Error in DiscoverySNPCallerPluginV2: No Chromosomes found in cutPosition tables
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ldbe...@ucdavis.edu
Aug 5, 2015, 3:23:17 PM8/5/15
to TASSEL - Trait Analysis by Association, Evolution and Linkage
Hi everyone,
I'm using the latest build of Tassel 5 (5.2.13).
So far all the steps went fine and the SAM file looks normal.
However, when I run the DiscoverySNPCallerPluginV2 I get an error saying 'No Chromosomes found in cutPosition tables'
I would appreciate help with this issue.
Here are the commands and log files:
-bash-3.2$ ./run_pipeline.pl -fork1 -DiscoverySNPCallerPluginV2 -db ./db/28LetGenV2.db -sC 1 -eC 9 -mnLCov 0.001 -mnMAF 0.001 -endPlugin -runfork1
./lib/biojava-core-4.0.0.jar:./lib/trove-3.0.3.jar:./lib/junit-4.10.jar:./lib/xercesImpl.jar:./lib/snappy-java-1.1.1.6.jar:./lib/batik-parser.jar:./lib/poi-3.0.1-FINAL-20070705.jar:./lib/slf4j-simple-1.7.10.jar:./lib/batik-svg-dom.jar:./lib/batik-util.jar:./lib/ejml-0.23.jar:./lib/jfreechart-1.0.3.jar:./lib/forester.jar:./lib/guava-14.0.1.jar:./lib/javax.json-1.0.4.jar:./lib/batik-gvt.jar:./lib/xmlParserAPIs.jar:./lib/batik-svggen.jar:./lib/biojava-phylo-4.0.0.jar:./lib/geronimo-spec-activation-1.0.2-rc4.jar:./lib/sqlite-jdbc-3.8.5-pre1.jar:./lib/batik-css.jar:./lib/biojava-alignment-4.0.0.jar:./lib/colt.jar:./lib/commons-codec-1.10.jar:./lib/batik-dom.jar:./lib/batik-xml.jar:./lib/log4j-1.2.13.jar:./lib/json-simple-1.1.1.jar:./lib/mail-1.4.jar:./lib/batik-ext.jar:./lib/itextpdf-5.1.0.jar:./lib/batik-awt-util.jar:./lib/batik-gui-util.jar:./lib/jcommon-1.0.6.jar:./lib/xml.jar:./lib/cisd-jhdf5-batteries_included_lin_win_mac.jar:./lib/commons-math3-3.4.1.jar:./lib/slf4j-api-1.7.10.jar:./lib/postgresql-9.4-1201.jdbc41.jar:./sTASSEL.jar
Memory Settings: -Xms25g -Xmx25g
Tassel Pipeline Arguments: -fork1 -DiscoverySNPCallerPluginV2 -db ./db/28LetGenV2.db -sC 1 -eC 9 -mnLCov 0.001 -mnMAF 0.001 -endPlugin -runfork1
[main] INFO net.maizegenetics.tassel.TasselLogging - Tassel Version: 5.2.13 Date: July 30, 2015
[main] INFO net.maizegenetics.tassel.TasselLogging - Max Available Memory Reported by JVM: 24533 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, -DiscoverySNPCallerPluginV2, -db, ./db/28LetGenV2.db, -sC, 1, -eC, 9, -mnLCov, 0.001, -mnMAF, 0.001, -endPlugin, -runfork1]
net.maizegenetics.analysis.gbs.v2.DiscoverySNPCallerPluginV2
[pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin - Starting net.maizegenetics.analysis.gbs.v2.DiscoverySNPCallerPluginV2: time: Aug 5, 2015 12:11:37
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.DiscoverySNPCallerPluginV2 - MinMAF:0.00100000
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.DiscoverySNPCallerPluginV2 - includeRare:false includeGaps:false
[pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin -
DiscoverySNPCallerPluginV2 Parameters
db: ./db/28LetGenV2.db
mnMAF: 0.001
mnLCov: 0.001
ref: null
sC: 1
eC: 9
inclRare: false
inclGaps: false
callBiSNPsWGap: false
gapAlignRatio: 1.0
maxTagsCutSite: 64
deleteOldData: false
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.DiscoverySNPCallerPluginV2 - Finding SNPs in ./db/28LetGenV2.db.
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.DiscoverySNPCallerPluginV2 - StartChr:1 EndChr:9
size of all tags in tag table=0
size of all tags in mappingApproach table=1
size of all taxa in taxa table=0
[pool-1-thread-1] ERROR net.maizegenetics.analysis.gbs.v2.DiscoverySNPCallerPluginV2 - No Chromosomes found in cutPosition tables
Closing SQLDB
[pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin - Finished net.maizegenetics.analysis.gbs.v2.DiscoverySNPCallerPluginV2: time: Aug 5, 2015 12:11:37
[pool-1-thread-1] INFO net.maizegenetics.pipeline.TasselPipeline - net.maizegenetics.analysis.gbs.v2.DiscoverySNPCallerPluginV2: time: Aug 5, 2015 12:11:37: progress: 100%
[pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin - net.maizegenetics.analysis.gbs.v2.DiscoverySNPCallerPluginV2 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.
Lynn Carol Johnson
Aug 5, 2015, 4:11:42 PM8/5/15
to tas...@googlegroups.com
The log data bellow shows there are no tags in your tag table, no taxa in the taxa table. It looks like the database you gave it is empty. Can you verify you ran the initial steps with this same database name? If yes, then re-run the initial steps
and check the output after each step for errors. Something has failed prior to the DiscoverySNPCallerPluginV2.
Thanks - Lynn
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ldbe...@ucdavis.edu
Aug 5, 2015, 4:22:36 PM8/5/15
to TASSEL - Trait Analysis by Association, Evolution and Linkage
Hi,
Thanks for your reply.
