool-worker-4] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:7000000 Reads with barcode and cut site overhang:1191682 rate:23275 ns/read
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:8000000 Reads with barcode and cut site overhang:2752463 rate:23568 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:9000000 Reads with barcode and cut site overhang:3880803 rate:23409 ns/read
[ForkJoinPool.commonPool-worker-2] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:10000000 Reads with barcode and cut site overhang:2674223 rate:23502 ns/read
[ForkJoinPool.commonPool-worker-4] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:11000000 Reads with barcode and cut site overhang:1900567 rate:23298 ns/read
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:11000000 Reads with barcode and cut site overhang:3833741 rate:23501 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:12000000 Reads with barcode and cut site overhang:5201645 rate:23512 ns/read
[ForkJoinPool.commonPool-worker-2] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:12000000 Reads with barcode and cut site overhang:3231738 rate:23511 ns/read
[ForkJoinPool.commonPool-worker-2] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:13000000 Reads with barcode and cut site overhang:3530582 rate:23463 ns/read
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:13000000 Reads with barcode and cut site overhang:4685876 rate:23483 ns/read
[ForkJoinPool.commonPool-worker-13] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:15000000 Reads with barcode and cut site overhang:973045 rate:23256 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:15000000 Reads with barcode and cut site overhang:6672919 rate:23435 ns/read
[ForkJoinPool.commonPool-worker-4] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:16000000 Reads with barcode and cut site overhang:2733492 rate:23251 ns/read
[ForkJoinPool.commonPool-worker-2] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:16000000 Reads with barcode and cut site overhang:4581295 rate:23393 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:16000000 Reads with barcode and cut site overhang:7181609 rate:23408 ns/read
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:17000000 Reads with barcode and cut site overhang:5913254 rate:23372 ns/read
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:17000000 Reads with barcode and cut site overhang:6523548 rate:23429 ns/read
[ForkJoinPool.commonPool-worker-6] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:18000000 Reads with barcode and cut site overhang:735177 rate:23195 ns/read
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:19000000 Reads with barcode and cut site overhang:6532646 rate:23373 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:19000000 Reads with barcode and cut site overhang:8618174 rate:23387 ns/read
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:19000000 Reads with barcode and cut site overhang:7435389 rate:23423 ns/read
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:20000000 Reads with barcode and cut site overhang:773478 rate:23060 ns/read
[ForkJoinPool.commonPool-worker-4] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:20000000 Reads with barcode and cut site overhang:3399119 rate:23294 ns/read
[ForkJoinPool.commonPool-worker-2] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:20000000 Reads with barcode and cut site overhang:5943837 rate:23401 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:20000000 Reads with barcode and cut site overhang:9097058 rate:23414 ns/read
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:20000000 Reads with barcode and cut site overhang:7820241 rate:23471 ns/read
[ForkJoinPool.commonPool-worker-6] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:21000000 Reads with barcode and cut site overhang:854402 rate:23148 ns/read
[ForkJoinPool.commonPool-worker-2] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:22000000 Reads with barcode and cut site overhang:6536063 rate:23329 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:22000000 Reads with barcode and cut site overhang:10067312 rate:23350 ns/read
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:22000000 Reads with barcode and cut site overhang:8604244 rate:23733 ns/read
[ForkJoinPool.commonPool-worker-6] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:23000000 Reads with barcode and cut site overhang:928973 rate:23103 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:23000000 Reads with barcode and cut site overhang:10542200 rate:23381 ns/read
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:23000000 Reads with barcode and cut site overhang:9027936 rate:23745 ns/read
[ForkJoinPool.commonPool-worker-2] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:24000000 Reads with barcode and cut site overhang:7169019 rate:23321 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:24000000 Reads with barcode and cut site overhang:11010456 rate:23362 ns/read
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:24000000 Reads with barcode and cut site overhang:9452773 rate:23709 ns/read
[ForkJoinPool.commonPool-worker-6] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of reads in lane=24853605
[ForkJoinPool.commonPool-worker-6] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of good barcoded reads=996511
[ForkJoinPool.commonPool-worker-6] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of low quality reads=1329705
[ForkJoinPool.commonPool-worker-6] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Timing process (sorting, collapsing, and writing TagCount to file).
[ForkJoinPool.commonPool-worker-6] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Process took 575985.78029 milliseconds for file /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol008-1-ACTTGA_L008-R1_fastq.fastq
[ForkJoinPool.commonPool-worker-4] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:25000000 Reads with barcode and cut site overhang:4301317 rate:23188 ns/read
[ForkJoinPool.commonPool-worker-2] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:25000000 Reads with barcode and cut site overhang:7483275 rate:23284 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:25000000 Reads with barcode and cut site overhang:11487748 rate:23314 ns/read
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:25000000 Reads with barcode and cut site overhang:9820938 rate:23599 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:26000000 Reads with barcode and cut site overhang:11979666 rate:23219 ns/read
[ForkJoinPool.commonPool-worker-4] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:27000000 Reads with barcode and cut site overhang:4653863 rate:22989 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:27000000 Reads with barcode and cut site overhang:12476830 rate:23105 ns/read
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:27000000 Reads with barcode and cut site overhang:8980369 rate:23113 ns/read
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:27000000 Reads with barcode and cut site overhang:10595427 rate:23367 ns/read
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of reads in lane=27627572
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of good barcoded reads=9091237
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of low quality reads=17031715
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Timing process (sorting, collapsing, and writing TagCount to file).
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Process took 636573.333103 milliseconds for file /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol5-1-ACAGTG_L008-R2_fastq.fastq
[ForkJoinPool.commonPool-worker-2] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:29000000 Reads with barcode and cut site overhang:8813457 rate:22764 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:29000000 Reads with barcode and cut site overhang:13480408 rate:22777 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:30000000 Reads with barcode and cut site overhang:14012618 rate:22584 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:31000000 Reads with barcode and cut site overhang:14537767 rate:22438 ns/read
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:31000000 Reads with barcode and cut site overhang:12273199 rate:22631 ns/read
[ForkJoinPool.commonPool-worker-4] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:32000000 Reads with barcode and cut site overhang:5528102 rate:22214 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:32000000 Reads with barcode and cut site overhang:15021858 rate:22285 ns/read
[ForkJoinPool.commonPool-worker-13] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of reads in lane=33746558
[ForkJoinPool.commonPool-worker-13] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of good barcoded reads=2175514
[ForkJoinPool.commonPool-worker-13] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of low quality reads=3679143
[ForkJoinPool.commonPool-worker-13] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Timing process (sorting, collapsing, and writing TagCount to file).
[ForkJoinPool.commonPool-worker-13] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Process took 740182.597661 milliseconds for file /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol011-1-GGCTAC_L008-R1_fastq.fastq
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:34000000 Reads with barcode and cut site overhang:13447593 rate:22127 ns/read
[ForkJoinPool.commonPool-worker-4] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:35000000 Reads with barcode and cut site overhang:6033507 rate:21698 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:35000000 Reads with barcode and cut site overhang:16522229 rate:21755 ns/read
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:36000000 Reads with barcode and cut site overhang:14131112 rate:21696 ns/read
[ForkJoinPool.commonPool-worker-2] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:37000000 Reads with barcode and cut site overhang:11793207 rate:21339 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:37000000 Reads with barcode and cut site overhang:17554205 rate:21345 ns/read
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:37000000 Reads with barcode and cut site overhang:14536094 rate:21495 ns/read
[ForkJoinPool.commonPool-worker-2] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:38000000 Reads with barcode and cut site overhang:12162279 rate:21173 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:38000000 Reads with barcode and cut site overhang:18046706 rate:21179 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:40000000 Reads with barcode and cut site overhang:19076200 rate:20854 ns/read
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of reads in lane=41312418
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of good barcoded reads=1581938
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of low quality reads=2293559
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Timing process (sorting, collapsing, and writing TagCount to file).
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Process took 846532.673444 milliseconds for file /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol007-1-CAGATC_L008-R1_fastq.fastq
[ForkJoinPool.commonPool-worker-2] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:41000000 Reads with barcode and cut site overhang:13303120 rate:20681 ns/read
[ForkJoinPool.commonPool-worker-4] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:42000000 Reads with barcode and cut site overhang:7221841 rate:20439 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:42000000 Reads with barcode and cut site overhang:20114831 rate:20474 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:43000000 Reads with barcode and cut site overhang:20645538 rate:20261 ns/read
[ForkJoinPool.commonPool-worker-2] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:43000000 Reads with barcode and cut site overhang:14102184 rate:20262 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:45000000 Reads with barcode and cut site overhang:21548355 rate:19875 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:46000000 Reads with barcode and cut site overhang:21738510 rate:19702 ns/read
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:46000000 Reads with barcode and cut site overhang:17955285 rate:19791 ns/read
[ForkJoinPool.commonPool-worker-4] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:47000000 Reads with barcode and cut site overhang:7967367 rate:19508 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:48000000 Reads with barcode and cut site overhang:22786244 rate:19367 ns/read
[ForkJoinPool.commonPool-worker-4] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of reads in lane=48312799
[ForkJoinPool.commonPool-worker-4] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of good barcoded reads=8188613
[ForkJoinPool.commonPool-worker-4] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of low quality reads=10941481
[ForkJoinPool.commonPool-worker-4] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Timing process (sorting, collapsing, and writing TagCount to file).
[ForkJoinPool.commonPool-worker-4] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Process took 932124.786952 milliseconds for file /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol013-1-AGTCAA_L008-R1_fastq.fastq
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:49000000 Reads with barcode and cut site overhang:18995509 rate:19229 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:50000000 Reads with barcode and cut site overhang:23803607 rate:18953 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:51000000 Reads with barcode and cut site overhang:24334846 rate:18756 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:52000000 Reads with barcode and cut site overhang:24746362 rate:18561 ns/read
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:52000000 Reads with barcode and cut site overhang:20010857 rate:18620 ns/read
[ForkJoinPool.commonPool-worker-2] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:53000000 Reads with barcode and cut site overhang:17722888 rate:18371 ns/read
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:53000000 Reads with barcode and cut site overhang:20432779 rate:18431 ns/read
[ForkJoinPool.commonPool-worker-2] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:54000000 Reads with barcode and cut site overhang:18116004 rate:18193 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:55000000 Reads with barcode and cut site overhang:26328801 rate:18029 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:58000000 Reads with barcode and cut site overhang:27878848 rate:17545 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of reads in lane=58322655
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of good barcoded reads=28039733
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of low quality reads=29202212
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Timing process (sorting, collapsing, and writing TagCount to file).
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Process took 1020589.631942 milliseconds for file /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol2-1-CGATGT_L008-R1_fastq.fastq
[ForkJoinPool.commonPool-worker-2] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:59000000 Reads with barcode and cut site overhang:20062764 rate:17358 ns/read
[ForkJoinPool.commonPool-worker-2] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:60000000 Reads with barcode and cut site overhang:20455709 rate:17169 ns/read
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:60000000 Reads with barcode and cut site overhang:22689065 rate:17206 ns/read
[ForkJoinPool.commonPool-worker-2] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:61000000 Reads with barcode and cut site overhang:20853728 rate:16984 ns/read
[ForkJoinPool.commonPool-worker-2] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:62000000 Reads with barcode and cut site overhang:21303005 rate:16804 ns/read
[ForkJoinPool.commonPool-worker-2] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of reads in lane=62268079
[ForkJoinPool.commonPool-worker-2] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of good barcoded reads=21409214
[ForkJoinPool.commonPool-worker-2] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of low quality reads=39011508
[ForkJoinPool.commonPool-worker-2] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Timing process (sorting, collapsing, and writing TagCount to file).
