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Robust detection of clinically relevant structural and copy number variation from whole genome sequencing data
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Error in Lumpy.depth.joined.sh in ClinSV v0.9: "Illegal division by zero at /opt/clinsv/clinSV/scripts/add-depth-to-PE-SR-calls.pl line 130." #51

Open avanbeelen opened 1 year ago

avanbeelen commented 1 year ago

Hello,

I am running a sample, which is mapped against reference hs37d5, and I got this issue at lumpy.depth.joined.sh. The error log is shown below.

Possible issues: 1) I used samtools view -s to sub sample the BAM file. 2) Regarding BWA MEM, I used the -Y to disable soft clipping for supplementary alignments.

Please help, I am at my wits end.

### executing: sh clinsv0.9/output/DCM_V_AVermeer/small_16D11813/SVs/joined/lumpy/sh/lumpy.depth.joined.sh &> clinsv0.9/output/DCM_V_AVermeer/small_16D11813/SVs/joined/lumpy/sh/lumpy.depth.joined.e  ...

 ### finished after (hh:mm:ss): 00:00:03
 ### exist status: 31744

 ***** error exist status != 0 (31744), please check clinsv0.9/output/DCM_V_AVermeer/small_16D11813/SVs/joined/lumpy/sh/lumpy.depth.joined.e for more information

Error log:

+ export PATH=/opt/clinsv/bin:/opt/clinsv/bin:/opt/clinsv/root/bin:/bin/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
+ PATH=/opt/clinsv/bin:/opt/clinsv/bin:/opt/clinsv/root/bin:/bin/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
+ perl -e 'while(<>){ if(/^#/){$h.=$_; next;} @_=split("\t",$_); $c=$_[0]; if(!exists($f{$c})){ open($f{$c},">clinsv0.9/output/DCM_V_AVermeer/small_16D11813/SVs/joined/lumpy/tmp/in.$c.vcf"); print {$f{$c}} $h; }
print {$f{$c}} $_; } foreach (values %f){close} ' clinsv0.9/output/DCM_V_AVermeer/small_16D11813/SVs/joined/lumpy/small_16D11813.MQ20.OpreProc.vcf
+ xargs -P 12 -t '-i{}' perl /opt/clinsv/clinSV/scripts/add-depth-to-PE-SR-calls.pl '{}' clinsv0.9/clinsv/refdata-b37/genome/human_g1k_v37_decoy.fasta clinsv0.9/output/DCM_V_AVermeer/small_16D11813 clinsv0.9/clinsv/refdata-b37/control/brkp 500 clinsv0.9/clinsv/refdata-b37/control/cnv/bw
+ ls clinsv0.9/output/DCM_V_AVermeer/small_16D11813/SVs/joined/lumpy/tmp/in.11.vcf clinsv0.9/output/DCM_V_AVermeer/small_16D11813/SVs/joined/lumpy/tmp/in.12.vcf clinsv0.9/output/DCM_V_AVermeer/small_16D11813/SVs/joined/lumpy/tmp/in.13.vcf clinsv0.9/output/DCM_V_AVermeer/small_16D11813/SVs/joined/lumpy/tmp/in.15.vcf clinsv0.9/output/DCM_V_AVermeer/small_16D11813/SVs/joined/lumpy/tmp/in.18.vcf clinsv0.9/output/DCM_V_AVermeer/small_16D11813/SVs/joined/lumpy/tmp/in.19.vcf clinsv0.9/output/DCM_V_AVermeer/small_16D11813/SVs/joined/lumpy/tmp/in.1.vcf clinsv0.9/output/DCM_V_AVermeer/small_16D11813/SVs/joined/lumpy/tmp/in.20.vcf clinsv0.9/output/DCM_V_AVermeer/small_16D11813/SVs/joined/lumpy/tmp/in.2.vcf clinsv0.9/output/DCM_V_AVermeer/small_16D11813/SVs/joined/lumpy/tmp/in.3.vcf clinsv0.9/output/DCM_V_AVermeer/small_16D11813/SVs/joined/lumpy/tmp/in.5.vcf clinsv0.9/output/DCM_V_AVermeer/small_16D11813/SVs/joined/lumpy/tmp/in.6.vcf clinsv0.9/output/DCM_V_AVermeer/small_16D11813/SVs/joined/lumpy/tmp/in.7.vcf
perl /opt/clinsv/clinSV/scripts/add-depth-to-PE-SR-calls.pl clinsv0.9/output/DCM_V_AVermeer/small_16D11813/SVs/joined/lumpy/tmp/in.11.vcf clinsv0.9/clinsv/refdata-b37/genome/human_g1k_v37_decoy.fasta clinsv0.9/output/DCM_V_AVermeer/small_16D11813 clinsv0.9/clinsv/refdata-b37/control/brkp 500 clinsv0.9/clinsv/refdata-b37/control/cnv/bw
perl /opt/clinsv/clinSV/scripts/add-depth-to-PE-SR-calls.pl clinsv0.9/output/DCM_V_AVermeer/small_16D11813/SVs/joined/lumpy/tmp/in.12.vcf clinsv0.9/clinsv/refdata-b37/genome/human_g1k_v37_decoy.fasta clinsv0.9/output/DCM_V_AVermeer/small_16D11813 clinsv0.9/clinsv/refdata-b37/control/brkp 500 clinsv0.9/clinsv/refdata-b37/control/cnv/bw
perl /opt/clinsv/clinSV/scripts/add-depth-to-PE-SR-calls.pl clinsv0.9/output/DCM_V_AVermeer/small_16D11813/SVs/joined/lumpy/tmp/in.13.vcf clinsv0.9/clinsv/refdata-b37/genome/human_g1k_v37_decoy.fasta clinsv0.9/output/DCM_V_AVermeer/small_16D11813 clinsv0.9/clinsv/refdata-b37/control/brkp 500 clinsv0.9/clinsv/refdata-b37/control/cnv/bw
perl /opt/clinsv/clinSV/scripts/add-depth-to-PE-SR-calls.pl clinsv0.9/output/DCM_V_AVermeer/small_16D11813/SVs/joined/lumpy/tmp/in.15.vcf clinsv0.9/clinsv/refdata-b37/genome/human_g1k_v37_decoy.fasta clinsv0.9/output/DCM_V_AVermeer/small_16D11813 clinsv0.9/clinsv/refdata-b37/control/brkp 500 clinsv0.9/clinsv/refdata-b37/control/cnv/bw