I think I am confused about the previous step (SAMToGBSdbPlugin). I don't understand what it does exactly and if I should input the same db file as generated in the GBSSeqToTagDBPlugin. Anyway, these are the commands and log files for each of the previous steps:
-bash-3.2$ ./run_pipeline.pl -fork1 -GBSSeqToTagDBPlugin -e AvaII -i ./fastq/28LetGen -db ./db/28LetGen.db -k ./keyfiles/Keyfile28LetGen.txt -endPlugin -runfork1
./lib/biojava-core-4.0.0.jar:./lib/trove-3.0.3.jar:./lib/junit-4.10.jar:./lib/xercesImpl.jar:./lib/snappy-java-1.1.1.6.jar:./lib/batik-parser.jar:./lib/poi-3.0.1-FINAL-20070705.jar:./lib/slf4j-simple-1.7.10.jar:./lib/batik-svg-dom.jar:./lib/batik-util.jar:./lib/ejml-0.23.jar:./lib/jfreechart-1.0.3.jar:./lib/forester.jar:./lib/guava-14.0.1.jar:./lib/javax.json-1.0.4.jar:./lib/batik-gvt.jar:./lib/xmlParserAPIs.jar:./lib/batik-svggen.jar:./lib/biojava-phylo-4.0.0.jar:./lib/geronimo-spec-activation-1.0.2-rc4.jar:./lib/sqlite-jdbc-3.8.5-pre1.jar:./lib/batik-css.jar:./lib/biojava-alignment-4.0.0.jar:./lib/colt.jar:./lib/commons-codec-1.10.jar:./lib/batik-dom.jar:./lib/batik-xml.jar:./lib/log4j-1.2.13.jar:./lib/json-simple-1.1.1.jar:./lib/mail-1.4.jar:./lib/batik-ext.jar:./lib/itextpdf-5.1.0.jar:./lib/batik-awt-util.jar:./lib/batik-gui-util.jar:./lib/jcommon-1.0.6.jar:./lib/xml.jar:./lib/cisd-jhdf5-batteries_included_lin_win_mac.jar:./lib/commons-math3-3.4.1.jar:./lib/slf4j-api-1.7.10.jar:./lib/postgresql-9.4-1201.jdbc41.jar:./sTASSEL.jar
Memory Settings: -Xms25g -Xmx25g
Tassel Pipeline Arguments: -fork1 -GBSSeqToTagDBPlugin -e AvaII -i ./fastq/28LetGen -db ./db/28LetGen.db -k ./keyfiles/Keyfile28LetGen.txt -endPlugin -runfork1
[main] INFO net.maizegenetics.tassel.TasselLogging - Tassel Version: 5.2.13 Date: July 30, 2015
[main] INFO net.maizegenetics.tassel.TasselLogging - Max Available Memory Reported by JVM: 24533 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, -GBSSeqToTagDBPlugin, -e, AvaII, -i, ./fastq/28LetGen, -db, ./db/28LetGen.db, -k, ./keyfiles/Keyfile28LetGen.txt, -endPlugin, -runfork1]
net.maizegenetics.analysis.gbs.v2.GBSSeqToTagDBPlugin
[pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin - Starting net.maizegenetics.analysis.gbs.v2.GBSSeqToTagDBPlugin: time: Aug 5, 2015 10:19:7
[pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin -
GBSSeqToTagDBPlugin Parameters
i: ./fastq/28LetGen
k: ./keyfiles/Keyfile28LetGen.txt
e: AvaII
kmerLength: 64
minKmerL: 20
c: 10
db: ./db/28LetGen.db
mnQS: 0
mxKmerNum: 50000000
batchSize: 8
deleteOldData: false
net.maizegenetics.analysis.gbs.v2.GBSSeqToTagDBPlugin
[pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin - Starting net.maizegenetics.analysis.gbs.v2.GBSSeqToTagDBPlugin: time: Aug 5, 2015 10:19:7
[pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin -
GBSSeqToTagDBPlugin Parameters
i: ./fastq/28LetGen
k: ./keyfiles/Keyfile28LetGen.txt
e: AvaII
kmerLength: 64
minKmerL: 20
c: 10
db: ./db/28LetGen.db
mnQS: 0
mxKmerNum: 50000000
batchSize: 8
deleteOldData: false
size of all tags in tag table=0
size of all tags in mappingApproach table=0
size of all taxa in taxa table=0
Start processing batch 1
Enzyme: AvaII
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.GBSSeqToTagDBPlugin - processing file /share/michelmore-scratch2/Tassel5/./fastq/28LetGen/28LetGen2P_2_fastq.gz
Enzyme: AvaII
[ForkJoinPool.commonPool-worker-57] INFO net.maizegenetics.analysis.gbs.v2.GBSSeqToTagDBPlugin - processing file /share/michelmore-scratch2/Tassel5/./fastq/28LetGen/28LetGen2P_1_fastq.gz
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.GBSUtils - /share/michelmore-scratch2/Tassel5/./fastq/28LetGen/28LetGen2P_2_fastq.gz: Quality score base:33
[ForkJoinPool.commonPool-worker-57] INFO net.maizegenetics.analysis.gbs.v2.GBSUtils - /share/michelmore-scratch2/Tassel5/./fastq/28LetGen/28LetGen2P_1_fastq.gz: Quality score base:33
[ForkJoinPool.commonPool-worker-57] INFO net.maizegenetics.analysis.gbs.v2.GBSSeqToTagDBPlugin - Total Reads:10000000 Reads with barcode and cut site overhang:8245124 rate:8678 ns/read. Current tag count:2680728
[ForkJoinPool.commonPool-worker-57] INFO net.maizegenetics.analysis.gbs.v2.GBSSeqToTagDBPlugin - Total Reads:20000000 Reads with barcode and cut site overhang:16527839 rate:8794 ns/read. Current tag count:4050155
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.GBSSeqToTagDBPlugin - Total Reads:20000000 Reads with barcode and cut site overhang:16503531 rate:8883 ns/read. Current tag count:4083787
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.GBSSeqToTagDBPlugin - Total Reads:30000000 Reads with barcode and cut site overhang:24754110 rate:8400 ns/read. Current tag count:5290525