[ForkJoinPool.commonPool-worker-2] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Process took 1043383.062723 milliseconds for file /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol1-1-ATCACG_L008-R1_fastq.fastq
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of reads in lane=62500553
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of good barcoded reads=23400053
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of low quality reads=36210925
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Timing process (sorting, collapsing, and writing TagCount to file).
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Process took 1045124.194128 milliseconds for file /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol6-1-GCCAAT_L008-R2_fastq.fastq
Finished processing batch 1
Start processing batch 2
Enzyme: ApeKI
Enzyme: ApeKI
Enzyme: ApeKI
Enzyme: ApeKI
Enzyme: ApeKI
Enzyme: ApeKI
Enzyme: ApeKI
Enzyme: ApeKI
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.GBSUtils - /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol009-1-GATCAG_L008-R2_fastq.fastq: Quality score base:33
[ForkJoinPool.commonPool-worker-13] INFO net.maizegenetics.analysis.gbs.v2.GBSUtils - /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol010-1-TAGCTT_L008-R2_fastq.fastq: Quality score base:33
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.GBSUtils - /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol4-1-TGACCA_L008-R1_fastq.fastq: Quality score base:33
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.GBSUtils - /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol010-1-TAGCTT_L008-R1_fastq.fastq: Quality score base:33
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.GBSUtils - /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol4-1-TGACCA_L008-R2_fastq.fastq: Quality score base:33
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.GBSUtils - /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol3-1-TTAGGC_L008-R1_fastq.fastq: Quality score base:33
[ForkJoinPool.commonPool-worker-4] INFO net.maizegenetics.analysis.gbs.v2.GBSUtils - /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol012-1-CTTGTA_L008-R1_fastq.fastq: Quality score base:33
[ForkJoinPool.commonPool-worker-6] INFO net.maizegenetics.analysis.gbs.v2.GBSUtils - /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/GBSPVD_2_fastq.fastq: Quality score base:33
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:3000000 Reads with barcode and cut site overhang:1237352 rate:23676 ns/read
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:6000000 Reads with barcode and cut site overhang:2481349 rate:23456 ns/read
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:6000000 Reads with barcode and cut site overhang:1859802 rate:24036 ns/read
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:6000000 Reads with barcode and cut site overhang:2502398 rate:24057 ns/read
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:7000000 Reads with barcode and cut site overhang:2974952 rate:23635 ns/read
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:7000000 Reads with barcode and cut site overhang:2290845 rate:24042 ns/read
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:8000000 Reads with barcode and cut site overhang:3448523 rate:23462 ns/read
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:8000000 Reads with barcode and cut site overhang:2674408 rate:23849 ns/read
[ForkJoinPool.commonPool-worker-6] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:9000000 Reads with barcode and cut site overhang:3254462 rate:21912 ns/read
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:9000000 Reads with barcode and cut site overhang:3897921 rate:23736 ns/read
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:10000000 Reads with barcode and cut site overhang:4341823 rate:23427 ns/read
[ForkJoinPool.commonPool-worker-6] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:11000000 Reads with barcode and cut site overhang:3991434 rate:21843 ns/read
[ForkJoinPool.commonPool-worker-6] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of reads in lane=12158498
[ForkJoinPool.commonPool-worker-6] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of good barcoded reads=4421065
[ForkJoinPool.commonPool-worker-6] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of low quality reads=6049864
[ForkJoinPool.commonPool-worker-6] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Timing process (sorting, collapsing, and writing TagCount to file).
[ForkJoinPool.commonPool-worker-6] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Process took 265867.889974 milliseconds for file /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/GBSPVD_2_fastq.fastq
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:12000000 Reads with barcode and cut site overhang:5267137 rate:23212 ns/read
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:12000000 Reads with barcode and cut site overhang:4036890 rate:23428 ns/read
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:13000000 Reads with barcode and cut site overhang:5754364 rate:23030 ns/read
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:13000000 Reads with barcode and cut site overhang:4400103 rate:23278 ns/read
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:15000000 Reads with barcode and cut site overhang:6746524 rate:22810 ns/read
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:16000000 Reads with barcode and cut site overhang:7222387 rate:22681 ns/read
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:19000000 Reads with barcode and cut site overhang:6286185 rate:22394 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:20000000 Reads with barcode and cut site overhang:1124955 rate:21973 ns/read
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:20000000 Reads with barcode and cut site overhang:9042387 rate:22243 ns/read
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:20000000 Reads with barcode and cut site overhang:6578340 rate:22262 ns/read
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:21000000 Reads with barcode and cut site overhang:9490519 rate:22016 ns/read
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:21000000 Reads with barcode and cut site overhang:6871289 rate:22139 ns/read
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:22000000 Reads with barcode and cut site overhang:9977484 rate:22028 ns/read
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:23000000 Reads with barcode and cut site overhang:7423653 rate:21989 ns/read
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:24000000 Reads with barcode and cut site overhang:10945502 rate:21794 ns/read
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of reads in lane=24404610
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of good barcoded reads=11174187
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of low quality reads=12657479
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Timing process (sorting, collapsing, and writing TagCount to file).
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Process took 534010.823697 milliseconds for file /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol3-1-TTAGGC_L008-R1_fastq.fastq
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:25000000 Reads with barcode and cut site overhang:11429298 rate:21697 ns/read
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of reads in lane=25527073
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of good barcoded reads=11697787
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of low quality reads=13299901
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Timing process (sorting, collapsing, and writing TagCount to file).
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Process took 551577.135421 milliseconds for file /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol4-1-TGACCA_L008-R1_fastq.fastq
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of reads in lane=25527073
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of good barcoded reads=8107465
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of low quality reads=15775883
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Timing process (sorting, collapsing, and writing TagCount to file).
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Process took 553715.934882 milliseconds for file /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol4-1-TGACCA_L008-R2_fastq.fastq
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:29000000 Reads with barcode and cut site overhang:1120859 rate:20430 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:31000000 Reads with barcode and cut site overhang:1574244 rate:19807 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of reads in lane=32237757
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of good barcoded reads=1596704
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of low quality reads=4074794
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Timing process (sorting, collapsing, and writing TagCount to file).
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Process took 628453.729928 milliseconds for file /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol009-1-GATCAG_L008-R2_fastq.fastq
[ForkJoinPool.commonPool-worker-13] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of reads in lane=38230971
[ForkJoinPool.commonPool-worker-13] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of good barcoded reads=958481
[ForkJoinPool.commonPool-worker-13] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of low quality reads=2220064
[ForkJoinPool.commonPool-worker-13] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Timing process (sorting, collapsing, and writing TagCount to file).
[ForkJoinPool.commonPool-worker-13] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Process took 681493.856418 milliseconds for file /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol010-1-TAGCTT_L008-R2_fastq.fastq
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of reads in lane=38230971
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of good barcoded reads=1450705
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of low quality reads=1851100
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Timing process (sorting, collapsing, and writing TagCount to file).
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Process took 681956.032733 milliseconds for file /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol010-1-TAGCTT_L008-R1_fastq.fastq
[ForkJoinPool.commonPool-worker-4] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of reads in lane=49082144
[ForkJoinPool.commonPool-worker-4] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of good barcoded reads=2501488
[ForkJoinPool.commonPool-worker-4] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of low quality reads=3314516
[ForkJoinPool.commonPool-worker-4] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Timing process (sorting, collapsing, and writing TagCount to file).
[ForkJoinPool.commonPool-worker-4] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Process took 714497.493646 milliseconds for file /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol012-1-CTTGTA_L008-R1_fastq.fastq
Finished processing batch 2
Start processing batch 3
Enzyme: ApeKI
Enzyme: ApeKI
Enzyme: ApeKI
Enzyme: ApeKI
Enzyme: ApeKI
Enzyme: ApeKI
Enzyme: ApeKI
Enzyme: ApeKI
[ForkJoinPool.commonPool-worker-3] INFO net.maizegenetics.analysis.gbs.v2.GBSUtils - /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol3-1-TTAGGC_L008-R2_fastq.fastq: Quality score base:33
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.GBSUtils - /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol009-1-GATCAG_L008-R1_fastq.fastq: Quality score base:33
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.GBSUtils - /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol6-1-GCCAAT_L008-R1_fastq.fastq: Quality score base:33
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.GBSUtils - /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol007-1-CAGATC_L008-R2_fastq.fastq: Quality score base:33
[ForkJoinPool.commonPool-worker-13] INFO net.maizegenetics.analysis.gbs.v2.GBSUtils - /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol011-1-GGCTAC_L008-R2_fastq.fastq: Quality score base:33
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.GBSUtils - /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol012-1-CTTGTA_L008-R2_fastq.fastq: Quality score base:33
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.GBSUtils - /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol1-1-ATCACG_L008-R2_fastq.fastq: Quality score base:33
[ForkJoinPool.commonPool-worker-6] INFO net.maizegenetics.analysis.gbs.v2.GBSUtils - /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/GBSPVD_1_fastq.fastq: Quality score base:33
[ForkJoinPool.commonPool-worker-3] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:1000000 Reads with barcode and cut site overhang:316918 rate:21181 ns/read
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:2000000 Reads with barcode and cut site overhang:884867 rate:23388 ns/read
[ForkJoinPool.commonPool-worker-6] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:3000000 Reads with barcode and cut site overhang:1409334 rate:22264 ns/read
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:3000000 Reads with barcode and cut site overhang:1324425 rate:23563 ns/read
[ForkJoinPool.commonPool-worker-3] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:5000000 Reads with barcode and cut site overhang:1359588 rate:22915 ns/read
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:5000000 Reads with barcode and cut site overhang:1937673 rate:23978 ns/read
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:6000000 Reads with barcode and cut site overhang:2577156 rate:23436 ns/read
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:7000000 Reads with barcode and cut site overhang:2657535 rate:23716 ns/read
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:8000000 Reads with barcode and cut site overhang:3064269 rate:23565 ns/read
[ForkJoinPool.commonPool-worker-6] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:9000000 Reads with barcode and cut site overhang:4243878 rate:21735 ns/read
[ForkJoinPool.commonPool-worker-3] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:9000000 Reads with barcode and cut site overhang:2723615 rate:23127 ns/read
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:10000000 Reads with barcode and cut site overhang:3780435 rate:23550 ns/read
[ForkJoinPool.commonPool-worker-6] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:11000000 Reads with barcode and cut site overhang:5177053 rate:21815 ns/read
[ForkJoinPool.commonPool-worker-3] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:11000000 Reads with barcode and cut site overhang:3311839 rate:23225 ns/read
[ForkJoinPool.commonPool-worker-6] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of reads in lane=12158498
[ForkJoinPool.commonPool-worker-6] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of good barcoded reads=5713902
[ForkJoinPool.commonPool-worker-6] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of low quality reads=5164922
[ForkJoinPool.commonPool-worker-6] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Timing process (sorting, collapsing, and writing TagCount to file).
