error: number of sites and genotypes do not agree

[Marlee Labroo]

Hi All,

I am running the ProductionSNPCaller Plugin with the following parameters:

run_pipeline.bat -Xmx7000m -fork1 -ProductionSNPCallerPluginV2 -db C:\Users\labroo2\GBS\GBSV2_MAF05_AVEDPTH10.db -e PstI-MspI -i C:\Users\labroo2\GBS\LongiMaster_Input -k C:\Users\labroo2\GBS\LongiMaster_Input\MasterKeyFile.txt -minPosQS 10 -o C:\Users\labroo2\GBS\LongiMaster_Output\LongiLibDepth10MAF05.h5 -endPlugin -runfork1

It is yielding an error, screenshot here:

It reads "error: number of sites and genotypes do not agree". Can someone explain it to me? I think the issue may really lie in my .db file and the quality scores-- I double-checked that the -qs file had the same number of positions as my output stats file, but maybe when I used the SNPQualityProfilerPlugin there was some disjunction in the sites and genotypes.

Thank you!

Marlee

[Lynn Carol Johnson]

Please run your command in debug mode send us information  as per the wiki here:

https://bytebucket.org/tasseladmin/tassel-5-source/wiki/docs/ReportingTassel5Issues.pdf

Thanks - Lynn

--
You received this message because you are subscribed to the Google Groups "TASSEL - Trait Analysis by Association, Evolution and Linkage" group.
To unsubscribe from this group and stop receiving emails from it, send an email to tassel+un...@googlegroups.com.
To post to this group, send email to tas...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/tassel/9a7ad55f-c76d-434b-9487-538b6af0b7e7%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

[Marlee Labroo]

Thanks Lynn! Did I report it correctly below?

Command: run_pipeline.bat -debug -Xmx7000m -fork1 -ProductionSNPCallerPluginV2 -db C:\Users\labroo2\GBS\GBSV2_MAF05_AVEDPTH10.db -e PstI-MspI -i C:\Users\labroo2\GBS\LongiMaster_Input -k C:\Users\labroo2\GBS\LongiMaster_Input\MasterKeyFile.txt -minPosQS 10 -o C:\Users\labroo2\GBS\LongiMaster_Output\LongiLibDepth10MAF05.h5 -endPlugin -runfork11

...

erhang:144320894 rate:10402 ns/read

[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPlug

inV2 - Total Reads:207000000 Reads with barcode and cut site overhang:202342008

rate:8920 ns/read

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Total Reads:150000000 Reads with barcode and cut site ov

erhang:145303782 rate:10403 ns/read

[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPlug

inV2 - Total Reads:208000000 Reads with barcode and cut site overhang:203323302

rate:8925 ns/read

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Total Reads:151000000 Reads with barcode and cut site ov

erhang:146281576 rate:10408 ns/read

[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPlug

inV2 - Total Reads:209000000 Reads with barcode and cut site overhang:204305988

rate:8925 ns/read

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Total Reads:152000000 Reads with barcode and cut site ov

erhang:147264071 rate:10409 ns/read

[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPlug

inV2 - Total Reads:210000000 Reads with barcode and cut site overhang:205286915

rate:8926 ns/read

[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPlug

inV2 - Total Reads:211000000 Reads with barcode and cut site overhang:206267566

rate:8932 ns/read

[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPlug

inV2 - Total Reads:212000000 Reads with barcode and cut site overhang:207247940

rate:8932 ns/read

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Total Reads:154000000 Reads with barcode and cut site ov

erhang:149225632 rate:10409 ns/read

[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPlug

inV2 - Total Reads:213000000 Reads with barcode and cut site overhang:208232219

rate:8935 ns/read

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Total Reads:155000000 Reads with barcode and cut site ov

erhang:150204713 rate:10411 ns/read

[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPlug

inV2 - Total Reads:214000000 Reads with barcode and cut site overhang:209216099

rate:8970 ns/read

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Total Reads:156000000 Reads with barcode and cut site ov

erhang:151188229 rate:10461 ns/read

[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPlug

inV2 - Total Reads:215000000 Reads with barcode and cut site overhang:210195588

rate:8969 ns/read

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Total Reads:157000000 Reads with barcode and cut site ov

erhang:152171661 rate:10462 ns/read

[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPlug

inV2 - Total Reads:216000000 Reads with barcode and cut site overhang:211174448

rate:8969 ns/read

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Total Reads:158000000 Reads with barcode and cut site ov