^[[ForkJoinPool.commonPool-worker-57] INFO net.maizegenetics.analysis.gbs.v2.GBSSeqToTagDBPlugin - Total Reads:40000000 Reads with barcode and cut site overhang:33059112 rate:8080 ns/read. Current tag count:6319887
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.GBSSeqToTagDBPlugin - Total Reads:40000000 Reads with barcode and cut site overhang:33027463 rate:8160 ns/read. Current tag count:6371310
[ForkJoinPool.commonPool-worker-57] INFO net.maizegenetics.analysis.gbs.v2.GBSSeqToTagDBPlugin - Total Reads:50000000 Reads with barcode and cut site overhang:41320761 rate:7902 ns/read. Current tag count:7356400
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.GBSSeqToTagDBPlugin - Total Reads:50000000 Reads with barcode and cut site overhang:41298001 rate:7991 ns/read. Current tag count:7422044
[ForkJoinPool.commonPool-worker-57] INFO net.maizegenetics.analysis.gbs.v2.GBSSeqToTagDBPlugin - Total Reads:60000000 Reads with barcode and cut site overhang:49584473 rate:7780 ns/read. Current tag count:8317036
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.GBSSeqToTagDBPlugin - Total Reads:60000000 Reads with barcode and cut site overhang:49557914 rate:7868 ns/read. Current tag count:8393461
[ForkJoinPool.commonPool-worker-57] INFO net.maizegenetics.analysis.gbs.v2.GBSSeqToTagDBPlugin - Total Reads:70000000 Reads with barcode and cut site overhang:57838589 rate:7678 ns/read. Current tag count:9658780
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.GBSSeqToTagDBPlugin - Total Reads:70000000 Reads with barcode and cut site overhang:57754574 rate:7803 ns/read. Current tag count:9843467
[ForkJoinPool.commonPool-worker-57] INFO net.maizegenetics.analysis.gbs.v2.GBSSeqToTagDBPlugin - Total Reads:80000000 Reads with barcode and cut site overhang:65980299 rate:7666 ns/read. Current tag count:10852283
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.GBSSeqToTagDBPlugin - Total Reads:80000000 Reads with barcode and cut site overhang:65996098 rate:7781 ns/read. Current tag count:10953449
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.GBSSeqToTagDBPlugin - Total Reads:90000000 Reads with barcode and cut site overhang:74277829 rate:7796 ns/read. Current tag count:12107774
[ForkJoinPool.commonPool-worker-57] INFO net.maizegenetics.analysis.gbs.v2.GBSSeqToTagDBPlugin - Total Reads:100000000 Reads with barcode and cut site overhang:82502109 rate:7585 ns/read. Current tag count:12902932
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.GBSSeqToTagDBPlugin - Total Reads:100000000 Reads with barcode and cut site overhang:82304149 rate:7976 ns/read. Current tag count:13427176
[ForkJoinPool.commonPool-worker-57] INFO net.maizegenetics.analysis.gbs.v2.GBSSeqToTagDBPlugin - Total Reads:110000000 Reads with barcode and cut site overhang:90786938 rate:7557 ns/read. Current tag count:13828354
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.GBSSeqToTagDBPlugin - Total Reads:110000000 Reads with barcode and cut site overhang:90565733 rate:7911 ns/read. Current tag count:14321053
[ForkJoinPool.commonPool-worker-57] INFO net.maizegenetics.analysis.gbs.v2.GBSSeqToTagDBPlugin - Total Reads:120000000 Reads with barcode and cut site overhang:99039754 rate:7525 ns/read. Current tag count:14708180
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.GBSSeqToTagDBPlugin - Total Reads:120000000 Reads with barcode and cut site overhang:98815304 rate:7851 ns/read. Current tag count:15165312
[ForkJoinPool.commonPool-worker-57] INFO net.maizegenetics.analysis.gbs.v2.GBSSeqToTagDBPlugin - Total Reads:130000000 Reads with barcode and cut site overhang:107313506 rate:7500 ns/read. Current tag count:15591007
[ForkJoinPool.commonPool-worker-57] INFO net.maizegenetics.analysis.gbs.v2.GBSSeqToTagDBPlugin - Summary for /share/michelmore-scratch2/Tassel5/./fastq/28LetGen/28LetGen2P_1_fastq.gz
Total number of reads in lane=134378204
Total number of good barcoded reads=110948301
Total number of low quality reads=0
Timing process (sorting, collapsing, and writing TagCount to file).
Process took 1007080.173 milliseconds.
tagCntMap size: 15999164
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.GBSSeqToTagDBPlugin - Total Reads:130000000 Reads with barcode and cut site overhang:107090100 rate:7816 ns/read. Current tag count:16065429
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.GBSSeqToTagDBPlugin - Summary for /share/michelmore-scratch2/Tassel5/./fastq/28LetGen/28LetGen2P_2_fastq.gz
Total number of reads in lane=134972857
Total number of good barcoded reads=111208879
Total number of low quality reads=0
Timing process (sorting, collapsing, and writing TagCount to file).