[ForkJoinPool.commonPool-worker-6] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Process took 264397.969293 milliseconds for file /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/GBSPVD_1_fastq.fastq
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:12000000 Reads with barcode and cut site overhang:5150971 rate:23237 ns/read
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:12000000 Reads with barcode and cut site overhang:4556625 rate:23304 ns/read
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:13000000 Reads with barcode and cut site overhang:5605011 rate:23024 ns/read
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:13000000 Reads with barcode and cut site overhang:4958895 rate:23125 ns/read
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:14000000 Reads with barcode and cut site overhang:6052820 rate:22860 ns/read
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:14000000 Reads with barcode and cut site overhang:5389819 rate:22918 ns/read
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:15000000 Reads with barcode and cut site overhang:5840279 rate:22720 ns/read
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:16000000 Reads with barcode and cut site overhang:7070172 rate:22505 ns/read
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:16000000 Reads with barcode and cut site overhang:6337652 rate:22545 ns/read
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:17000000 Reads with barcode and cut site overhang:7569794 rate:22427 ns/read
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:18000000 Reads with barcode and cut site overhang:7285975 rate:22305 ns/read
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:18000000 Reads with barcode and cut site overhang:8075230 rate:22330 ns/read
[ForkJoinPool.commonPool-worker-3] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:19000000 Reads with barcode and cut site overhang:5631460 rate:22135 ns/read
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:19000000 Reads with barcode and cut site overhang:8575747 rate:22245 ns/read
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:20000000 Reads with barcode and cut site overhang:597887 rate:21886 ns/read
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:20000000 Reads with barcode and cut site overhang:1377496 rate:21923 ns/read
[ForkJoinPool.commonPool-worker-3] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:20000000 Reads with barcode and cut site overhang:5917778 rate:22031 ns/read
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:20000000 Reads with barcode and cut site overhang:9034543 rate:22142 ns/read
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:22000000 Reads with barcode and cut site overhang:9953503 rate:21936 ns/read
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:22000000 Reads with barcode and cut site overhang:8998935 rate:21967 ns/read
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:23000000 Reads with barcode and cut site overhang:1579063 rate:21708 ns/read
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:24000000 Reads with barcode and cut site overhang:9901670 rate:21845 ns/read
[ForkJoinPool.commonPool-worker-3] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of reads in lane=24404610
[ForkJoinPool.commonPool-worker-3] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of good barcoded reads=6986692
[ForkJoinPool.commonPool-worker-3] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of low quality reads=15624016
[ForkJoinPool.commonPool-worker-3] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Timing process (sorting, collapsing, and writing TagCount to file).
[ForkJoinPool.commonPool-worker-3] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Process took 530056.571209 milliseconds for file /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol3-1-TTAGGC_L008-R2_fastq.fastq
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:25000000 Reads with barcode and cut site overhang:10327496 rate:21697 ns/read
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:25000000 Reads with barcode and cut site overhang:11380193 rate:21726 ns/read
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:26000000 Reads with barcode and cut site overhang:10715627 rate:21546 ns/read
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:27000000 Reads with barcode and cut site overhang:12328287 rate:21433 ns/read
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:28000000 Reads with barcode and cut site overhang:1914714 rate:21110 ns/read
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:28000000 Reads with barcode and cut site overhang:12825961 rate:21267 ns/read
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:28000000 Reads with barcode and cut site overhang:11600288 rate:21277 ns/read
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:29000000 Reads with barcode and cut site overhang:13317062 rate:21116 ns/read
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:29000000 Reads with barcode and cut site overhang:12073805 rate:21126 ns/read
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:30000000 Reads with barcode and cut site overhang:12563912 rate:20985 ns/read
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:32000000 Reads with barcode and cut site overhang:14837633 rate:20771 ns/read
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of reads in lane=32237757
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of good barcoded reads=2171977
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of low quality reads=3682205
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Timing process (sorting, collapsing, and writing TagCount to file).
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Process took 665281.582289 milliseconds for file /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol009-1-GATCAG_L008-R1_fastq.fastq
[ForkJoinPool.commonPool-worker-13] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of reads in lane=33746558
[ForkJoinPool.commonPool-worker-13] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of good barcoded reads=1433058
[ForkJoinPool.commonPool-worker-13] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of low quality reads=4219957
[ForkJoinPool.commonPool-worker-13] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Timing process (sorting, collapsing, and writing TagCount to file).
[ForkJoinPool.commonPool-worker-13] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Process took 688732.100247 milliseconds for file /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol011-1-GGCTAC_L008-R2_fastq.fastq
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:34000000 Reads with barcode and cut site overhang:15832741 rate:20380 ns/read
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:34000000 Reads with barcode and cut site overhang:14348269 rate:20392 ns/read
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:36000000 Reads with barcode and cut site overhang:15088785 rate:19893 ns/read
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:36000000 Reads with barcode and cut site overhang:16815573 rate:19907 ns/read
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:37000000 Reads with barcode and cut site overhang:15555884 rate:19675 ns/read
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:38000000 Reads with barcode and cut site overhang:16026525 rate:19461 ns/read
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:40000000 Reads with barcode and cut site overhang:16886694 rate:19081 ns/read
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of reads in lane=41312418
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of good barcoded reads=1094894
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of low quality reads=2654430
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Timing process (sorting, collapsing, and writing TagCount to file).
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Process took 773970.71309 milliseconds for file /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol007-1-CAGATC_L008-R2_fastq.fastq
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:41000000 Reads with barcode and cut site overhang:19335695 rate:18895 ns/read
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:43000000 Reads with barcode and cut site overhang:18154165 rate:18415 ns/read
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:47000000 Reads with barcode and cut site overhang:19958871 rate:17595 ns/read
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:48000000 Reads with barcode and cut site overhang:22808719 rate:17407 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of reads in lane=49082144
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of good barcoded reads=1807034
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of low quality reads=3838814
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Timing process (sorting, collapsing, and writing TagCount to file).
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Process took 841932.735109 milliseconds for file /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol012-1-CTTGTA_L008-R2_fastq.fastq
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:51000000 Reads with barcode and cut site overhang:21548499 rate:16769 ns/read
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:53000000 Reads with barcode and cut site overhang:25000735 rate:16357 ns/read
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:53000000 Reads with barcode and cut site overhang:22383514 rate:16357 ns/read
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:54000000 Reads with barcode and cut site overhang:22862918 rate:16161 ns/read
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:56000000 Reads with barcode and cut site overhang:26424926 rate:15792 ns/read
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:57000000 Reads with barcode and cut site overhang:26930617 rate:15615 ns/read
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:59000000 Reads with barcode and cut site overhang:27990444 rate:15283 ns/read
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:60000000 Reads with barcode and cut site overhang:28522015 rate:15126 ns/read
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:60000000 Reads with barcode and cut site overhang:25082888 rate:15126 ns/read
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:61000000 Reads with barcode and cut site overhang:28981366 rate:14973 ns/read
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:61000000 Reads with barcode and cut site overhang:25523782 rate:14974 ns/read
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of reads in lane=62268079
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of good barcoded reads=25825559
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of low quality reads=32192312
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Timing process (sorting, collapsing, and writing TagCount to file).
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Process took 921142.937374 milliseconds for file /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol1-1-ATCACG_L008-R2_fastq.fastq
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of reads in lane=62500553
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of good barcoded reads=29775658
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of low quality reads=31632914
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Timing process (sorting, collapsing, and writing TagCount to file).
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Process took 921829.248553 milliseconds for file /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol6-1-GCCAAT_L008-R1_fastq.fastq
Finished processing batch 3
Start processing batch 4
Enzyme: ApeKI
Enzyme: ApeKI
Enzyme: ApeKI
Enzyme: ApeKI
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.GBSUtils - /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol5-1-ACAGTG_L008-R1_fastq.fastq: Quality score base:33
[ForkJoinPool.commonPool-worker-13] INFO net.maizegenetics.analysis.gbs.v2.GBSUtils - /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol008-1-ACTTGA_L008-R2_fastq.fastq: Quality score base:33
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.GBSUtils - /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol013-1-AGTCAA_L008-R2_fastq.fastq: Quality score base:33
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.GBSUtils - /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol2-1-CGATGT_L008-R2_fastq.fastq: Quality score base:33
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:1000000 Reads with barcode and cut site overhang:415271 rate:11160 ns/read
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:2000000 Reads with barcode and cut site overhang:814889 rate:11291 ns/read
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:3000000 Reads with barcode and cut site overhang:1207316 rate:11419 ns/read
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:4000000 Reads with barcode and cut site overhang:1605974 rate:11450 ns/read
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:4000000 Reads with barcode and cut site overhang:1437704 rate:11661 ns/read
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:6000000 Reads with barcode and cut site overhang:2423622 rate:11484 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:7000000 Reads with barcode and cut site overhang:890161 rate:11634 ns/read
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:9000000 Reads with barcode and cut site overhang:2971903 rate:11571 ns/read
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:11000000 Reads with barcode and cut site overhang:3612099 rate:11590 ns/read
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:12000000 Reads with barcode and cut site overhang:5153809 rate:11548 ns/read
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:12000000 Reads with barcode and cut site overhang:3931257 rate:11607 ns/read
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:14000000 Reads with barcode and cut site overhang:4743413 rate:11619 ns/read
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:15000000 Reads with barcode and cut site overhang:5199355 rate:11579 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:16000000 Reads with barcode and cut site overhang:2068821 rate:11561 ns/read
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:16000000 Reads with barcode and cut site overhang:5628864 rate:11593 ns/read
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:17000000 Reads with barcode and cut site overhang:7534051 rate:11548 ns/read
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:18000000 Reads with barcode and cut site overhang:6438060 rate:11602 ns/read
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:19000000 Reads with barcode and cut site overhang:8494581 rate:11562 ns/read
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:19000000 Reads with barcode and cut site overhang:6783122 rate:11599 ns/read
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:20000000 Reads with barcode and cut site overhang:8983660 rate:11554 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:20000000 Reads with barcode and cut site overhang:2584410 rate:11572 ns/read
[ForkJoinPool.commonPool-worker-13] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:21000000 Reads with barcode and cut site overhang:652002 rate:11802 ns/read
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:22000000 Reads with barcode and cut site overhang:9758533 rate:11560 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:22000000 Reads with barcode and cut site overhang:2843322 rate:11575 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:23000000 Reads with barcode and cut site overhang:2989576 rate:11569 ns/read
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:23000000 Reads with barcode and cut site overhang:8291684 rate:11590 ns/read
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:24000000 Reads with barcode and cut site overhang:8616788 rate:11589 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:25000000 Reads with barcode and cut site overhang:3295271 rate:11578 ns/read
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:25000000 Reads with barcode and cut site overhang:8969613 rate:11587 ns/read
[ForkJoinPool.commonPool-worker-13] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of reads in lane=24853605
[ForkJoinPool.commonPool-worker-13] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of good barcoded reads=716748
[ForkJoinPool.commonPool-worker-13] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of low quality reads=1530844
[ForkJoinPool.commonPool-worker-13] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Timing process (sorting, collapsing, and writing TagCount to file).