erhang:153151346 rate:10463 ns/read

[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPlug

inV2 - Total Reads:217000000 Reads with barcode and cut site overhang:212153573

rate:8967 ns/read

[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPlug

inV2 - Total Reads:218000000 Reads with barcode and cut site overhang:213136114

rate:8966 ns/read

[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPlug

inV2 - Total Reads:219000000 Reads with barcode and cut site overhang:214119714

rate:8969 ns/read

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Total Reads:160000000 Reads with barcode and cut site ov

erhang:155113799 rate:10467 ns/read

[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPlug

inV2 - Total Reads:220000000 Reads with barcode and cut site overhang:215099434

rate:8976 ns/read

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Total Reads:161000000 Reads with barcode and cut site ov

erhang:156096111 rate:10477 ns/read

[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPlug

inV2 - Total Reads:221000000 Reads with barcode and cut site overhang:216079980

rate:8982 ns/read

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Total Reads:162000000 Reads with barcode and cut site ov

erhang:157074662 rate:10481 ns/read

[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPlug

inV2 - Total Reads:222000000 Reads with barcode and cut site overhang:217059543

rate:8981 ns/read

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Total Reads:163000000 Reads with barcode and cut site ov

erhang:158057399 rate:10481 ns/read

[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPlug

inV2 - Total Reads:223000000 Reads with barcode and cut site overhang:218040489

rate:8981 ns/read

[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPlug

inV2 - Total number of reads in lane=223816750

[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPlug

inV2 - Total number of good barcoded reads=218840835

[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPlug

inV2 - Total number of low quality reads=0

[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPlug

inV2 - Timing process (sorting, collapsing, and writing TagCount to file).

[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPlug

inV2 - Process took 2010043.251492 milliseconds for file C:\Users\labroo2\GBS\Lo

ngiMaster_Input\D00653_4_fastq.gz

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Total Reads:164000000 Reads with barcode and cut site ov

erhang:159036185 rate:10482 ns/read

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Total Reads:165000000 Reads with barcode and cut site ov

erhang:160018725 rate:10466 ns/read

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Total Reads:166000000 Reads with barcode and cut site ov

erhang:160997031 rate:10449 ns/read

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Total Reads:167000000 Reads with barcode and cut site ov

erhang:161979898 rate:10431 ns/read

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Total Reads:168000000 Reads with barcode and cut site ov

erhang:162963187 rate:10415 ns/read

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Total Reads:169000000 Reads with barcode and cut site ov

erhang:163942203 rate:10399 ns/read

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Total Reads:170000000 Reads with barcode and cut site ov

erhang:164925559 rate:10383 ns/read

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Total Reads:171000000 Reads with barcode and cut site ov

erhang:165905543 rate:10366 ns/read

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Total Reads:172000000 Reads with barcode and cut site ov

erhang:166888657 rate:10351 ns/read

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Total Reads:173000000 Reads with barcode and cut site ov

erhang:167867376 rate:10335 ns/read

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Total Reads:174000000 Reads with barcode and cut site ov

erhang:168850586 rate:10319 ns/read

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Total Reads:175000000 Reads with barcode and cut site ov

erhang:169829073 rate:10303 ns/read

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Total Reads:176000000 Reads with barcode and cut site ov

erhang:170812757 rate:10290 ns/read

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Total Reads:177000000 Reads with barcode and cut site ov

erhang:171796427 rate:10274 ns/read

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Total Reads:178000000 Reads with barcode and cut site ov

erhang:172776043 rate:10259 ns/read

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Total Reads:179000000 Reads with barcode and cut site ov

erhang:173759333 rate:10246 ns/read

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Total Reads:180000000 Reads with barcode and cut site ov

erhang:174738889 rate:10232 ns/read

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Total Reads:182000000 Reads with barcode and cut site ov

erhang:176702297 rate:10205 ns/read

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Total Reads:183000000 Reads with barcode and cut site ov

erhang:177685279 rate:10194 ns/read

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Total Reads:184000000 Reads with barcode and cut site ov

erhang:178664528 rate:10184 ns/read

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Total Reads:185000000 Reads with barcode and cut site ov

erhang:179647541 rate:10170 ns/read

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Total Reads:186000000 Reads with barcode and cut site ov

erhang:180630894 rate:10158 ns/read

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Total Reads:187000000 Reads with barcode and cut site ov

erhang:181609930 rate:10145 ns/read

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Total Reads:188000000 Reads with barcode and cut site ov

erhang:182593809 rate:10180 ns/read

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Total Reads:189000000 Reads with barcode and cut site ov