Process took 1050717.317 milliseconds.
tagCntMap size: 16313872
Kmers are added from batch 1. Total batch number: 1
Current number: 16313872. Max kmer number: 50000000
0.32627743 of max tag number
Map Tags:16,313,872 Memory:2,123,146,658 TotalDepth:222,157,180 AvgDepthPerTag:13
Starting removeTagsWithoutReplication. Current tag number: 16313872
Finished removeTagsWithoutReplication. tagsRemoved = 14774938. Current tag number: 1538934
Map Tags:1,538,934 Memory:635,831,860 TotalDepth:197,265,414 AvgDepthPerTag:128
Kmer number is reduced to 1538934
Total memory: 24.0 Gb
Free memory: 15.0 Gb
Max memory: 24.0 Gb
All the batch are processed
By removing kmers with minCount of 10Kmer number is reduced to 1365525
Enzyme: AvaII
GBSSeqToTagDBPlugin.removeSecondCutSitesFromMap started Initial Size:1365525
After removal tagCntMap.size() = 903945
After removal shortTags.size() = 283831
belowMinSize = 70299
shortExisting = 107450
After combining again tagCntMap.size() = 1187776
size of all taxa in taxa table=58
tagInsertPS.executeBatch() 100001
tagInsertPS.executeBatch() 100001
tagInsertPS.executeBatch() 100001
tagInsertPS.executeBatch() 100001
tagInsertPS.executeBatch() 100001
tagInsertPS.executeBatch() 100001
tagInsertPS.executeBatch() 100001
tagInsertPS.executeBatch() 100001
tagInsertPS.executeBatch() 100001
tagInsertPS.executeBatch() 100001
tagInsertPS.executeBatch() 100001
size of all tags in tag table=1187776
putTaxaDistribution next100001
putTaxaDistribution next100001
putTaxaDistribution next100001
putTaxaDistribution next100001
putTaxaDistribution next100001
putTaxaDistribution next100001
putTaxaDistribution next100001
putTaxaDistribution next100001
putTaxaDistribution next100001
putTaxaDistribution next100001
putTaxaDistribution next100001
Closing SQLDB
[pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin - Finished net.maizegenetics.analysis.gbs.v2.GBSSeqToTagDBPlugin: time: Aug 5, 2015 10:40:38
[pool-1-thread-1] INFO net.maizegenetics.pipeline.TasselPipeline - net.maizegenetics.analysis.gbs.v2.GBSSeqToTagDBPlugin: time: Aug 5, 2015 10:40:38: progress: 100%
Enzyme: AvaII
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.GBSSeqToTagDBPlugin - processing file /share/michelmore-scratch2/Tassel5/./fastq/28LetGen/28LetGen2P_2_fastq.gz
Enzyme: AvaII
[ForkJoinPool.commonPool-worker-57] INFO net.maizegenetics.analysis.gbs.v2.GBSSeqToTagDBPlugin - processing file /share/michelmore-scratch2/Tassel5/./fastq/28LetGen/28LetGen2P_1_fastq.gz
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.GBSUtils - /share/michelmore-scratch2/Tassel5/./fastq/28LetGen/28LetGen2P_2_fastq.gz: Quality score base:33
[ForkJoinPool.commonPool-worker-57] INFO net.maizegenetics.analysis.gbs.v2.GBSUtils - /share/michelmore-scratch2/Tassel5/./fastq/28LetGen/28LetGen2P_1_fastq.gz: Quality score base:33
[ForkJoinPool.commonPool-worker-57] INFO net.maizegenetics.analysis.gbs.v2.GBSSeqToTagDBPlugin - Total Reads:10000000 Reads with barcode and cut site overhang:8245124 rate:8678 ns/read. Current tag count:2680728
[ForkJoinPool.commonPool-worker-57] INFO net.maizegenetics.analysis.gbs.v2.GBSSeqToTagDBPlugin - Total Reads:20000000 Reads with barcode and cut site overhang:16527839 rate:8794 ns/read. Current tag count:4050155
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.GBSSeqToTagDBPlugin - Total Reads:20000000 Reads with barcode and cut site overhang:16503531 rate:8883 ns/read. Current tag count:4083787
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.GBSSeqToTagDBPlugin - Total Reads:30000000 Reads with barcode and cut site overhang:24754110 rate:8400 ns/read. Current tag count:5290525
^[[ForkJoinPool.commonPool-worker-57] INFO net.maizegenetics.analysis.gbs.v2.GBSSeqToTagDBPlugin - Total Reads:40000000 Reads with barcode and cut site overhang:33059112 rate:8080 ns/read. Current tag count:6319887
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.GBSSeqToTagDBPlugin - Total Reads:40000000 Reads with barcode and cut site overhang:33027463 rate:8160 ns/read. Current tag count:6371310
[ForkJoinPool.commonPool-worker-57] INFO net.maizegenetics.analysis.gbs.v2.GBSSeqToTagDBPlugin - Total Reads:50000000 Reads with barcode and cut site overhang:41320761 rate:7902 ns/read. Current tag count:7356400
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.GBSSeqToTagDBPlugin - Total Reads:50000000 Reads with barcode and cut site overhang:41298001 rate:7991 ns/read. Current tag count:7422044
[ForkJoinPool.commonPool-worker-57] INFO net.maizegenetics.analysis.gbs.v2.GBSSeqToTagDBPlugin - Total Reads:60000000 Reads with barcode and cut site overhang:49584473 rate:7780 ns/read. Current tag count:8317036
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.GBSSeqToTagDBPlugin - Total Reads:60000000 Reads with barcode and cut site overhang:49557914 rate:7868 ns/read. Current tag count:8393461
[ForkJoinPool.commonPool-worker-57] INFO net.maizegenetics.analysis.gbs.v2.GBSSeqToTagDBPlugin - Total Reads:70000000 Reads with barcode and cut site overhang:57838589 rate:7678 ns/read. Current tag count:9658780
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.GBSSeqToTagDBPlugin - Total Reads:70000000 Reads with barcode and cut site overhang:57754574 rate:7803 ns/read. Current tag count:9843467