[ForkJoinPool.commonPool-worker-13] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Process took 293209.451315 milliseconds for file /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol008-1-ACTTGA_L008-R2_fastq.fastq
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:27000000 Reads with barcode and cut site overhang:12157192 rate:11384 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:27000000 Reads with barcode and cut site overhang:3553818 rate:11397 ns/read
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:27000000 Reads with barcode and cut site overhang:9715171 rate:11406 ns/read
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of reads in lane=27627572
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of good barcoded reads=12473904
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of low quality reads=14636326
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Timing process (sorting, collapsing, and writing TagCount to file).
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Process took 312754.31718 milliseconds for file /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol5-1-ACAGTG_L008-R1_fastq.fastq
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:28000000 Reads with barcode and cut site overhang:3684489 rate:11260 ns/read
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:29000000 Reads with barcode and cut site overhang:10495434 rate:11072 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:35000000 Reads with barcode and cut site overhang:4539563 rate:10170 ns/read
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:38000000 Reads with barcode and cut site overhang:13552955 rate:9830 ns/read
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:39000000 Reads with barcode and cut site overhang:13866086 rate:9727 ns/read
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:40000000 Reads with barcode and cut site overhang:14231978 rate:9630 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:42000000 Reads with barcode and cut site overhang:5236201 rate:9446 ns/read
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:44000000 Reads with barcode and cut site overhang:15632588 rate:9281 ns/read
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:45000000 Reads with barcode and cut site overhang:15902867 rate:9205 ns/read
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:46000000 Reads with barcode and cut site overhang:16290239 rate:9131 ns/read
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:47000000 Reads with barcode and cut site overhang:16581236 rate:9062 ns/read
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:48000000 Reads with barcode and cut site overhang:16911506 rate:8994 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of reads in lane=48312799
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of good barcoded reads=5643335
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of low quality reads=12704945
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Timing process (sorting, collapsing, and writing TagCount to file).
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Process took 433386.048592 milliseconds for file /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol013-1-AGTCAA_L008-R2_fastq.fastq
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:50000000 Reads with barcode and cut site overhang:17615397 rate:8766 ns/read
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:54000000 Reads with barcode and cut site overhang:18772604 rate:8332 ns/read
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:55000000 Reads with barcode and cut site overhang:19159328 rate:8234 ns/read
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of reads in lane=58322655
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of good barcoded reads=19952138
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of low quality reads=35196217
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Timing process (sorting, collapsing, and writing TagCount to file).
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Process took 462507.370558 milliseconds for file /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol2-1-CGATGT_L008-R2_fastq.fastq
Finished processing batch 4
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 -
Writing ReadsPerSample log file...
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - ReadsPerSample log file: /home/facon/GBS_PVd_unified_analysis/GBS_PVd_unifiedfile_ReadsPerSample.log
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 -
Total number of SNPs processed with minimum quality score 20 was 2200875.
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - ...done
[pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin - Finished net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2: time: Dec 18, 2015 20:26:12
[pool-1-thread-1] INFO net.maizegenetics.pipeline.TasselPipeline - net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2: time: Dec 18, 2015 20:26:12: progress: 100%
[pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin - net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 Citation: Bradbury PJ, Zhang Z, Kroon DE, Casstevens TM, Ramdoss Y, Buckler ES. (2007) TASSEL: Software for association mapping of complex traits in diverse samples. Bioinformatics 23:2633-2635.
Thank you,
Sincerely,
Debora
Lynn Carol Johnson
Dec 22, 2015, 8:45:12 AM12/22/15
to tas...@googlegroups.com
Hi Debora -
You are correct – it is not necessary to import SNP position quality information. That step can be skipped.
Regarding your h5 file issue: Do you get an error when running ProductionSNPCallerPluginV2 without the –ko option? How did you determine it terminated before the end? Using the –ko option to get around this isn’t working as the file appears to have
problems with the taxalist when attempting to close.
Can you run the ProductionSNPCallerPluginV2 with debug and without the –ko option and show me that output?
Thanks - Lynn
To view this discussion on the web visit
https://groups.google.com/d/msgid/tassel/a5392ea5-bd23-4d27-9474-d3881dffaec2%40googlegroups.com.
Debora Santo
Dec 22, 2015, 10:58:38 AM12/22/15
to TASSEL - Trait Analysis by Association, Evolution and Linkage
Hi Lynn,
I ran the ProductionSNPCallerPluginV2 without the -ko option and attached the debug output at the bottom. I get an error without the -ko option set, too (the default for it is "false", according to the Bitbucket Wiki).
I concluded that the Plugin has terminated before the end from the comparison of the amounts of processed data in the two debug files (with differently set -ko) - it looks like the Plugin stops processing at a certain batch in the closed .h5 file and throws an ERROR, while for the open .h5 file it runs longer (through more batches of data).
Since you have mentioned that the closing of the .h5 file is due to a problem with the taxalist, do you know what could be the exact cause? I did notice that the number of taxa that is shown to be imported into the open .h5 file (which is correct, according to our experiment/input and equals 297 individuals/taxa) doesn't match the number of taxa in the debug file when attempting to close the .h5 file (and is significantly lower). No errors prior to this step occur, but if needed, I could re-run the data through the whole pipeline to provide debug files for each plugin (in case there might be a hidden reason for something wrong in previous steps, but which is not pointed out with an error message).
Apart from trying to run the ProductionSNPCallerPluginV2 with differently set -ko, I also tried switching between the -do options, to create a .vcf file instead of the .h5 one (which gave me the following error message in the TASSEL GUI java.lang.ArrayIndexOutOfBoundsException -1; I see that other users have this same issue with .vcf files), using earlier TASSEL versions with which I have successfully created datasets in .h5 format and also running it on subsets of my data for which I already had good .h5 datasets created (and are part of the larger population now being analysed). Nothing I could think of solved the issue. It might also be due to some changes in the environment on the cluster I am using, since they have made some maintenance lately or just something I am overlooking due to my lack of deeper experience in this field.
Thanks for looking into this issue!
Thanks for looking into this issue!
Debora
Here is the debug file for the ProductionSNPCallerPluginV2 with no -ko set:
Here is the debug file for the ProductionSNPCallerPluginV2 with no -ko set:
[main] INFO net.maizegenetics.tassel.TasselLogging - Tassel Version: 5.2.18 Date: December 10, 2015
[main] INFO net.maizegenetics.tassel.TasselLogging - Max Available Memory Reported by JVM: 13653 MB
[main] INFO net.maizegenetics.tassel.TasselLogging - Java Version: 1.8.0_45
[main] INFO net.maizegenetics.tassel.TasselLogging - OS: Linux
[main] INFO net.maizegenetics.tassel.TasselLogging - Number of Processors: 16
[main] INFO net.maizegenetics.pipeline.TasselPipeline - Tassel Pipeline Arguments: [-fork1, -ProductionSNPCallerPluginV2, -db, ./GBSPVDunified.db, -e, ApeKI, -i, ./AllFastqFiles/, -k, ./GBS_PVd_unified_keyfile.txt, -kmerLength, 126, -mnQS, 20, -o, GBSPVdUnified.h5, -endplugin, -runfork1]
net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2
[pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin - Starting net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2: time: Dec 22, 2015 15:09:28
Enzyme: ApeKI
[pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin -
ProductionSNPCallerPluginV2 Parameters
i: ./AllFastqFiles/
k: ./GBS_PVd_unified_keyfile.txt
e: ApeKI
db: ./GBSPVDunified.db
o: GBSPVdUnified.h5
eR: 0.01
d: 0
ko: false
do: true
kmerLength: 126
minPosQS: 0.0
batchSize: 8
mnQS: 20
size of all tags in tag table=600431
size of all tissues in tissue table=0
size of all tags in mappingApproach table=2
size of all taxa in taxa table=297
ProductionSNPCallerPluginV2: Total batches to process: 4
size of all positions in snpPosition table=207913
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 -
The target HDF5 file:
GBSPVdUnified.h5
does not exist. A new HDF5 file of that name will be created
to hold the genotypes from this run.