erhang:183574391 rate:10168 ns/read

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Total Reads:190000000 Reads with barcode and cut site ov

erhang:184557275 rate:10156 ns/read

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Total Reads:191000000 Reads with barcode and cut site ov

erhang:185536390 rate:10142 ns/read

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Total Reads:192000000 Reads with barcode and cut site ov

erhang:186519864 rate:10129 ns/read

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Total Reads:193000000 Reads with barcode and cut site ov

erhang:187498579 rate:10116 ns/read

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Total Reads:194000000 Reads with barcode and cut site ov

erhang:188482248 rate:10103 ns/read

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Total Reads:195000000 Reads with barcode and cut site ov

erhang:189466131 rate:10091 ns/read

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Total Reads:196000000 Reads with barcode and cut site ov

erhang:190446651 rate:10078 ns/read

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Total Reads:197000000 Reads with barcode and cut site ov

erhang:191430095 rate:10066 ns/read

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Total Reads:198000000 Reads with barcode and cut site ov

erhang:192408523 rate:10053 ns/read

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Total Reads:199000000 Reads with barcode and cut site ov

erhang:193391901 rate:10041 ns/read

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Total Reads:200000000 Reads with barcode and cut site ov

erhang:194371022 rate:10029 ns/read

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Total Reads:201000000 Reads with barcode and cut site ov

erhang:195354528 rate:10018 ns/read

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Total Reads:202000000 Reads with barcode and cut site ov

erhang:196337447 rate:10006 ns/read

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Total Reads:203000000 Reads with barcode and cut site ov

erhang:197317751 rate:9994 ns/read

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Total Reads:204000000 Reads with barcode and cut site ov

erhang:198301422 rate:9983 ns/read

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Total Reads:205000000 Reads with barcode and cut site ov

erhang:199279905 rate:9971 ns/read

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Total Reads:206000000 Reads with barcode and cut site ov

erhang:200262742 rate:9959 ns/read

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Total Reads:207000000 Reads with barcode and cut site ov

erhang:201242086 rate:9950 ns/read

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Total Reads:208000000 Reads with barcode and cut site ov

erhang:202225237 rate:9940 ns/read

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Total number of reads in lane=208959551

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Total number of good barcoded reads=203165179

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Total number of low quality reads=0

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Timing process (sorting, collapsing, and writing TagCoun

t to file).

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Process took 2075288.583816 milliseconds for file C:\Use

rs\labroo2\GBS\LongiMaster_Input\D00553R_3_fastq.gz

[pool-1-thread-1] DEBUG net.maizegenetics.plugindef.AbstractPlugin - Number of s

ites and genotypes do not agree

java.lang.IndexOutOfBoundsException: Number of sites and genotypes do not agree

        at net.maizegenetics.dna.snp.GenotypeTableBuilder.addTaxon(GenotypeTable

Builder.java:569)

        at net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2.callGen

otypes(ProductionSNPCallerPluginV2.java:294)

        at net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2.lambda$

processData$105(ProductionSNPCallerPluginV2.java:264)

        at java.util.Iterator.forEachRemaining(Unknown Source)

        at java.util.Spliterators$IteratorSpliterator.forEachRemaining(Unknown S

ource)

        at java.util.stream.ReferencePipeline$Head.forEach(Unknown Source)

        at net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2.process

Data(ProductionSNPCallerPluginV2.java:263)

        at net.maizegenetics.plugindef.AbstractPlugin.performFunction(AbstractPl

ugin.java:110)

        at net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPl

ugin.java:1645)

        at net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPlugin

Listener.java:29)

        at java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)

        at java.util.concurrent.FutureTask.run(Unknown Source)

        at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)

        at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)

        at java.lang.Thread.run(Unknown Source)

[pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin -

Usage:

ProductionSNPCallerPluginV2 <options>

-i <Input Directory> : Input directory containing fastq AND/OR qseq files. (requ

ired)

-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 i

nstead. (required)

-eR <Ave Seq Error Rate> : Average sequencing error rate per base (used to decid

e between heterozygous and homozygous calls) (Default: 0.01)

-d <Max Divergence> : Maximum divergence (edit distance) between new read and pr

eviously mapped read (Default: 0 = perfect matches only) (Default: 0)

-ko <true | false> : Only applicable to hdf5 output files: Keep hdf5 genotypes o

pen 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 ge

notypes 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 t

o be included (Default: 0.0)

-batchSize <Batch size of fastq files> : Number of flow cells being processed si

multaneously (Default: 8)

-mnQS <Minimum quality score> : Minimum quality score within the barcode and rea

d length to be accepted (Default: 0)

[pool-1-thread-1] ERROR net.maizegenetics.plugindef.AbstractPlugin - Number of s

ites and genotypes do not agree

C:\Users\labroo2\TASSEL5>

[Lynn Carol Johnson]

HI Marlee -

What happens if you run ProductionSNPCallerPluginV2 without specifying the minPosQS parameter (i.e., default to all positions)?  Does that run without error?