[ForkJoinPool.commonPool-worker-57] INFO net.maizegenetics.analysis.gbs.v2.GBSSeqToTagDBPlugin - Total Reads:80000000 Reads with barcode and cut site overhang:65980299 rate:7666 ns/read. Current tag count:10852283
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.GBSSeqToTagDBPlugin - Total Reads:80000000 Reads with barcode and cut site overhang:65996098 rate:7781 ns/read. Current tag count:10953449
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.GBSSeqToTagDBPlugin - Total Reads:90000000 Reads with barcode and cut site overhang:74277829 rate:7796 ns/read. Current tag count:12107774
[ForkJoinPool.commonPool-worker-57] INFO net.maizegenetics.analysis.gbs.v2.GBSSeqToTagDBPlugin - Total Reads:100000000 Reads with barcode and cut site overhang:82502109 rate:7585 ns/read. Current tag count:12902932
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.GBSSeqToTagDBPlugin - Total Reads:100000000 Reads with barcode and cut site overhang:82304149 rate:7976 ns/read. Current tag count:13427176
[ForkJoinPool.commonPool-worker-57] INFO net.maizegenetics.analysis.gbs.v2.GBSSeqToTagDBPlugin - Total Reads:110000000 Reads with barcode and cut site overhang:90786938 rate:7557 ns/read. Current tag count:13828354
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.GBSSeqToTagDBPlugin - Total Reads:110000000 Reads with barcode and cut site overhang:90565733 rate:7911 ns/read. Current tag count:14321053
[ForkJoinPool.commonPool-worker-57] INFO net.maizegenetics.analysis.gbs.v2.GBSSeqToTagDBPlugin - Total Reads:120000000 Reads with barcode and cut site overhang:99039754 rate:7525 ns/read. Current tag count:14708180
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.GBSSeqToTagDBPlugin - Total Reads:120000000 Reads with barcode and cut site overhang:98815304 rate:7851 ns/read. Current tag count:15165312
[ForkJoinPool.commonPool-worker-57] INFO net.maizegenetics.analysis.gbs.v2.GBSSeqToTagDBPlugin - Total Reads:130000000 Reads with barcode and cut site overhang:107313506 rate:7500 ns/read. Current tag count:15591007
[ForkJoinPool.commonPool-worker-57] INFO net.maizegenetics.analysis.gbs.v2.GBSSeqToTagDBPlugin - Summary for /share/michelmore-scratch2/Tassel5/./fastq/28LetGen/28LetGen2P_1_fastq.gz
Total number of reads in lane=134378204
Total number of good barcoded reads=110948301
Total number of low quality reads=0
Timing process (sorting, collapsing, and writing TagCount to file).
Process took 1007080.173 milliseconds.
tagCntMap size: 15999164
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.GBSSeqToTagDBPlugin - Total Reads:130000000 Reads with barcode and cut site overhang:107090100 rate:7816 ns/read. Current tag count:16065429
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.GBSSeqToTagDBPlugin - Summary for /share/michelmore-scratch2/Tassel5/./fastq/28LetGen/28LetGen2P_2_fastq.gz
Total number of reads in lane=134972857
Total number of good barcoded reads=111208879
Total number of low quality reads=0
Timing process (sorting, collapsing, and writing TagCount to file).
Process took 1050717.317 milliseconds.
tagCntMap size: 16313872
Kmers are added from batch 1. Total batch number: 1
Current number: 16313872. Max kmer number: 50000000
0.32627743 of max tag number
Map Tags:16,313,872 Memory:2,123,146,658 TotalDepth:222,157,180 AvgDepthPerTag:13
Starting removeTagsWithoutReplication. Current tag number: 16313872
Finished removeTagsWithoutReplication. tagsRemoved = 14774938. Current tag number: 1538934
Map Tags:1,538,934 Memory:635,831,860 TotalDepth:197,265,414 AvgDepthPerTag:128
Kmer number is reduced to 1538934
Total memory: 24.0 Gb
Free memory: 15.0 Gb
Max memory: 24.0 Gb
All the batch are processed
By removing kmers with minCount of 10Kmer number is reduced to 1365525
Enzyme: AvaII
GBSSeqToTagDBPlugin.removeSecondCutSitesFromMap started Initial Size:1365525
After removal tagCntMap.size() = 903945
After removal shortTags.size() = 283831
belowMinSize = 70299
shortExisting = 107450
After combining again tagCntMap.size() = 1187776
size of all taxa in taxa table=58
tagInsertPS.executeBatch() 100001
tagInsertPS.executeBatch() 100001
tagInsertPS.executeBatch() 100001
tagInsertPS.executeBatch() 100001
tagInsertPS.executeBatch() 100001
tagInsertPS.executeBatch() 100001
tagInsertPS.executeBatch() 100001
tagInsertPS.executeBatch() 100001
tagInsertPS.executeBatch() 100001
tagInsertPS.executeBatch() 100001
tagInsertPS.executeBatch() 100001
size of all tags in tag table=1187776
putTaxaDistribution next100001
putTaxaDistribution next100001
putTaxaDistribution next100001
putTaxaDistribution next100001
putTaxaDistribution next100001
putTaxaDistribution next100001
putTaxaDistribution next100001
putTaxaDistribution next100001
putTaxaDistribution next100001
putTaxaDistribution next100001
putTaxaDistribution next100001
Closing SQLDB
[pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin - Finished net.maizegenetics.analysis.gbs.v2.GBSSeqToTagDBPlugin: time: Aug 5, 2015 10:40:38
[pool-1-thread-1] INFO net.maizegenetics.pipeline.TasselPipeline - net.maizegenetics.analysis.gbs.v2.GBSSeqToTagDBPlugin: time: Aug 5, 2015 10:40:38: progress: 100%
[pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin - net.maizegenetics.analysis.gbs.v2.GBSSeqToTagDBPlugin 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.