size of all positions in snpPosition table=207913
size of all alleles in allele table=448635
Start processing batch 1
Enzyme: ApeKI
Enzyme: ApeKI
Enzyme: ApeKI
Enzyme: ApeKI
Enzyme: ApeKI
Enzyme: ApeKI
Enzyme: ApeKI
[ForkJoinPool.commonPool-worker-4] INFO net.maizegenetics.analysis.gbs.v2.GBSUtils - /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol011-1-GGCTAC_L008-R1_fastq.fastq: Quality score base:33
[ForkJoinPool.commonPool-worker-6] INFO net.maizegenetics.analysis.gbs.v2.GBSUtils - /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol6-1-GCCAAT_L008-R2_fastq.fastq: Quality score base:33
[ForkJoinPool.commonPool-worker-2] INFO net.maizegenetics.analysis.gbs.v2.GBSUtils - /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol1-1-ATCACG_L008-R1_fastq.fastq: Quality score base:33
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.GBSUtils - /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol007-1-CAGATC_L008-R1_fastq.fastq: Quality score base:33
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.GBSUtils - /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol5-1-ACAGTG_L008-R2_fastq.fastq: Quality score base:33
Enzyme: ApeKI
[ForkJoinPool.commonPool-worker-13] INFO net.maizegenetics.analysis.gbs.v2.GBSUtils - /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol013-1-AGTCAA_L008-R1_fastq.fastq: Quality score base:33
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.GBSUtils - /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol008-1-ACTTGA_L008-R1_fastq.fastq: Quality score base:33
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.GBSUtils - /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol2-1-CGATGT_L008-R1_fastq.fastq: Quality score base:33
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:1000000 Reads with barcode and cut site overhang:355967 rate:25951 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:1000000 Reads with barcode and cut site overhang:457862 rate:25926 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:3000000 Reads with barcode and cut site overhang:1344680 rate:24270 ns/read
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:3000000 Reads with barcode and cut site overhang:972443 rate:24618 ns/read
[ForkJoinPool.commonPool-worker-6] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:4000000 Reads with barcode and cut site overhang:1563205 rate:23392 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:4000000 Reads with barcode and cut site overhang:1778118 rate:24046 ns/read
[ForkJoinPool.commonPool-worker-6] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:6000000 Reads with barcode and cut site overhang:2200560 rate:23300 ns/read
[ForkJoinPool.commonPool-worker-13] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:7000000 Reads with barcode and cut site overhang:1191682 rate:23412 ns/read
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:8000000 Reads with barcode and cut site overhang:2752463 rate:23795 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:9000000 Reads with barcode and cut site overhang:3880803 rate:23814 ns/read
[ForkJoinPool.commonPool-worker-2] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:10000000 Reads with barcode and cut site overhang:2674223 rate:23025 ns/read
[ForkJoinPool.commonPool-worker-13] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:11000000 Reads with barcode and cut site overhang:1900567 rate:23305 ns/read
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:11000000 Reads with barcode and cut site overhang:3833741 rate:23645 ns/read
[ForkJoinPool.commonPool-worker-2] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:12000000 Reads with barcode and cut site overhang:3231738 rate:23062 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:12000000 Reads with barcode and cut site overhang:5201645 rate:23748 ns/read
[ForkJoinPool.commonPool-worker-2] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:13000000 Reads with barcode and cut site overhang:3530582 rate:23057 ns/read
[ForkJoinPool.commonPool-worker-6] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:13000000 Reads with barcode and cut site overhang:4685876 rate:23389 ns/read
[ForkJoinPool.commonPool-worker-4] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:15000000 Reads with barcode and cut site overhang:973045 rate:22921 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:15000000 Reads with barcode and cut site overhang:6672919 rate:23640 ns/read
[ForkJoinPool.commonPool-worker-2] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:16000000 Reads with barcode and cut site overhang:4581295 rate:23053 ns/read
[ForkJoinPool.commonPool-worker-13] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:16000000 Reads with barcode and cut site overhang:2733492 rate:23240 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:16000000 Reads with barcode and cut site overhang:7181609 rate:23584 ns/read
[ForkJoinPool.commonPool-worker-6] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:17000000 Reads with barcode and cut site overhang:6523548 rate:23371 ns/read
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:17000000 Reads with barcode and cut site overhang:5913254 rate:23575 ns/read
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:18000000 Reads with barcode and cut site overhang:735177 rate:23240 ns/read
[ForkJoinPool.commonPool-worker-6] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:19000000 Reads with barcode and cut site overhang:7435389 rate:23365 ns/read
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:19000000 Reads with barcode and cut site overhang:6532646 rate:23552 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:19000000 Reads with barcode and cut site overhang:8618174 rate:23637 ns/read
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:20000000 Reads with barcode and cut site overhang:773478 rate:23073 ns/read
[ForkJoinPool.commonPool-worker-2] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:20000000 Reads with barcode and cut site overhang:5943837 rate:23098 ns/read
[ForkJoinPool.commonPool-worker-13] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:20000000 Reads with barcode and cut site overhang:3399119 rate:23235 ns/read
[ForkJoinPool.commonPool-worker-6] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:20000000 Reads with barcode and cut site overhang:7820241 rate:23405 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:20000000 Reads with barcode and cut site overhang:9097058 rate:23703 ns/read
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:21000000 Reads with barcode and cut site overhang:854402 rate:23281 ns/read
[ForkJoinPool.commonPool-worker-2] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:22000000 Reads with barcode and cut site overhang:6536063 rate:23091 ns/read
[ForkJoinPool.commonPool-worker-6] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:22000000 Reads with barcode and cut site overhang:8604244 rate:23322 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:22000000 Reads with barcode and cut site overhang:10067312 rate:23679 ns/read
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:23000000 Reads with barcode and cut site overhang:928973 rate:23222 ns/read
[ForkJoinPool.commonPool-worker-6] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:23000000 Reads with barcode and cut site overhang:9027936 rate:23347 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:23000000 Reads with barcode and cut site overhang:10542200 rate:23638 ns/read
[ForkJoinPool.commonPool-worker-2] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:24000000 Reads with barcode and cut site overhang:7169019 rate:23110 ns/read
[ForkJoinPool.commonPool-worker-6] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:24000000 Reads with barcode and cut site overhang:9452773 rate:23316 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:24000000 Reads with barcode and cut site overhang:11010456 rate:23654 ns/read
[ForkJoinPool.commonPool-worker-2] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:25000000 Reads with barcode and cut site overhang:7483275 rate:23094 ns/read
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of reads in lane=24853605
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of good barcoded reads=996511
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of low quality reads=1329705
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Timing process (sorting, collapsing, and writing TagCount to file).
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Process took 578910.095277 milliseconds for file /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol008-1-ACTTGA_L008-R1_fastq.fastq
[ForkJoinPool.commonPool-worker-13] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:25000000 Reads with barcode and cut site overhang:4301317 rate:23251 ns/read
[ForkJoinPool.commonPool-worker-6] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:25000000 Reads with barcode and cut site overhang:9820938 rate:23334 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:25000000 Reads with barcode and cut site overhang:11487748 rate:23567 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:26000000 Reads with barcode and cut site overhang:11979666 rate:23418 ns/read
[ForkJoinPool.commonPool-worker-13] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:27000000 Reads with barcode and cut site overhang:4653863 rate:23043 ns/read
[ForkJoinPool.commonPool-worker-6] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:27000000 Reads with barcode and cut site overhang:10595427 rate:23121 ns/read
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:27000000 Reads with barcode and cut site overhang:8980369 rate:23182 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:27000000 Reads with barcode and cut site overhang:12476830 rate:23336 ns/read
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of reads in lane=27627572
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of good barcoded reads=9091237
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of low quality reads=17031715
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Timing process (sorting, collapsing, and writing TagCount to file).
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Process took 639301.036088 milliseconds for file /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol5-1-ACAGTG_L008-R2_fastq.fastq
[ForkJoinPool.commonPool-worker-2] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:29000000 Reads with barcode and cut site overhang:8813457 rate:22615 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:29000000 Reads with barcode and cut site overhang:13480408 rate:22956 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:30000000 Reads with barcode and cut site overhang:14012618 rate:22792 ns/read
[ForkJoinPool.commonPool-worker-6] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:31000000 Reads with barcode and cut site overhang:12273199 rate:22442 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:31000000 Reads with barcode and cut site overhang:14537767 rate:22634 ns/read
[ForkJoinPool.commonPool-worker-13] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:32000000 Reads with barcode and cut site overhang:5528102 rate:22220 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:32000000 Reads with barcode and cut site overhang:15021858 rate:22467 ns/read
[ForkJoinPool.commonPool-worker-4] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of reads in lane=33746558
[ForkJoinPool.commonPool-worker-4] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of good barcoded reads=2175514
[ForkJoinPool.commonPool-worker-4] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of low quality reads=3679143
[ForkJoinPool.commonPool-worker-4] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Timing process (sorting, collapsing, and writing TagCount to file).
[ForkJoinPool.commonPool-worker-4] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Process took 736742.380462 milliseconds for file /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol011-1-GGCTAC_L008-R1_fastq.fastq
[ForkJoinPool.commonPool-worker-6] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:34000000 Reads with barcode and cut site overhang:13447593 rate:21954 ns/read
[ForkJoinPool.commonPool-worker-13] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:35000000 Reads with barcode and cut site overhang:6033507 rate:21697 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:35000000 Reads with barcode and cut site overhang:16522229 rate:21878 ns/read
[ForkJoinPool.commonPool-worker-6] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:36000000 Reads with barcode and cut site overhang:14131112 rate:21543 ns/read
[ForkJoinPool.commonPool-worker-2] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:37000000 Reads with barcode and cut site overhang:11793207 rate:21221 ns/read
[ForkJoinPool.commonPool-worker-6] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:37000000 Reads with barcode and cut site overhang:14536094 rate:21351 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:37000000 Reads with barcode and cut site overhang:17554205 rate:21477 ns/read
[ForkJoinPool.commonPool-worker-2] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:38000000 Reads with barcode and cut site overhang:12162279 rate:21053 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:38000000 Reads with barcode and cut site overhang:18046706 rate:21290 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:40000000 Reads with barcode and cut site overhang:19076200 rate:20959 ns/read
[ForkJoinPool.commonPool-worker-2] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:41000000 Reads with barcode and cut site overhang:13303120 rate:20578 ns/read
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of reads in lane=41312418
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of good barcoded reads=1581938
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of low quality reads=2293559
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Timing process (sorting, collapsing, and writing TagCount to file).
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Process took 847904.568675 milliseconds for file /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol007-1-CAGATC_L008-R1_fastq.fastq
[ForkJoinPool.commonPool-worker-13] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:42000000 Reads with barcode and cut site overhang:7221841 rate:20430 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:42000000 Reads with barcode and cut site overhang:20114831 rate:20563 ns/read
[ForkJoinPool.commonPool-worker-2] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:43000000 Reads with barcode and cut site overhang:14102184 rate:20183 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:43000000 Reads with barcode and cut site overhang:20645538 rate:20348 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:45000000 Reads with barcode and cut site overhang:21548355 rate:19960 ns/read
[ForkJoinPool.commonPool-worker-6] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:46000000 Reads with barcode and cut site overhang:17955285 rate:19703 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:46000000 Reads with barcode and cut site overhang:21738510 rate:19783 ns/read
[ForkJoinPool.commonPool-worker-13] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:47000000 Reads with barcode and cut site overhang:7967367 rate:19485 ns/read
[ForkJoinPool.commonPool-worker-13] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of reads in lane=48312799
[ForkJoinPool.commonPool-worker-13] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of good barcoded reads=8188613
[ForkJoinPool.commonPool-worker-13] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of low quality reads=10941481
[ForkJoinPool.commonPool-worker-13] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Timing process (sorting, collapsing, and writing TagCount to file).
[ForkJoinPool.commonPool-worker-13] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Process took 931064.56337 milliseconds for file /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol013-1-AGTCAA_L008-R1_fastq.fastq
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:48000000 Reads with barcode and cut site overhang:22786244 rate:19430 ns/read
[ForkJoinPool.commonPool-worker-6] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:49000000 Reads with barcode and cut site overhang:18995509 rate:19156 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:50000000 Reads with barcode and cut site overhang:23803607 rate:19000 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:51000000 Reads with barcode and cut site overhang:24334846 rate:18797 ns/read
[ForkJoinPool.commonPool-worker-6] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:52000000 Reads with barcode and cut site overhang:20010857 rate:18553 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:52000000 Reads with barcode and cut site overhang:24746362 rate:18606 ns/read
[ForkJoinPool.commonPool-worker-2] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:53000000 Reads with barcode and cut site overhang:17722888 rate:18325 ns/read
[ForkJoinPool.commonPool-worker-6] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:53000000 Reads with barcode and cut site overhang:20432779 rate:18366 ns/read
[ForkJoinPool.commonPool-worker-2] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:54000000 Reads with barcode and cut site overhang:18116004 rate:18143 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:55000000 Reads with barcode and cut site overhang:26328801 rate:18067 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:58000000 Reads with barcode and cut site overhang:27878848 rate:17583 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of reads in lane=58322655
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of good barcoded reads=28039733
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of low quality reads=29202212
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Timing process (sorting, collapsing, and writing TagCount to file).