perl /opt/clinsv/clinSV/scripts/add-depth-to-PE-SR-calls.pl clinsv0.9/output/DCM_V_AVermeer/small_16D11813/SVs/joined/lumpy/tmp/in.18.vcf clinsv0.9/clinsv/refdata-b37/genome/human_g1k_v37_decoy.fasta clinsv0.9/output/DCM_V_AVermeer/small_16D11813 clinsv0.9/clinsv/refdata-b37/control/brkp 500 clinsv0.9/clinsv/refdata-b37/control/cnv/bw
perl /opt/clinsv/clinSV/scripts/add-depth-to-PE-SR-calls.pl clinsv0.9/output/DCM_V_AVermeer/small_16D11813/SVs/joined/lumpy/tmp/in.19.vcf clinsv0.9/clinsv/refdata-b37/genome/human_g1k_v37_decoy.fasta clinsv0.9/output/DCM_V_AVermeer/small_16D11813 clinsv0.9/clinsv/refdata-b37/control/brkp 500 clinsv0.9/clinsv/refdata-b37/control/cnv/bw
perl /opt/clinsv/clinSV/scripts/add-depth-to-PE-SR-calls.pl clinsv0.9/output/DCM_V_AVermeer/small_16D11813/SVs/joined/lumpy/tmp/in.1.vcf clinsv0.9/clinsv/refdata-b37/genome/human_g1k_v37_decoy.fasta clinsv0.9/output/DCM_V_AVermeer/small_16D11813 clinsv0.9/clinsv/refdata-b37/control/brkp 500 clinsv0.9/clinsv/refdata-b37/control/cnv/bw
perl /opt/clinsv/clinSV/scripts/add-depth-to-PE-SR-calls.pl clinsv0.9/output/DCM_V_AVermeer/small_16D11813/SVs/joined/lumpy/tmp/in.20.vcf clinsv0.9/clinsv/refdata-b37/genome/human_g1k_v37_decoy.fasta clinsv0.9/output/DCM_V_AVermeer/small_16D11813 clinsv0.9/clinsv/refdata-b37/control/brkp 500 clinsv0.9/clinsv/refdata-b37/control/cnv/bw
perl /opt/clinsv/clinSV/scripts/add-depth-to-PE-SR-calls.pl clinsv0.9/output/DCM_V_AVermeer/small_16D11813/SVs/joined/lumpy/tmp/in.2.vcf clinsv0.9/clinsv/refdata-b37/genome/human_g1k_v37_decoy.fasta clinsv0.9/output/DCM_V_AVermeer/small_16D11813 clinsv0.9/clinsv/refdata-b37/control/brkp 500 clinsv0.9/clinsv/refdata-b37/control/cnv/bw
perl /opt/clinsv/clinSV/scripts/add-depth-to-PE-SR-calls.pl clinsv0.9/output/DCM_V_AVermeer/small_16D11813/SVs/joined/lumpy/tmp/in.3.vcf clinsv0.9/clinsv/refdata-b37/genome/human_g1k_v37_decoy.fasta clinsv0.9/output/DCM_V_AVermeer/small_16D11813 clinsv0.9/clinsv/refdata-b37/control/brkp 500 clinsv0.9/clinsv/refdata-b37/control/cnv/bw
perl /opt/clinsv/clinSV/scripts/add-depth-to-PE-SR-calls.pl clinsv0.9/output/DCM_V_AVermeer/small_16D11813/SVs/joined/lumpy/tmp/in.5.vcf clinsv0.9/clinsv/refdata-b37/genome/human_g1k_v37_decoy.fasta clinsv0.9/output/DCM_V_AVermeer/small_16D11813 clinsv0.9/clinsv/refdata-b37/control/brkp 500 clinsv0.9/clinsv/refdata-b37/control/cnv/bw
perl /opt/clinsv/clinSV/scripts/add-depth-to-PE-SR-calls.pl clinsv0.9/output/DCM_V_AVermeer/small_16D11813/SVs/joined/lumpy/tmp/in.6.vcf clinsv0.9/clinsv/refdata-b37/genome/human_g1k_v37_decoy.fasta clinsv0.9/output/DCM_V_AVermeer/small_16D11813 clinsv0.9/clinsv/refdata-b37/control/brkp 500 clinsv0.9/clinsv/refdata-b37/control/cnv/bw
local perl lib: /opt/clinsv/clinSV/scripts/../../perlib
local perl lib: /opt/clinsv/clinSV/scripts/../../perlib
local perl lib: /opt/clinsv/clinSV/scripts/../../perlib
local perl lib: /opt/clinsv/clinSV/scripts/../../perlib
local perl lib: /opt/clinsv/clinSV/scripts/../../perlib
# running add-depth-to-PE-SR-calls-v4.pl
# in VCF: clinsv0.9/output/DCM_V_AVermeer/small_16D11813/SVs/joined/lumpy/tmp/in.1.vcf
# out VCF: clinsv0.9/output/DCM_V_AVermeer/small_16D11813/SVs/joined/lumpy/tmp/in.1.out
# in SR control: clinsv0.9/clinsv/refdata-b37/control/brkp/SR.brkp.gz
# in PE control: clinsv0.9/clinsv/refdata-b37/control/brkp/PE.brkp.gz
create tabix vcf to extract the copy neutral deletion duplications...
local perl lib: /opt/clinsv/clinSV/scripts/../../perlib
local perl lib: /opt/clinsv/clinSV/scripts/../../perlib