-bash-3.2$
Second command:
-bash-3.2$ ./run_pipeline.pl -fork1 -TagExportToFastqPlugin -db ./db/28LetGen.db -o ./fastq/28LetGen/tagsforAlign_28LetGen.fastq.gz -c 1 -endPlugin -runfork1
./lib/biojava-core-4.0.0.jar:./lib/trove-3.0.3.jar:./lib/junit-4.10.jar:./lib/xercesImpl.jar:./lib/snappy-java-1.1.1.6.jar:./lib/batik-parser.jar:./lib/poi-3.0.1-FINAL-20070705.jar:./lib/slf4j-simple-1.7.10.jar:./lib/batik-svg-dom.jar:./lib/batik-util.jar:./lib/ejml-0.23.jar:./lib/jfreechart-1.0.3.jar:./lib/forester.jar:./lib/guava-14.0.1.jar:./lib/javax.json-1.0.4.jar:./lib/batik-gvt.jar:./lib/xmlParserAPIs.jar:./lib/batik-svggen.jar:./lib/biojava-phylo-4.0.0.jar:./lib/geronimo-spec-activation-1.0.2-rc4.jar:./lib/sqlite-jdbc-3.8.5-pre1.jar:./lib/batik-css.jar:./lib/biojava-alignment-4.0.0.jar:./lib/colt.jar:./lib/commons-codec-1.10.jar:./lib/batik-dom.jar:./lib/batik-xml.jar:./lib/log4j-1.2.13.jar:./lib/json-simple-1.1.1.jar:./lib/mail-1.4.jar:./lib/batik-ext.jar:./lib/itextpdf-5.1.0.jar:./lib/batik-awt-util.jar:./lib/batik-gui-util.jar:./lib/jcommon-1.0.6.jar:./lib/xml.jar:./lib/cisd-jhdf5-batteries_included_lin_win_mac.jar:./lib/commons-math3-3.4.1.jar:./lib/slf4j-api-1.7.10.jar:./lib/postgresql-9.4-1201.jdbc41.jar:./sTASSEL.jar
Memory Settings: -Xms25g -Xmx25g
Tassel Pipeline Arguments: -fork1 -TagExportToFastqPlugin -db ./db/28LetGen.db -o ./fastq/28LetGen/tagsforAlign_28LetGen.fastq.gz -c 1 -endPlugin -runfork1
[main] INFO net.maizegenetics.tassel.TasselLogging - Tassel Version: 5.2.13 Date: July 30, 2015
[main] INFO net.maizegenetics.tassel.TasselLogging - Max Available Memory Reported by JVM: 24533 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, -TagExportToFastqPlugin, -db, ./db/28LetGen.db, -o, ./fastq/28LetGen/tagsforAlign_28LetGen.fastq.gz, -c, 1, -endPlugin, -runfork1]
net.maizegenetics.analysis.gbs.v2.TagExportToFastqPlugin
[pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin - Starting net.maizegenetics.analysis.gbs.v2.TagExportToFastqPlugin: time: Aug 5, 2015 10:45:50
[pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin -
TagExportToFastqPlugin Parameters
db: ./db/28LetGen.db
o: ./fastq/28LetGen/tagsforAlign_28LetGen.fastq.gz
c: 1
size of all tags in tag table=1187776
net.maizegenetics.analysis.gbs.v2.TagExportToFastqPlugin
[pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin - Starting net.maizegenetics.analysis.gbs.v2.TagExportToFastqPlugin: time: Aug 5, 2015 10:45:50
[pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin -
TagExportToFastqPlugin Parameters
db: ./db/28LetGen.db
o: ./fastq/28LetGen/tagsforAlign_28LetGen.fastq.gz
c: 1
size of all tags in tag table=1187776
size of all tags in mappingApproach table=1
size of all taxa in taxa table=58
Closing SQLDB
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.TagExportToFastqPlugin - Finished converting binary tag count file to fastq.
Total number of tags written: 1187776 (above minCount of 1)
Ouput fastq file: ./fastq/28LetGen/tagsforAlign_28LetGen.fastq.gz
[pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin - Finished net.maizegenetics.analysis.gbs.v2.TagExportToFastqPlugin: time: Aug 5, 2015 10:46:31
[pool-1-thread-1] INFO net.maizegenetics.pipeline.TasselPipeline - net.maizegenetics.analysis.gbs.v2.TagExportToFastqPlugin: time: Aug 5, 2015 10:46:31: progress: 100%
[pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin - net.maizegenetics.analysis.gbs.v2.TagExportToFastqPlugin 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.
Closing SQLDB
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.TagExportToFastqPlugin - Finished converting binary tag count file to fastq.
Total number of tags written: 1187776 (above minCount of 1)
Ouput fastq file: ./fastq/28LetGen/tagsforAlign_28LetGen.fastq.gz
[pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin - Finished net.maizegenetics.analysis.gbs.v2.TagExportToFastqPlugin: time: Aug 5, 2015 10:46:31
[pool-1-thread-1] INFO net.maizegenetics.pipeline.TasselPipeline - net.maizegenetics.analysis.gbs.v2.TagExportToFastqPlugin: time: Aug 5, 2015 10:46:31: progress: 100%
[pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin - net.maizegenetics.analysis.gbs.v2.TagExportToFastqPlugin 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.