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Process took 1022790.290861 milliseconds for file /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol2-1-CGATGT_L008-R1_fastq.fastq
[ForkJoinPool.commonPool-worker-2] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:59000000 Reads with barcode and cut site overhang:20062764 rate:17339 ns/read
[ForkJoinPool.commonPool-worker-2] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:60000000 Reads with barcode and cut site overhang:20455709 rate:17147 ns/read
[ForkJoinPool.commonPool-worker-6] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:60000000 Reads with barcode and cut site overhang:22689065 rate:17179 ns/read
[ForkJoinPool.commonPool-worker-2] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:61000000 Reads with barcode and cut site overhang:20853728 rate:16962 ns/read
[ForkJoinPool.commonPool-worker-2] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:62000000 Reads with barcode and cut site overhang:21303005 rate:16782 ns/read
[ForkJoinPool.commonPool-worker-2] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of reads in lane=62268079
[ForkJoinPool.commonPool-worker-2] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of good barcoded reads=21409214
[ForkJoinPool.commonPool-worker-2] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of low quality reads=39011508
[ForkJoinPool.commonPool-worker-2] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Timing process (sorting, collapsing, and writing TagCount to file).
[ForkJoinPool.commonPool-worker-2] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Process took 1042062.086406 milliseconds for file /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol1-1-ATCACG_L008-R1_fastq.fastq
[ForkJoinPool.commonPool-worker-6] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of reads in lane=62500553
[ForkJoinPool.commonPool-worker-6] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of good barcoded reads=23400053
[ForkJoinPool.commonPool-worker-6] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of low quality reads=36210925
[ForkJoinPool.commonPool-worker-6] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Timing process (sorting, collapsing, and writing TagCount to file).
[ForkJoinPool.commonPool-worker-6] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Process took 1043664.055963 milliseconds for file /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol6-1-GCCAAT_L008-R2_fastq.fastq
Finished processing batch 1
Start processing batch 2
Enzyme: ApeKI
Enzyme: ApeKI
Enzyme: ApeKI
Enzyme: ApeKI
Enzyme: ApeKI
Enzyme: ApeKI
Enzyme: ApeKI
Enzyme: ApeKI
[ForkJoinPool.commonPool-worker-4] INFO net.maizegenetics.analysis.gbs.v2.GBSUtils - /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol4-1-TGACCA_L008-R2_fastq.fastq: Quality score base:33
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.GBSUtils - /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol010-1-TAGCTT_L008-R2_fastq.fastq: Quality score base:33
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.GBSUtils - /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol010-1-TAGCTT_L008-R1_fastq.fastq: Quality score base:33
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.GBSUtils - /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol4-1-TGACCA_L008-R1_fastq.fastq: Quality score base:33
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.GBSUtils - /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol009-1-GATCAG_L008-R2_fastq.fastq: Quality score base:33
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.GBSUtils - /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol3-1-TTAGGC_L008-R1_fastq.fastq: Quality score base:33
[ForkJoinPool.commonPool-worker-13] INFO net.maizegenetics.analysis.gbs.v2.GBSUtils - /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol012-1-CTTGTA_L008-R1_fastq.fastq: Quality score base:33
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.GBSUtils - /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/GBSPVD_2_fastq.fastq: Quality score base:33
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:3000000 Reads with barcode and cut site overhang:1237352 rate:24134 ns/read
[ForkJoinPool.commonPool-worker-4] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:6000000 Reads with barcode and cut site overhang:1859802 rate:23268 ns/read
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:6000000 Reads with barcode and cut site overhang:2502398 rate:23751 ns/read
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:6000000 Reads with barcode and cut site overhang:2481349 rate:23777 ns/read
[ForkJoinPool.commonPool-worker-4] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:7000000 Reads with barcode and cut site overhang:2290845 rate:23502 ns/read
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:7000000 Reads with barcode and cut site overhang:2974952 rate:23629 ns/read
[ForkJoinPool.commonPool-worker-4] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:8000000 Reads with barcode and cut site overhang:2674408 rate:23374 ns/read
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:8000000 Reads with barcode and cut site overhang:3448523 rate:23486 ns/read
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:9000000 Reads with barcode and cut site overhang:3254462 rate:21764 ns/read
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:9000000 Reads with barcode and cut site overhang:3897921 rate:23577 ns/read
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:10000000 Reads with barcode and cut site overhang:4341823 rate:23498 ns/read
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:11000000 Reads with barcode and cut site overhang:3991434 rate:21657 ns/read
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of reads in lane=12158498
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of good barcoded reads=4421065
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of low quality reads=6049864
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Timing process (sorting, collapsing, and writing TagCount to file).
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Process took 263941.613539 milliseconds for file /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/GBSPVD_2_fastq.fastq
[ForkJoinPool.commonPool-worker-4] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:12000000 Reads with barcode and cut site overhang:4036890 rate:23287 ns/read
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:12000000 Reads with barcode and cut site overhang:5267137 rate:23298 ns/read
[ForkJoinPool.commonPool-worker-4] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:13000000 Reads with barcode and cut site overhang:4400103 rate:23020 ns/read
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:13000000 Reads with barcode and cut site overhang:5754364 rate:23128 ns/read
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:15000000 Reads with barcode and cut site overhang:6746524 rate:22762 ns/read
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:16000000 Reads with barcode and cut site overhang:7222387 rate:22578 ns/read
[ForkJoinPool.commonPool-worker-4] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:19000000 Reads with barcode and cut site overhang:6286185 rate:22210 ns/read
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:20000000 Reads with barcode and cut site overhang:1124955 rate:21867 ns/read
[ForkJoinPool.commonPool-worker-4] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:20000000 Reads with barcode and cut site overhang:6578340 rate:22097 ns/read
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:20000000 Reads with barcode and cut site overhang:9042387 rate:22152 ns/read
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:21000000 Reads with barcode and cut site overhang:9490519 rate:22037 ns/read
[ForkJoinPool.commonPool-worker-4] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:21000000 Reads with barcode and cut site overhang:6871289 rate:22043 ns/read
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:22000000 Reads with barcode and cut site overhang:9977484 rate:21992 ns/read
[ForkJoinPool.commonPool-worker-4] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:23000000 Reads with barcode and cut site overhang:7423653 rate:21849 ns/read
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:24000000 Reads with barcode and cut site overhang:10945502 rate:21807 ns/read
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of reads in lane=24404610
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of good barcoded reads=11174187
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of low quality reads=12657479
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Timing process (sorting, collapsing, and writing TagCount to file).
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Process took 532133.105123 milliseconds for file /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol3-1-TTAGGC_L008-R1_fastq.fastq
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:25000000 Reads with barcode and cut site overhang:11429298 rate:21711 ns/read
[ForkJoinPool.commonPool-worker-4] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of reads in lane=25527073
[ForkJoinPool.commonPool-worker-4] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of good barcoded reads=8107465
[ForkJoinPool.commonPool-worker-4] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of low quality reads=15775883
[ForkJoinPool.commonPool-worker-4] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Timing process (sorting, collapsing, and writing TagCount to file).
[ForkJoinPool.commonPool-worker-4] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Process took 551044.060314 milliseconds for file /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol4-1-TGACCA_L008-R2_fastq.fastq
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of reads in lane=25527073
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of good barcoded reads=11697787
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of low quality reads=13299901
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Timing process (sorting, collapsing, and writing TagCount to file).
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Process took 551879.336801 milliseconds for file /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol4-1-TGACCA_L008-R1_fastq.fastq
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:29000000 Reads with barcode and cut site overhang:1120859 rate:20309 ns/read
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:31000000 Reads with barcode and cut site overhang:1574244 rate:19766 ns/read
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of reads in lane=32237757
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of good barcoded reads=1596704
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of low quality reads=4074794
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Timing process (sorting, collapsing, and writing TagCount to file).
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Process took 627020.575218 milliseconds for file /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol009-1-GATCAG_L008-R2_fastq.fastq
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of reads in lane=38230971
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of good barcoded reads=958481
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of low quality reads=2220064
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Timing process (sorting, collapsing, and writing TagCount to file).
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Process took 678508.500848 milliseconds for file /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol010-1-TAGCTT_L008-R2_fastq.fastq
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of reads in lane=38230971
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of good barcoded reads=1450705
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of low quality reads=1851100
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Timing process (sorting, collapsing, and writing TagCount to file).
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Process took 678753.458972 milliseconds for file /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol010-1-TAGCTT_L008-R1_fastq.fastq
[ForkJoinPool.commonPool-worker-13] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of reads in lane=49082144
[ForkJoinPool.commonPool-worker-13] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of good barcoded reads=2501488
[ForkJoinPool.commonPool-worker-13] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of low quality reads=3314516
[ForkJoinPool.commonPool-worker-13] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Timing process (sorting, collapsing, and writing TagCount to file).
[ForkJoinPool.commonPool-worker-13] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Process took 710881.36816 milliseconds for file /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol012-1-CTTGTA_L008-R1_fastq.fastq
Finished processing batch 2
Start processing batch 3
Enzyme: ApeKI
Enzyme: ApeKI
Enzyme: ApeKI
Enzyme: ApeKI
Enzyme: ApeKI
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.GBSUtils - /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol6-1-GCCAAT_L008-R1_fastq.fastq: Quality score base:33
[ForkJoinPool.commonPool-worker-10] INFO net.maizegenetics.analysis.gbs.v2.GBSUtils - /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol3-1-TTAGGC_L008-R2_fastq.fastq: Quality score base:33
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.GBSUtils - /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/GBSPVD_1_fastq.fastq: Quality score base:33
Enzyme: ApeKI
Enzyme: ApeKI
[ForkJoinPool.commonPool-worker-4] INFO net.maizegenetics.analysis.gbs.v2.GBSUtils - /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol009-1-GATCAG_L008-R1_fastq.fastq: Quality score base:33
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.GBSUtils - /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol011-1-GGCTAC_L008-R2_fastq.fastq: Quality score base:33
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.GBSUtils - /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol012-1-CTTGTA_L008-R2_fastq.fastq: Quality score base:33
Enzyme: ApeKI
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.GBSUtils - /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol1-1-ATCACG_L008-R2_fastq.fastq: Quality score base:33
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.GBSUtils - /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol007-1-CAGATC_L008-R2_fastq.fastq: Quality score base:33
[ForkJoinPool.commonPool-worker-10] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:1000000 Reads with barcode and cut site overhang:316918 rate:21769 ns/read
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:2000000 Reads with barcode and cut site overhang:884867 rate:22526 ns/read
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:3000000 Reads with barcode and cut site overhang:1409334 rate:21536 ns/read
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:3000000 Reads with barcode and cut site overhang:1324425 rate:22461 ns/read
[ForkJoinPool.commonPool-worker-10] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:5000000 Reads with barcode and cut site overhang:1359588 rate:23054 ns/read
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:5000000 Reads with barcode and cut site overhang:1937673 rate:23624 ns/read
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:6000000 Reads with barcode and cut site overhang:2577156 rate:23048 ns/read
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:7000000 Reads with barcode and cut site overhang:2657535 rate:23536 ns/read
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:8000000 Reads with barcode and cut site overhang:3064269 rate:23404 ns/read
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:9000000 Reads with barcode and cut site overhang:4243878 rate:21444 ns/read
[ForkJoinPool.commonPool-worker-10] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:9000000 Reads with barcode and cut site overhang:2723615 rate:23099 ns/read
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:10000000 Reads with barcode and cut site overhang:3780435 rate:23475 ns/read
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:11000000 Reads with barcode and cut site overhang:5177053 rate:21463 ns/read
[ForkJoinPool.commonPool-worker-10] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:11000000 Reads with barcode and cut site overhang:3311839 rate:23161 ns/read
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of reads in lane=12158498
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of good barcoded reads=5713902
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of low quality reads=5164922
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Timing process (sorting, collapsing, and writing TagCount to file).