Lynn

To view this discussion on the web visit https://groups.google.com/d/msgid/tassel/3876f644-ae6c-40fe-a74d-d4679c2c6763%40googlegroups.com.

[Marlee Labroo]

Hi Lynn, actually I get a different error doing that: ERROR net.maizegenetics.plugindef.AbstractPlugin - Taxon [] al

ready exists in the HDF5 file.  Duplicated taxa not allowed.

Thanks!

Command: run_pipeline.bat -debug -Xmx7000m -fork1 -ProductionSNPCallerPluginV2 -db C:\Users\labroo2\GBS\GBSV2_MAF05_AVEDPTH10.db -e PstI-MspI -i C:\Users\labroo2\GBS\LongiMaster_Input -k C:\Users\labroo2\GBS\LongiMaster_Input\MasterKeyFile.txt -o C:\Users\labroo2\GBS\LongiMaster_Output\LongiLibDepth10MAF05_test.h5 -endPlugin -runfork1

rate:8841 ns/read

[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPlug

inV2 - Total Reads:204000000 Reads with barcode and cut site overhang:199413510

rate:8846 ns/read

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Total Reads:154000000 Reads with barcode and cut site ov

erhang:149225632 rate:10290 ns/read

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Total Reads:155000000 Reads with barcode and cut site ov

erhang:150204713 rate:10293 ns/read

[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPlug

inV2 - Total Reads:206000000 Reads with barcode and cut site overhang:201364932

rate:9041 ns/read

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Total Reads:156000000 Reads with barcode and cut site ov

erhang:151188229 rate:10662 ns/read

[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPlug

inV2 - Total Reads:207000000 Reads with barcode and cut site overhang:202342008

rate:9130 ns/read

[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPlug

inV2 - Total Reads:208000000 Reads with barcode and cut site overhang:203323302

rate:9138 ns/read

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Total Reads:157000000 Reads with barcode and cut site ov

erhang:152171661 rate:10672 ns/read

[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPlug

inV2 - Total Reads:209000000 Reads with barcode and cut site overhang:204305988

rate:9141 ns/read

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Total Reads:158000000 Reads with barcode and cut site ov

erhang:153151346 rate:10678 ns/read

[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPlug

inV2 - Total Reads:210000000 Reads with barcode and cut site overhang:205286915

rate:9144 ns/read

[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPlug

inV2 - Total Reads:211000000 Reads with barcode and cut site overhang:206267566

rate:9142 ns/read

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Total Reads:160000000 Reads with barcode and cut site ov

erhang:155113799 rate:10679 ns/read

[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPlug

inV2 - Total Reads:212000000 Reads with barcode and cut site overhang:207247940

rate:9144 ns/read

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Total Reads:161000000 Reads with barcode and cut site ov

erhang:156096111 rate:10680 ns/read

[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPlug

inV2 - Total Reads:213000000 Reads with barcode and cut site overhang:208232219

rate:9143 ns/read

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Total Reads:162000000 Reads with barcode and cut site ov

erhang:157074662 rate:10678 ns/read

[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPlug

inV2 - Total Reads:214000000 Reads with barcode and cut site overhang:209216099

rate:9144 ns/read

[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPlug

inV2 - Total Reads:215000000 Reads with barcode and cut site overhang:210195588

rate:9145 ns/read

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Total Reads:163000000 Reads with barcode and cut site ov

erhang:158057399 rate:10677 ns/read

[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPlug

inV2 - Total Reads:216000000 Reads with barcode and cut site overhang:211174448

rate:9144 ns/read

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Total Reads:164000000 Reads with barcode and cut site ov

erhang:159036185 rate:10676 ns/read

[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPlug

inV2 - Total Reads:217000000 Reads with barcode and cut site overhang:212153573

rate:9146 ns/read

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Total Reads:165000000 Reads with barcode and cut site ov

erhang:160018725 rate:10679 ns/read

[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPlug

inV2 - Total Reads:218000000 Reads with barcode and cut site overhang:213136114

rate:9144 ns/read

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Total Reads:166000000 Reads with barcode and cut site ov

