Open cfljam opened 7 years ago
@cfljam
Can you point me to your notebook?
Thanks
Helge
I have reproduced this at /workspace/cfljam/HighHealth/PoolSeq/alignEA/
with CL
$NXF_HOME/nextflow run \
PlantandFoodResearch/VariantAnalysis/align.nf \
--genus 'Actinidia' \
--input_dir $INPUTDIR\
--genome $EAFASTA \
--design ./design.config \
--output_dir $EAOUTPUTDIR
Notebook visible at /workspace/cfljam/HighHealth/PoolSeq/2016-10-23AlignPoolsEANextFlow.html/workspace/cfljam/HighHealth/PoolSeq/2016-10-23AlignPoolsEANextFlow.html
Config file is same as https://github.com/Actinidia/HighHealth/blob/master/PoolSeq/design.config
Here is another possible issue:
ad position: EA01_02_scaffold378265:1
INFO 2016-10-24 19:59:19 MarkDuplicates Tracking 425633 as yet unmatched pairs. 3160 records in RAM.
INFO 2016-10-24 20:12:15 MarkDuplicates Read 116811705 records. 0 pairs never matched.
INFO 2016-10-24 20:12:27 MarkDuplicates After buildSortedReadEndLists freeMemory: 2309320448; totalMemory: 17644388352; maxMemory: 30542397440
INFO 2016-10-24 20:12:27 MarkDuplicates Will retain up to 954449920 duplicate indices before spilling to disk.
[Mon Oct 24 20:12:49 NZDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 1,837.42 minutes.
Runtime.totalMemory()=24965545984
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
Exception in thread "main" java.lang.OutOfMemoryError: Java heap space
at htsjdk.samtools.util.SortingLongCollection.<init>(SortingLongCollection.java:112)
at picard.sam.markduplicates.MarkDuplicates.generateDuplicateIndexes(MarkDuplicates.java:570)
at picard.sam.markduplicates.MarkDuplicates.doWork(MarkDuplicates.java:195)
at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:209)
at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:95)
at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:105)
When i run the alignment template there is a some zombie data I presume from the default/demo data coming through in the output
My config file looks like this:
but there is spurious mystery output:
2 issues