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Process took 260550.067585 milliseconds for file /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/GBSPVD_1_fastq.fastq
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:12000000 Reads with barcode and cut site overhang:5150971 rate:22967 ns/read
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:12000000 Reads with barcode and cut site overhang:4556625 rate:23268 ns/read
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:13000000 Reads with barcode and cut site overhang:5605011 rate:22695 ns/read
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:13000000 Reads with barcode and cut site overhang:4958895 rate:23032 ns/read
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:14000000 Reads with barcode and cut site overhang:6052820 rate:22571 ns/read
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:14000000 Reads with barcode and cut site overhang:5389819 rate:22865 ns/read
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:15000000 Reads with barcode and cut site overhang:5840279 rate:22688 ns/read
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:16000000 Reads with barcode and cut site overhang:7070172 rate:22227 ns/read
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:16000000 Reads with barcode and cut site overhang:6337652 rate:22524 ns/read
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:17000000 Reads with barcode and cut site overhang:7569794 rate:22167 ns/read
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:18000000 Reads with barcode and cut site overhang:8075230 rate:22057 ns/read
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:18000000 Reads with barcode and cut site overhang:7285975 rate:22315 ns/read
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:19000000 Reads with barcode and cut site overhang:8575747 rate:21993 ns/read
[ForkJoinPool.commonPool-worker-10] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:19000000 Reads with barcode and cut site overhang:5631460 rate:22026 ns/read
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:20000000 Reads with barcode and cut site overhang:9034543 rate:21888 ns/read
[ForkJoinPool.commonPool-worker-10] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:20000000 Reads with barcode and cut site overhang:5917778 rate:21925 ns/read
[ForkJoinPool.commonPool-worker-4] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:20000000 Reads with barcode and cut site overhang:1377496 rate:21944 ns/read
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:20000000 Reads with barcode and cut site overhang:597887 rate:22067 ns/read
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:22000000 Reads with barcode and cut site overhang:9953503 rate:21763 ns/read
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:22000000 Reads with barcode and cut site overhang:8998935 rate:21990 ns/read
[ForkJoinPool.commonPool-worker-4] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:23000000 Reads with barcode and cut site overhang:1579063 rate:21716 ns/read
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:24000000 Reads with barcode and cut site overhang:9901670 rate:21868 ns/read
[ForkJoinPool.commonPool-worker-10] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of reads in lane=24404610
[ForkJoinPool.commonPool-worker-10] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of good barcoded reads=6986692
[ForkJoinPool.commonPool-worker-10] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of low quality reads=15624016
[ForkJoinPool.commonPool-worker-10] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Timing process (sorting, collapsing, and writing TagCount to file).
[ForkJoinPool.commonPool-worker-10] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Process took 527972.006192 milliseconds for file /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol3-1-TTAGGC_L008-R2_fastq.fastq
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:25000000 Reads with barcode and cut site overhang:11380193 rate:21513 ns/read
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:25000000 Reads with barcode and cut site overhang:10327496 rate:21698 ns/read
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:26000000 Reads with barcode and cut site overhang:10715627 rate:21553 ns/read
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:27000000 Reads with barcode and cut site overhang:12328287 rate:21209 ns/read
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:28000000 Reads with barcode and cut site overhang:12825961 rate:21073 ns/read
[ForkJoinPool.commonPool-worker-4] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:28000000 Reads with barcode and cut site overhang:1914714 rate:21113 ns/read
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:28000000 Reads with barcode and cut site overhang:11600288 rate:21252 ns/read
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:29000000 Reads with barcode and cut site overhang:13317062 rate:20924 ns/read
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:29000000 Reads with barcode and cut site overhang:12073805 rate:21101 ns/read
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:30000000 Reads with barcode and cut site overhang:12563912 rate:20978 ns/read
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:32000000 Reads with barcode and cut site overhang:14837633 rate:20637 ns/read
[ForkJoinPool.commonPool-worker-4] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of reads in lane=32237757
[ForkJoinPool.commonPool-worker-4] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of good barcoded reads=2171977
[ForkJoinPool.commonPool-worker-4] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of low quality reads=3682205
[ForkJoinPool.commonPool-worker-4] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Timing process (sorting, collapsing, and writing TagCount to file).
[ForkJoinPool.commonPool-worker-4] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Process took 664634.879651 milliseconds for file /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol009-1-GATCAG_L008-R1_fastq.fastq
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of reads in lane=33746558
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of good barcoded reads=1433058
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of low quality reads=4219957
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Timing process (sorting, collapsing, and writing TagCount to file).
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Process took 686299.055937 milliseconds for file /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol011-1-GGCTAC_L008-R2_fastq.fastq
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:34000000 Reads with barcode and cut site overhang:15832741 rate:20288 ns/read
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:34000000 Reads with barcode and cut site overhang:14348269 rate:20360 ns/read
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:36000000 Reads with barcode and cut site overhang:16815573 rate:19795 ns/read
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:36000000 Reads with barcode and cut site overhang:15088785 rate:19867 ns/read
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:37000000 Reads with barcode and cut site overhang:15555884 rate:19639 ns/read
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:38000000 Reads with barcode and cut site overhang:16026525 rate:19436 ns/read
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:40000000 Reads with barcode and cut site overhang:16886694 rate:19048 ns/read
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:41000000 Reads with barcode and cut site overhang:19335695 rate:18812 ns/read
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of reads in lane=41312418
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of good barcoded reads=1094894
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of low quality reads=2654430
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Timing process (sorting, collapsing, and writing TagCount to file).
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Process took 775139.069221 milliseconds for file /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol007-1-CAGATC_L008-R2_fastq.fastq
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:43000000 Reads with barcode and cut site overhang:18154165 rate:18405 ns/read
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:47000000 Reads with barcode and cut site overhang:19958871 rate:17586 ns/read
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:48000000 Reads with barcode and cut site overhang:22808719 rate:17359 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of reads in lane=49082144
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of good barcoded reads=1807034
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of low quality reads=3838814
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Timing process (sorting, collapsing, and writing TagCount to file).
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Process took 842594.565066 milliseconds for file /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol012-1-CTTGTA_L008-R2_fastq.fastq
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:51000000 Reads with barcode and cut site overhang:21548499 rate:16766 ns/read
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:53000000 Reads with barcode and cut site overhang:25000735 rate:16329 ns/read
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:53000000 Reads with barcode and cut site overhang:22383514 rate:16354 ns/read
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:54000000 Reads with barcode and cut site overhang:22862918 rate:16159 ns/read
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:56000000 Reads with barcode and cut site overhang:26424926 rate:15769 ns/read
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:57000000 Reads with barcode and cut site overhang:26930617 rate:15592 ns/read
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:59000000 Reads with barcode and cut site overhang:27990444 rate:15261 ns/read
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:60000000 Reads with barcode and cut site overhang:28522015 rate:15106 ns/read
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:60000000 Reads with barcode and cut site overhang:25082888 rate:15120 ns/read
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:61000000 Reads with barcode and cut site overhang:28981366 rate:14952 ns/read
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:61000000 Reads with barcode and cut site overhang:25523782 rate:14969 ns/read
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of reads in lane=62268079
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of good barcoded reads=25825559
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of low quality reads=32192312
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Timing process (sorting, collapsing, and writing TagCount to file).
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Process took 920385.358958 milliseconds for file /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol1-1-ATCACG_L008-R2_fastq.fastq
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of reads in lane=62500553
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of good barcoded reads=29775658
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of low quality reads=31632914
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Timing process (sorting, collapsing, and writing TagCount to file).
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Process took 920681.30706 milliseconds for file /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol6-1-GCCAAT_L008-R1_fastq.fastq
Finished processing batch 3
Start processing batch 4
Enzyme: ApeKI
Enzyme: ApeKI
Enzyme: ApeKI
Enzyme: ApeKI
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.GBSUtils - /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol008-1-ACTTGA_L008-R2_fastq.fastq: Quality score base:33
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.GBSUtils - /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol5-1-ACAGTG_L008-R1_fastq.fastq: Quality score base:33
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.GBSUtils - /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol2-1-CGATGT_L008-R2_fastq.fastq: Quality score base:33
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.GBSUtils - /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol013-1-AGTCAA_L008-R2_fastq.fastq: Quality score base:33
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:1000000 Reads with barcode and cut site overhang:415271 rate:11756 ns/read
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:2000000 Reads with barcode and cut site overhang:814889 rate:11781 ns/read
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:3000000 Reads with barcode and cut site overhang:1207316 rate:11747 ns/read
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:4000000 Reads with barcode and cut site overhang:1605974 rate:11664 ns/read
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:4000000 Reads with barcode and cut site overhang:1437704 rate:11823 ns/read
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:6000000 Reads with barcode and cut site overhang:2423622 rate:11670 ns/read
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:7000000 Reads with barcode and cut site overhang:890161 rate:11726 ns/read
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:9000000 Reads with barcode and cut site overhang:2971903 rate:11758 ns/read
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:11000000 Reads with barcode and cut site overhang:3612099 rate:11743 ns/read
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:12000000 Reads with barcode and cut site overhang:5153809 rate:11653 ns/read
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:12000000 Reads with barcode and cut site overhang:3931257 rate:11717 ns/read
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:14000000 Reads with barcode and cut site overhang:4743413 rate:11721 ns/read
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:15000000 Reads with barcode and cut site overhang:5199355 rate:11692 ns/read
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:16000000 Reads with barcode and cut site overhang:2068821 rate:11667 ns/read
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:16000000 Reads with barcode and cut site overhang:5628864 rate:11707 ns/read
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:17000000 Reads with barcode and cut site overhang:7534051 rate:11646 ns/read
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:18000000 Reads with barcode and cut site overhang:6438060 rate:11704 ns/read
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:19000000 Reads with barcode and cut site overhang:8494581 rate:11669 ns/read
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:19000000 Reads with barcode and cut site overhang:6783122 rate:11695 ns/read
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:20000000 Reads with barcode and cut site overhang:2584410 rate:11650 ns/read
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:20000000 Reads with barcode and cut site overhang:8983660 rate:11663 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:21000000 Reads with barcode and cut site overhang:652002 rate:11567 ns/read
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:22000000 Reads with barcode and cut site overhang:2843322 rate:11641 ns/read
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:22000000 Reads with barcode and cut site overhang:9758533 rate:11653 ns/read
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:23000000 Reads with barcode and cut site overhang:2989576 rate:11637 ns/read
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:23000000 Reads with barcode and cut site overhang:8291684 rate:11687 ns/read
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:24000000 Reads with barcode and cut site overhang:8616788 rate:11681 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of reads in lane=24853605
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of good barcoded reads=716748
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of low quality reads=1530844
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Timing process (sorting, collapsing, and writing TagCount to file).
