Hello,
I'm trying to run the GBS pipeline on some data I was given, but something is going wrong with either the first or second step. The first command I run is
run_pipeline.pl -Xmx15G -fork1 -GBSSeqToTagDBPlugin -e PstI-MspI -i /FQ -db tags.db -k keyfile.tsv -mnQS 10 -kmerLength 80 -minKmerL 20 -mxKmerNum 100000000 -c 1 -endPlugin -runfork1
which seems to run fine. There are a couple errors in the log file. This one appears near the beginning, but it doesn't seem to stop the rest of the script from running:
[SQLITE_ERROR] SQL error or missing database (table tag already exists)
org.sqlite.SQLiteException: [SQLITE_ERROR] SQL error or missing database (table tag already exists)
at org.sqlite.core.DB.newSQLException(DB.java:1135)
at org.sqlite.core.DB.newSQLException(DB.java:1146)
at org.sqlite.core.DB.throwex(DB.java:1106)
at org.sqlite.core.NativeDB._exec_utf8(Native Method)
at org.sqlite.core.NativeDB._exec(NativeDB.java:86)
at org.sqlite.jdbc3.JDBC3Statement.executeLargeUpdate(JDBC3Statement.java:97)
at org.sqlite.jdbc3.JDBC3Statement.executeUpdate(JDBC3Statement.java:78)
at net.maizegenetics.dna.tag.TagDataSQLite.<init>(TagDataSQLite.java:98)
at net.maizegenetics.analysis.gbs.v2.GBSSeqToTagDBPlugin.processData(GBSSeqToTagDBPlugin.java:218)
at net.maizegenetics.plugindef.AbstractPlugin.performFunction(AbstractPlugin.java:111)
at net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:2017)
at net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:572)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:317)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1144)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:642)
at java.base/java.lang.Thread.run(Thread.java:1583)
The other error is a single "sequence at line failed the length test" error, but I don't know that that should hurt anything.
Otherwise, the log looks good from the first step. Here's a little output from the end:
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.GBSSeqToTagDBPlugin - Summary for /FQ/1-sw-54_HVKFWDRX3_S54_2_fastq.txt.gz
Total number of reads in lane=440273
Total number of good barcoded reads=413698
Total number of low quality reads=19326
Timing process (sorting, collapsing, and writing TagCount to file).
Process took 2855.360497 milliseconds.
tagCntMap size: 2046683
[pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin - Finished net.maizegenetics.analysis.gbs.v2.GBSSeqToTagDBPlugin: time: May 1, 2024 14:16:16
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.GBSSeqToTagDBPlugin - Summary for /FQ/1-sw-54_HVKFWDRX3_S54_2_fastq.txt.gz
Total number of reads in lane=440273
Total number of good barcoded reads=413698
Total number of low quality reads=19326
Timing process (sorting, collapsing, and writing TagCount to file).
Process took 2772.697447 milliseconds.
tagCntMap size: 2046683
[pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin - Finished net.maizegenetics.analysis.gbs.v2.GBSSeqToTagDBPlugin: time: May 1, 2024 14:16:16
However, the tag db produced is only 112kb, which seems too small. Then when I run the next step:
run_pipeline.pl -Xmx15G -fork1 -TagExportToFastqPlugin -db tags.db -o tags.fa.gz -c 1 -endPlugin -runfork1
I get this:
size of all tags in tag table=0
size of all tissues in tissue table=0
size of all tags in mappingApproach table=1
size of all taxa in taxa table=0
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: 0 (above minCount of 1)
Ouput fastq file: tags.fa.gz
So for some reason nothing is getting written to the tag database. I sort of wonder if I'm running out of memory, but there doesn't seem to be anything indicating that in the log. Does anyone have any other ideas what might be going wrong?