erhang:160997031 rate:10681 ns/read

[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPlug

inV2 - Total Reads:219000000 Reads with barcode and cut site overhang:214119714

rate:9145 ns/read

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Total Reads:167000000 Reads with barcode and cut site ov

erhang:161979898 rate:10681 ns/read

[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPlug

inV2 - Total Reads:220000000 Reads with barcode and cut site overhang:215099434

rate:9144 ns/read

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Total Reads:168000000 Reads with barcode and cut site ov

erhang:162963187 rate:10679 ns/read

[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPlug

inV2 - Total Reads:221000000 Reads with barcode and cut site overhang:216079980

rate:9148 ns/read

[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPlug

inV2 - Total Reads:222000000 Reads with barcode and cut site overhang:217059543

rate:9158 ns/read

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Total Reads:169000000 Reads with barcode and cut site ov

erhang:163942203 rate:10695 ns/read

[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPlug

inV2 - Total Reads:223000000 Reads with barcode and cut site overhang:218040489

rate:9160 ns/read

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Total Reads:170000000 Reads with barcode and cut site ov

erhang:164925559 rate:10696 ns/read

[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPlug

inV2 - Total number of reads in lane=223816750

[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPlug

inV2 - Total number of good barcoded reads=218840835

[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPlug

inV2 - Total number of low quality reads=0

[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPlug

inV2 - Timing process (sorting, collapsing, and writing TagCount to file).

[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPlug

inV2 - Process took 2051095.121253 milliseconds for file C:\Users\labroo2\GBS\Lo

ngiMaster_Input\D00653_4_fastq.gz

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Total Reads:171000000 Reads with barcode and cut site ov

erhang:165905543 rate:10692 ns/read

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Total Reads:172000000 Reads with barcode and cut site ov

erhang:166888657 rate:10675 ns/read

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Total Reads:173000000 Reads with barcode and cut site ov

erhang:167867376 rate:10657 ns/read

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Total Reads:174000000 Reads with barcode and cut site ov

erhang:168850586 rate:10639 ns/read

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Total Reads:175000000 Reads with barcode and cut site ov

erhang:169829073 rate:10624 ns/read

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Total Reads:176000000 Reads with barcode and cut site ov

erhang:170812757 rate:10606 ns/read

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Total Reads:177000000 Reads with barcode and cut site ov

erhang:171796427 rate:10589 ns/read

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Total Reads:178000000 Reads with barcode and cut site ov

erhang:172776043 rate:10572 ns/read

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Total Reads:179000000 Reads with barcode and cut site ov

erhang:173759333 rate:10557 ns/read

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Total Reads:180000000 Reads with barcode and cut site ov

erhang:174738889 rate:10541 ns/read

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Total Reads:182000000 Reads with barcode and cut site ov

erhang:176702297 rate:10512 ns/read

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Total Reads:183000000 Reads with barcode and cut site ov

erhang:177685279 rate:10496 ns/read

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Total Reads:184000000 Reads with barcode and cut site ov

erhang:178664528 rate:10480 ns/read

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Total Reads:185000000 Reads with barcode and cut site ov

erhang:179647541 rate:10466 ns/read

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Total Reads:186000000 Reads with barcode and cut site ov

erhang:180630894 rate:10451 ns/read

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Total Reads:187000000 Reads with barcode and cut site ov

erhang:181609930 rate:10435 ns/read

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Total Reads:188000000 Reads with barcode and cut site ov

erhang:182593809 rate:10422 ns/read

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Total Reads:189000000 Reads with barcode and cut site ov

erhang:183574391 rate:10407 ns/read

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Total Reads:190000000 Reads with barcode and cut site ov

erhang:184557275 rate:10392 ns/read

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Total Reads:191000000 Reads with barcode and cut site ov

erhang:185536390 rate:10379 ns/read

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Total Reads:192000000 Reads with barcode and cut site ov

erhang:186519864 rate:11340 ns/read

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Total Reads:193000000 Reads with barcode and cut site ov

erhang:187498579 rate:11596 ns/read

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Total Reads:194000000 Reads with barcode and cut site ov

erhang:188482248 rate:11588 ns/read

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Total Reads:195000000 Reads with barcode and cut site ov

erhang:189466131 rate:11567 ns/read

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Total Reads:196000000 Reads with barcode and cut site ov

erhang:190446651 rate:11546 ns/read

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Total Reads:197000000 Reads with barcode and cut site ov