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Process took 287647.460362 milliseconds for file /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol008-1-ACTTGA_L008-R2_fastq.fastq
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:25000000 Reads with barcode and cut site overhang:3295271 rate:11616 ns/read
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:25000000 Reads with barcode and cut site overhang:8969613 rate:11636 ns/read
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:27000000 Reads with barcode and cut site overhang:12157192 rate:11399 ns/read
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:27000000 Reads with barcode and cut site overhang:3553818 rate:11404 ns/read
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:27000000 Reads with barcode and cut site overhang:9715171 rate:11423 ns/read
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of reads in lane=27627572
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of good barcoded reads=12473904
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of low quality reads=14636326
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Timing process (sorting, collapsing, and writing TagCount to file).
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Process took 313163.915666 milliseconds for file /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol5-1-ACAGTG_L008-R1_fastq.fastq
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:28000000 Reads with barcode and cut site overhang:3684489 rate:11266 ns/read
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:29000000 Reads with barcode and cut site overhang:10495434 rate:11087 ns/read
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:35000000 Reads with barcode and cut site overhang:4539563 rate:10175 ns/read
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:38000000 Reads with barcode and cut site overhang:13552955 rate:9839 ns/read
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:39000000 Reads with barcode and cut site overhang:13866086 rate:9736 ns/read
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:40000000 Reads with barcode and cut site overhang:14231978 rate:9639 ns/read
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:42000000 Reads with barcode and cut site overhang:5236201 rate:9451 ns/read
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:44000000 Reads with barcode and cut site overhang:15632588 rate:9287 ns/read
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:45000000 Reads with barcode and cut site overhang:15902867 rate:9210 ns/read
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:46000000 Reads with barcode and cut site overhang:16290239 rate:9136 ns/read
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:47000000 Reads with barcode and cut site overhang:16581236 rate:9066 ns/read
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:48000000 Reads with barcode and cut site overhang:16911506 rate:8999 ns/read
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of reads in lane=48312799
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of good barcoded reads=5643335
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of low quality reads=12704945
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Timing process (sorting, collapsing, and writing TagCount to file).
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Process took 433605.385598 milliseconds for file /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol013-1-AGTCAA_L008-R2_fastq.fastq
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:50000000 Reads with barcode and cut site overhang:17615397 rate:8771 ns/read
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:54000000 Reads with barcode and cut site overhang:18772604 rate:8337 ns/read
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:55000000 Reads with barcode and cut site overhang:19159328 rate:8238 ns/read
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of reads in lane=58322655
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of good barcoded reads=19952138
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of low quality reads=35196217
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Timing process (sorting, collapsing, and writing TagCount to file).
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Process took 462747.457207 milliseconds for file /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol2-1-CGATGT_L008-R2_fastq.fastq
Finished processing batch 4
Number of taxa in HDF5 file:106
[pool-1-thread-1] ERROR net.maizegenetics.plugindef.AbstractPlugin - null
[pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin -
Usage:
ProductionSNPCallerPluginV2 <options>
-i <Input Directory> : Input directory containing fastq AND/OR qseq files. (required)
-k <Key File> : Key file listing barcodes distinguishing the samples (required)
-e <Enzyme> : Enzyme used to create the GBS library (required)
-db <Input GBS Database> : Input Database file if using SQLite (required)
-o <Output Genotypes File> : Output (target) genotypes file to produce. Default output file type is VCF. If file suffix is .h5, an hdf5 file will be created instead. (required)
-eR <Ave Seq Error Rate> : Average sequencing error rate per base (used to decide between heterozygous and homozygous calls) (Default: 0.01)
-d <Max Divergence> : Maximum divergence (edit distance) between new read and previously mapped read (Default: 0 = perfect matches only) (Default: 0)
-ko <true | false> : Only applicable to hdf5 output files: Keep hdf5 genotypes open for future runs that add more taxa or more depth (Default: false)
-do <true | false> : Depth output: True means write depths to the output hdf5 genotypes file, false means do NOT write depths to the hdf5 file (Default: true)
-kmerLength <Maximum Kmer Length> : Length of kmers to process (Default: 64)
-minPosQS <Minimun snp quality score> : Minimum quality score for snp position to be included (Default: 0.0)
-batchSize <Batch size of fastq files> : Number of flow cells being processed simultaneously (Default: 8)
-mnQS <Minimum quality score> : Minimum quality score within the barcode and read length to be accepted (Default: 0)
[pool-1-thread-1] DEBUG net.maizegenetics.plugindef.AbstractPlugin - null
java.lang.NullPointerException
at net.maizegenetics.taxa.TaxaArrayList.<init>(TaxaArrayList.java:33)
at net.maizegenetics.taxa.TaxaListBuilder.build(TaxaListBuilder.java:116)
at net.maizegenetics.taxa.TaxaListBuilder.buildFromHDF5(TaxaListBuilder.java:149)
at net.maizegenetics.dna.snp.depth.HDF5AlleleDepth.<init>(HDF5AlleleDepth.java:39)
at net.maizegenetics.dna.snp.depth.AlleleDepthBuilder.getExistingHDF5Instance(AlleleDepthBuilder.java:90)
at net.maizegenetics.dna.snp.GenotypeTableBuilder.getInstance(GenotypeTableBuilder.java:449)
at net.maizegenetics.dna.snp.GenotypeTableBuilder.build(GenotypeTableBuilder.java:661)
at net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2.processData(ProductionSNPCallerPluginV2.java:275)
at net.maizegenetics.plugindef.AbstractPlugin.performFunction(AbstractPlugin.java:110)
at net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:1631)
at net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
********************************************************************************************
On Tuesday, December 22, 2015 at 2:45:12 PM UTC+1, Lynn Johnson wrote:
Hi Debora -
...
Debora Santo
Dec 22, 2015, 11:04:12 AM12/22/15
to TASSEL - Trait Analysis by Association, Evolution and Linkage
It seems that the end of my previous message was cut, maybe the debug text was too long.
Here I am re-sending just the end of the debug output with the details of the error in the message and the whole debug output file attached.
***************************************************************************************************
*************************************************************************************************************************************************
Thanks
Debora
Lynn Carol Johnson
Dec 22, 2015, 4:25:46 PM12/22/15
to tas...@googlegroups.com
Debora -
There’s a problem with the allele depths calculation when building the final genotype table in ProductionSNPCallerPluginV2. The reason you don’t see the error when the –ko open is used is because this step is skipped until the file is closed. (which
is why you see it when you run the plugin to close the file)
Can you give me specifics on how you ran the pipeline? Did you start with a specific set of fastQ files when running the Discovery steps (From GBSSeqToTagDBPlugin through DiscoverySNPCallerPluginV2)? Are you using different fastQ files when you run ProductionSNPCallerPluginV2?
Is it the same key file and taxa list?
What happens if you run ProductionSNPCallerPluginV2 using a single fastQ file that you ran during Discovery? I’m not suggesting this is a fix, I’m trying to narrow the problem.
Thanks - Lynn
From: <tas...@googlegroups.com> on behalf of Debora Santo <debora....@gmail.com>
Reply-To: "tas...@googlegroups.com" <tas...@googlegroups.com>
Date: Tuesday, December 22, 2015 at 11:04 AM
To: "TASSEL - Trait Analysis by Association, Evolution and Linkage" <tas...@googlegroups.com>
Subject: Re: [TASSEL-Group] Re: UpdateSNPPositionQualityPlugin error
Reply-To: "tas...@googlegroups.com" <tas...@googlegroups.com>
Date: Tuesday, December 22, 2015 at 11:04 AM
To: "TASSEL - Trait Analysis by Association, Evolution and Linkage" <tas...@googlegroups.com>
Subject: Re: [TASSEL-Group] Re: UpdateSNPPositionQualityPlugin error
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Debora Santo
Dec 23, 2015, 10:51:18 AM12/23/15
to TASSEL - Trait Analysis by Association, Evolution and Linkage
Hi Lynn,
At least, we now know what is wrong, so we are closer to solving the issue.
Attached is the file with the pipeline commands used on the cluster. I also attached the keyfile, so you can see the amount and organization of the data, if needed.
Just a quick background for the data: samples are divided into pools of 24 and sequenced in 3 lanes with paired end sequencing of 150 bp (2 fastq files are produced per pool). There are 13 pools in total, some samples are in 2 pools (in case they needed resequencing for additional data). The first lane was run on MiSeq as a trial, so it contains only one pool. The other two were run on Illumina HiSeq, 6 in the first one (it includes the first pool and five more) and 7 in the second (some samples from the first lane are re-sequenced in the last pools).
What I see as a potential issue is perhaps the fact that some samples with the same names in the keyfile are repeated due to re-sequencing, but then again, even when I tried to process only the first trial pool of samples, I got the same error - that was done on two fastq files with a keyfile for them that used to work well before, using commands and TASSEL v5.2.11 like when the data was first used to produce a SNP dataset. Could there be something wrong with the fastq files perhaps? I had to change their location, so maybe they weren't moved properly? Also, I know that the reference genome fastq file needs to be indexed before used, I used BWA for this purpose. Do the GBS sequence files need to be indexed as well, or not? Does it make a difference? I have got conflicting instructions on this topic.
For the whole dataset, I ran all the 28 fastq files at once (2*13 files, two per each of the pools + 2 files for the trial pool repeated) and used the same keyfile in any plugin where it was needed. Maybe an alternative approach would be a multiple step filling of the database or joining of separate databases - if the amount or organization of the data is the problem? But then again, even when working with only 2 fastq from the trial, the same problem remained. I can try running it on a single fastq file though, just to see what happens.
Thanks
Debora
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Lynn Carol Johnson
Jan 3, 2016, 2:53:16 PM1/3/16
to tas...@googlegroups.com
Hi Debora -
Nothing is jumping out at me. Was your database created without error? If you send me privately your gbsv2 database created from the first step in the pipelines, and the 2 fastq files that will create the problem, I will debug and get back to you.
One other question: Was the gbsv2 db created with a different tassel 5 load than the one used to run ProductionSNPCallerPluginV2? I note you said this worked with the tassel v5.2.11 load (built on June 4th). There have been changes to the code the last
few month. I’m curious to know if you have problems when the entire pipeline is run on a consistent load.
Thanks - Lynn
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Debora Santo
Jan 5, 2016, 9:26:59 AM1/5/16
to TASSEL - Trait Analysis by Association, Evolution and Linkage
Dear Lynn,
I had no error when creating the database, everything looked fine. The only problem that is visible seems to be the closing of the file. It is either unfinished when -ko set to false, or seems to be good with -ko set to true, but then when closed cannot be viewed in the TASSEL GUI (it is the issue that seems to be connected with the depth of the reads, as you have said). I think that I also tried making a file without writing in the depths of the reads, but the problem persisted.
I have used the latest build of TASSEL whenever I used this software, ranging from 5.2.11 to 5.2.18. The latest analyses I tried in 5.2.17 and 5.2.18 and I only used the 5.2.11 that used to work well for me before to check if the issue remains even with that build and with data I already got good results for.
I am not sure where can I see/find your email, can you send it in response here (or write to debora...@gmail.com and I will send the files in the reply)? In the meanwhile I will try to run the pipeline again and see what happens.
Sincerely,
Debora
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