-bash-3.2$
bwa alignment:
-bash-3.2$ bwa aln -t 4 Lsat.1.v6.Reference.fa ./fastq/28LetGen/tagsforAlign_28LetGen.fastq.gz > ./fastq/28LetGen/tagsForAlign_28LetGen.sai
[bwa_aln] 17bp reads: max_diff = 2
[bwa_aln] 38bp reads: max_diff = 3
[bwa_aln] 64bp reads: max_diff = 4
[bwa_aln] 93bp reads: max_diff = 5
[bwa_aln] 124bp reads: max_diff = 6
[bwa_aln] 157bp reads: max_diff = 7
[bwa_aln] 190bp reads: max_diff = 8
[bwa_aln] 225bp reads: max_diff = 9
[bwa_aln_core] calculate SA coordinate... 250.57 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 155.34 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 180.87 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 159.10 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 86.03 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 1187776 sequences have been processed.
[main] Version: 0.7.4-r385
[main] CMD: bwa aln -t 4 Lsat.1.v6.Reference.fa ./fastq/28LetGen/tagsforAlign_28LetGen.fastq.gz
[bwa_aln] 17bp reads: max_diff = 2
[bwa_aln] 38bp reads: max_diff = 3
[bwa_aln] 64bp reads: max_diff = 4
[bwa_aln] 93bp reads: max_diff = 5
[bwa_aln] 124bp reads: max_diff = 6
[bwa_aln] 157bp reads: max_diff = 7
[bwa_aln] 190bp reads: max_diff = 8
[bwa_aln] 225bp reads: max_diff = 9
[bwa_aln_core] calculate SA coordinate... 250.57 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 155.34 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 180.87 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 159.10 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 86.03 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 1187776 sequences have been processed.
[main] Version: 0.7.4-r385
[main] CMD: bwa aln -t 4 Lsat.1.v6.Reference.fa ./fastq/28LetGen/tagsforAlign_28LetGen.fastq.gz
[main] Real time: 245.746 sec; CPU: 838.098 sec
amash-3.2$ bwa samse ./Lsat.1.v6.Reference.fa ./fastq/28LetGen/tagsForAlign_28LetGen.sai ./fastq/28LetGen/tagsforAlign_28LetGen.fastq.gz > ./fastq/28LetGen/tagsForAlign_28LetGen.s
[bwa_aln_core] convert to sequence coordinate... 6.13 sec
[bwa_aln_core] refine gapped alignments... 1.51 sec
[bwa_aln_core] print alignments... 0.92 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_aln_core] convert to sequence coordinate... 5.99 sec
[bwa_aln_core] refine gapped alignments... 1.45 sec
[bwa_aln_core] print alignments... 0.92 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_aln_core] convert to sequence coordinate... 5.95 sec
[bwa_aln_core] refine gapped alignments... 1.45 sec
[bwa_aln_core] print alignments... 0.92 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_aln_core] convert to sequence coordinate... 6.78 sec
[bwa_aln_core] refine gapped alignments... 1.51 sec
[bwa_aln_core] print alignments... 0.92 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_aln_core] convert to sequence coordinate... 5.27 sec
[bwa_aln_core] refine gapped alignments... 1.13 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 1187776 sequences have been processed.
[main] Version: 0.7.4-r385
[main] CMD: bwa samse ./Lsat.1.v6.Reference.fa ./fastq/28LetGen/tagsForAlign_28LetGen.sai ./fastq/28LetGen/tagsforAlign_28LetGen.fastq.gz
[bwa_aln_core] convert to sequence coordinate... 6.13 sec
[bwa_aln_core] refine gapped alignments... 1.51 sec
[bwa_aln_core] print alignments... 0.92 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_aln_core] convert to sequence coordinate... 5.99 sec
[bwa_aln_core] refine gapped alignments... 1.45 sec
[bwa_aln_core] print alignments... 0.92 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_aln_core] convert to sequence coordinate... 5.95 sec
[bwa_aln_core] refine gapped alignments... 1.45 sec
[bwa_aln_core] print alignments... 0.92 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_aln_core] convert to sequence coordinate... 6.78 sec
[bwa_aln_core] refine gapped alignments... 1.51 sec
[bwa_aln_core] print alignments... 0.92 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_aln_core] convert to sequence coordinate... 5.27 sec
[bwa_aln_core] refine gapped alignments... 1.13 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 1187776 sequences have been processed.