erhang:191430095 rate:11527 ns/read

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Total Reads:198000000 Reads with barcode and cut site ov

erhang:192408523 rate:11506 ns/read

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Total Reads:199000000 Reads with barcode and cut site ov

erhang:193391901 rate:11491 ns/read

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Total Reads:200000000 Reads with barcode and cut site ov

erhang:194371022 rate:11475 ns/read

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Total Reads:201000000 Reads with barcode and cut site ov

erhang:195354528 rate:11459 ns/read

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Total Reads:202000000 Reads with barcode and cut site ov

erhang:196337447 rate:11440 ns/read

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Total Reads:203000000 Reads with barcode and cut site ov

erhang:197317751 rate:11421 ns/read

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Total Reads:204000000 Reads with barcode and cut site ov

erhang:198301422 rate:11402 ns/read

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Total Reads:205000000 Reads with barcode and cut site ov

erhang:199279905 rate:11383 ns/read

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Total Reads:206000000 Reads with barcode and cut site ov

erhang:200262742 rate:11366 ns/read

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Total Reads:207000000 Reads with barcode and cut site ov

erhang:201242086 rate:11350 ns/read

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Total Reads:208000000 Reads with barcode and cut site ov

erhang:202225237 rate:11333 ns/read

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Total number of reads in lane=208959551

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Total number of good barcoded reads=203165179

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Total number of low quality reads=0

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Timing process (sorting, collapsing, and writing TagCoun

t to file).

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.Produc

tionSNPCallerPluginV2 - Process took 2366178.455396 milliseconds for file C:\Use

rs\labroo2\GBS\LongiMaster_Input\D00553R_3_fastq.gz

[pool-1-thread-1] DEBUG net.maizegenetics.plugindef.AbstractPlugin - Taxon [] al

ready exists in the HDF5 file.  Duplicated taxa not allowed.

java.lang.IllegalStateException: Taxon [] already exists in the HDF5 file.  Dupl

icated taxa not allowed.

        at net.maizegenetics.dna.snp.GenotypeTableBuilder.addTaxon(GenotypeTable

Builder.java:743)

        at net.maizegenetics.dna.snp.GenotypeTableBuilder.addTaxon(GenotypeTable

Builder.java:575)

[pool-1-thread-1] ERROR net.maizegenetics.plugindef.AbstractPlugin - Taxon [] al

ready exists in the HDF5 file.  Duplicated taxa not allowed.

C:\Users\labroo2\TASSEL5>

[Lynn Carol Johnson]

Hi Marlee -

To verify:  Are you running the Production leg using the same key file/taxa list used when you created the db, and the db for Production is the one used throughout the pipeline ?

Have you been able to successfully run ProductionSNPCallerPLuginV2 previously ( on any db), or is this your first attempt?  Are the input fastq files the same or different from those you used when running the Discovery plugins?

Lynn

To view this discussion on the web visit https://groups.google.com/d/msgid/tassel/3469ee20-53fd-4ab4-a4e5-9bf110dca399%40googlegroups.com.

[Marlee Labroo]

Hi Lynn-- yes, it is the same key file, but I made three copies of my original db from the pipeline to apply various filtering parameters. I think I just hit copy, paste, and renamed it. I successfully ran the Production Caller on one of my libraries included in this pipeline in the past; the input fastq files are the same as in other plugins.

I will try rerunning the Production line on my original .db file. Thanks! -Marlee

...

[Lynn Carol Johnson]

The copies with changes could be an issue.  Let me know what happens.

Thanks - Lynn

--

You received this message because you are subscribed to the Google Groups "TASSEL - Trait Analysis by Association, Evolution and Linkage" group.
To unsubscribe from this group and stop receiving emails from it, send an email to tassel+un...@googlegroups.com.
To post to this group, send email to tas...@googlegroups.com.

To view this discussion on the web visit https://groups.google.com/d/msgid/tassel/50290665-7a02-4f56-b519-eb1d407ddb5f%40googlegroups.com.

[Marlee Labroo]

Lynn-- using the original db as generated from the beginning of the pipeline, I get the exact same error (duplicated taxa not allowed). I may get started trying to regenerate the db file from scratch. What do you think?

...

[Marlee Labroo]

Hi Lynn-- In my initial key file, my control well is named "blank" for all 4 libraries. I bet this is causing the issue. Will changing the name in the key file alone resolve it, or are the identical names stuck in the fasta files too? Will I need to rerun the pipeline after renaming the blanks in my key file?

I should have caught this earlier- thanks for your patience and help.

...