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brentp / smoove

structural variant calling and genotyping with existing tools, but, smoothly.
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([E]lumpy-filter) mv: cannot stat ‘SmooveTest_out/001MS.split.bam.tmp.bam’: No such file or directory #158

Closed nitha26 closed 3 years ago

nitha26 commented 3 years ago

Hi @brentp, I am running smoove in conda version in cluster. When I try to do test run for 10 samples (CRAM file ) in parallel getting following error

Command used in python: smoove call --outdir SmooveTest_out --exclude exclude_reg/exclude.cnvnator_100bp.GRCh38.20170403.bed --name "+x[int]+" --fasta ref-gen/GRCh38_full_analysis_set_plus_decoy_hla.fa -p 1 --genotype CRAM/"+x[int]+".cram

`[smoove] 2021/07/05 12:39:25 calculating bam stats for 1 bams [smoove] 2021/07/05 12:39:29 done calculating bam stats [smoove]: ([E]lumpy-filter) 2021/07/05 13:27:07 mv: cannot stat ‘SmooveTest_out/001MS.split.bam.tmp.bam’: No such file or directory [smoove]:2021/07/05 13:27:07 finished process: lumpy-filter (lumpy_filter -f ref-gen/GRCh38_full_analysis_set_plus_decoy_hla.fa CRAM/001MS.cram SmooveTest_out/00) in user-time:47m18.254711s system-time:21.227666s [smoove]:2021/07/05 13:27:07 error running command: lumpy_filter -f ref-gen/GRCh38_full_analysis_set_plus_decoy_hla.fa CRAM/001MS.cram SmooveTest_out/001MS.split.bam.tmp.bam SmooveTest_out/001MS.disc.bam.tmp.bam 2 && mv SmooveTest_out/001MS.split.bam.tmp.bam SmooveTest_out/001MS.split.bam && mv SmooveTest_out/001MS.disc.bam.tmp.bam SmooveTest_out/001MS.disc.bam -> exit status 1 panic: exit status 1

goroutine 1 [running]: github.com/brentp/smoove/lumpy.Lumpy(0x7fffa7423c68, 0x5, 0x7fffa7423c76, 0x32, 0x7fffa7423c11, 0xe, 0xc420131430, 0x1, 0x1, 0xc420197f40, ...) /home/brentp/go/src/github.com/brentp/smoove/lumpy/lumpy.go:115 +0x556 github.com/brentp/smoove/lumpy.Main() /home/brentp/go/src/github.com/brentp/smoove/lumpy/lumpy.go:275 +0x23a main.main() /home/brentp/go/src/github.com/brentp/smoove/cmd/smoove/smoove.go:115 +0x1dd m/brentp/smoove/cmd/smoove/smoove.go:115 +0x1dd`

Could you please help me? Thanks!

brentp commented 3 years ago

Hi, here are some things you can check:

  1. if this has run before remove all stale files in SmooveTest_out
  2. make sure that the process has permission to create and write to SmooveTest_out
  3. check if the cram file that is erroring is very small or check if it is not readable.
nitha26 commented 3 years ago

@brentp,I tried re-running smoove (docker version running in HPC) this time in bash script after the above correction for 7 cram files. But this time I'm facing different types of errors. The error file is attached. smoove_7samptestrunLog.txt

Command used: 

#!/bin/bash  
FILES="/gpfs/data/SV_test/smoove_SVcalling/CRAM/*.cram"; for f in $FILES; do smoove call --outdir /gpfs/data/SV_test/smoove_SVcalling/7_out/ --exclude /gpfs/data/SV_test/smoove_SVcalling/exclude_reg/exclude.cnvnator_100bp.GRCh38.20170403.bed  --name "$f"_new --fasta /gpfs/data/SV_test/smoove_SVcalling/ref-gen/GRCh38_full_analysis_set_plus_decoy_hla.fa -p 1 --genotype "$f" &>>smoove_Test7cram; done

Could you please guide me whether the command used is correct.

Thanks!

brentp commented 3 years ago

Hi, please update to the latest version of smoove and re-try with clean directories. You have a very old version of smoove.

nitha26 commented 3 years ago

Thank you. I will check it

nitha26 commented 3 years ago

@brentp could you please redirect me to the link where I can find the latest docker version of smoove. Thanks

brentp commented 3 years ago

https://www.google.com/search?q=docker+smoove