[main] Version: 0.7.4-r385
[main] CMD: bwa samse ./Lsat.1.v6.Reference.fa ./fastq/28LetGen/tagsForAlign_28LetGen.sai ./fastq/28LetGen/tagsforAlign_28LetGen.fastq.gz
[main] Real time: 45.099 sec; CPU: 44.521 sec
SAMToGBSdbPlugin : not sure what this does
-bash-3.2$ ./run_pipeline.pl -fork1 -SAMToGBSdbPlugin -i ./fastq/28LetGen/tagsForAlign_28LetGen.sam -db ./db/28LetGenV2.db -aProp 0.0 -aLen 0 -endPlugin -runfork1
./lib/biojava-core-4.0.0.jar:./lib/trove-3.0.3.jar:./lib/junit-4.10.jar:./lib/xercesImpl.jar:./lib/snappy-java-1.1.1.6.jar:./lib/batik-parser.jar:./lib/poi-3.0.1-FINAL-20070705.jar:./lib/slf4j-simple-1.7.10.jar:./lib/batik-svg-dom.jar:./lib/batik-util.jar:./lib/ejml-0.23.jar:./lib/jfreechart-1.0.3.jar:./lib/forester.jar:./lib/guava-14.0.1.jar:./lib/javax.json-1.0.4.jar:./lib/batik-gvt.jar:./lib/xmlParserAPIs.jar:./lib/batik-svggen.jar:./lib/biojava-phylo-4.0.0.jar:./lib/geronimo-spec-activation-1.0.2-rc4.jar:./lib/sqlite-jdbc-3.8.5-pre1.jar:./lib/batik-css.jar:./lib/biojava-alignment-4.0.0.jar:./lib/colt.jar:./lib/commons-codec-1.10.jar:./lib/batik-dom.jar:./lib/batik-xml.jar:./lib/log4j-1.2.13.jar:./lib/json-simple-1.1.1.jar:./lib/mail-1.4.jar:./lib/batik-ext.jar:./lib/itextpdf-5.1.0.jar:./lib/batik-awt-util.jar:./lib/batik-gui-util.jar:./lib/jcommon-1.0.6.jar:./lib/xml.jar:./lib/cisd-jhdf5-batteries_included_lin_win_mac.jar:./lib/commons-math3-3.4.1.jar:./lib/slf4j-api-1.7.10.jar:./lib/postgresql-9.4-1201.jdbc41.jar:./sTASSEL.jar
Memory Settings: -Xms25g -Xmx25g
Memory Settings: -Xms25g -Xmx25g
Tassel Pipeline Arguments: -fork1 -SAMToGBSdbPlugin -i ./fastq/28LetGen/tagsForAlign_28LetGen.sam -db ./db/28LetGenV2.db -aProp 0.0 -aLen 0 -endPlugin -runfork1
[main] INFO net.maizegenetics.tassel.TasselLogging - Tassel Version: 5.2.13 Date: July 30, 2015
[main] INFO net.maizegenetics.tassel.TasselLogging - Max Available Memory Reported by JVM: 24533 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, -SAMToGBSdbPlugin, -i, ./fastq/28LetGen/tagsForAlign_28LetGen.sam, -db, ./db/28LetGenV2.db, -aProp, 0.0, -aLen, 0, -endPlugin, -runfork1]
net.maizegenetics.analysis.gbs.v2.SAMToGBSdbPlugin
[pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin - Starting net.maizegenetics.analysis.gbs.v2.SAMToGBSdbPlugin: time: Aug 5, 2015 12:08:57
[pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin -
SAMToGBSdbPlugin Parameters
i: ./fastq/28LetGen/tagsForAlign_28LetGen.sam
db: ./db/28LetGenV2.db
aProp: 0.0
aLen: 0
deleteOldData: false
net.maizegenetics.analysis.gbs.v2.SAMToGBSdbPlugin
[pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin - Starting net.maizegenetics.analysis.gbs.v2.SAMToGBSdbPlugin: time: Aug 5, 2015 12:08:57
[pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin -
SAMToGBSdbPlugin Parameters
i: ./fastq/28LetGen/tagsForAlign_28LetGen.sam
db: ./db/28LetGenV2.db
aProp: 0.0
aLen: 0
deleteOldData: false
size of all tags in tag table=0
size of all tags in mappingApproach table=0
size of all taxa in taxa table=0
Unobserved tags were found in the SAM file count= 1187776
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.SAMToGBSdbPlugin - Finished reading SAM file. No Tags added to DB as 1187776 unobserved tags were found.
Please ensure all tags in the SAM file already exist in the DB.
Closing SQLDB
[pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin - Finished net.maizegenetics.analysis.gbs.v2.SAMToGBSdbPlugin: time: Aug 5, 2015 12:09:23
[pool-1-thread-1] INFO net.maizegenetics.pipeline.TasselPipeline - net.maizegenetics.analysis.gbs.v2.SAMToGBSdbPlugin: time: Aug 5, 2015 12:09:23: progress: 100%
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.SAMToGBSdbPlugin - Finished reading SAM file. No Tags added to DB as 1187776 unobserved tags were found.
Please ensure all tags in the SAM file already exist in the DB.
Closing SQLDB
[pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin - Finished net.maizegenetics.analysis.gbs.v2.SAMToGBSdbPlugin: time: Aug 5, 2015 12:09:23
[pool-1-thread-1] INFO net.maizegenetics.pipeline.TasselPipeline - net.maizegenetics.analysis.gbs.v2.SAMToGBSdbPlugin: time: Aug 5, 2015 12:09:23: progress: 100%
[pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin - net.maizegenetics.analysis.gbs.v2.SAMToGBSdbPlugin 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.
ldbe...@ucdavis.edu
Aug 5, 2015, 4:45:17 PM8/5/15
to TASSEL - Trait Analysis by Association, Evolution and Linkage
Hi,
I think I figured it out. I did not realize that the SAMToGBSdbPlugin updates the existing .db file with cut positions. I had given a new filename for the .db file in the SAMToGBSdbPlugin step and therefore it did not work for the DiscoverySNPCaller. I ran the SAMToGBSdbPlugin again using the existing .db file and it worked fine. I am now running the DiscoverySNPCaller and it seems to be running fine.
Thank you,
Lien
Lynn Carol Johnson
Aug 5, 2015, 4:54:40 PM8/5/15
to tas...@googlegroups.com
Glad you found the problem.
Yes, the same database is used for all steps in the pipeline. Each step adds additional data relating to tags, their taxa distribution, SNP positions, etc. Please take a look at the wiki and let me know if there are clarifications needed for any of the
steps.
From: <tas...@googlegroups.com> on behalf of "ldbe...@ucdavis.edu" <ldbe...@ucdavis.edu>
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Date: Wednesday, August 5, 2015 at 4:45 PM
To: "TASSEL - Trait Analysis by Association, Evolution and Linkage" <tas...@googlegroups.com>
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Date: Wednesday, August 5, 2015 at 4:45 PM
To: "TASSEL - Trait Analysis by Association, Evolution and Linkage" <tas...@googlegroups.com>
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