# running add-depth-to-PE-SR-calls-v4.pl
local perl lib: /opt/clinsv/clinSV/scripts/../../perlib
local perl lib: /opt/clinsv/clinSV/scripts/../../perlib
local perl lib: /opt/clinsv/clinSV/scripts/../../perlib
# running add-depth-to-PE-SR-calls-v4.pl
# in VCF: clinsv0.9/output/DCM_V_AVermeer/small_16D11813/SVs/joined/lumpy/tmp/in.18.vcf
# out VCF: clinsv0.9/output/DCM_V_AVermeer/small_16D11813/SVs/joined/lumpy/tmp/in.18.out
# in SR control: clinsv0.9/clinsv/refdata-b37/control/brkp/SR.brkp.gz
# in PE control: clinsv0.9/clinsv/refdata-b37/control/brkp/PE.brkp.gz
create tabix vcf to extract the copy neutral deletion duplications...
local perl lib: /opt/clinsv/clinSV/scripts/../../perlib
local perl lib: /opt/clinsv/clinSV/scripts/../../perlib
# running add-depth-to-PE-SR-calls-v4.pl
# in VCF: clinsv0.9/output/DCM_V_AVermeer/small_16D11813/SVs/joined/lumpy/tmp/in.12.vcf
# out VCF: clinsv0.9/output/DCM_V_AVermeer/small_16D11813/SVs/joined/lumpy/tmp/in.12.out
# in SR control: clinsv0.9/clinsv/refdata-b37/control/brkp/SR.brkp.gz
# in PE control: clinsv0.9/clinsv/refdata-b37/control/brkp/PE.brkp.gz
create tabix vcf to extract the copy neutral deletion duplications...
# running add-depth-to-PE-SR-calls-v4.pl
# in VCF: clinsv0.9/output/DCM_V_AVermeer/small_16D11813/SVs/joined/lumpy/tmp/in.3.vcf
# out VCF: clinsv0.9/output/DCM_V_AVermeer/small_16D11813/SVs/joined/lumpy/tmp/in.3.out
# in SR control: clinsv0.9/clinsv/refdata-b37/control/brkp/SR.brkp.gz
# in PE control: clinsv0.9/clinsv/refdata-b37/control/brkp/PE.brkp.gz
create tabix vcf to extract the copy neutral deletion duplications...
# in VCF: clinsv0.9/output/DCM_V_AVermeer/small_16D11813/SVs/joined/lumpy/tmp/in.5.vcf
# out VCF: clinsv0.9/output/DCM_V_AVermeer/small_16D11813/SVs/joined/lumpy/tmp/in.5.out
# running add-depth-to-PE-SR-calls-v4.pl
# in VCF: clinsv0.9/output/DCM_V_AVermeer/small_16D11813/SVs/joined/lumpy/tmp/in.13.vcf
# out VCF: clinsv0.9/output/DCM_V_AVermeer/small_16D11813/SVs/joined/lumpy/tmp/in.13.out
# in SR control: clinsv0.9/clinsv/refdata-b37/control/brkp/SR.brkp.gz
# in PE control: clinsv0.9/clinsv/refdata-b37/control/brkp/PE.brkp.gz
create tabix vcf to extract the copy neutral deletion duplications...
# running add-depth-to-PE-SR-calls-v4.pl
# in VCF: clinsv0.9/output/DCM_V_AVermeer/small_16D11813/SVs/joined/lumpy/tmp/in.2.vcf
# out VCF: clinsv0.9/output/DCM_V_AVermeer/small_16D11813/SVs/joined/lumpy/tmp/in.2.out
# in SR control: clinsv0.9/clinsv/refdata-b37/control/brkp/SR.brkp.gz
# in PE control: clinsv0.9/clinsv/refdata-b37/control/brkp/PE.brkp.gz
create tabix vcf to extract the copy neutral deletion duplications...
# running add-depth-to-PE-SR-calls-v4.pl
# in VCF: clinsv0.9/output/DCM_V_AVermeer/small_16D11813/SVs/joined/lumpy/tmp/in.20.vcf
# out VCF: clinsv0.9/output/DCM_V_AVermeer/small_16D11813/SVs/joined/lumpy/tmp/in.20.out
# in SR control: clinsv0.9/clinsv/refdata-b37/control/brkp/SR.brkp.gz
# in PE control: clinsv0.9/clinsv/refdata-b37/control/brkp/PE.brkp.gz
create tabix vcf to extract the copy neutral deletion duplications...
# running add-depth-to-PE-SR-calls-v4.pl
# in VCF: clinsv0.9/output/DCM_V_AVermeer/small_16D11813/SVs/joined/lumpy/tmp/in.19.vcf
# out VCF: clinsv0.9/output/DCM_V_AVermeer/small_16D11813/SVs/joined/lumpy/tmp/in.19.out
# in SR control: clinsv0.9/clinsv/refdata-b37/control/brkp/SR.brkp.gz
# in PE control: clinsv0.9/clinsv/refdata-b37/control/brkp/PE.brkp.gz
create tabix vcf to extract the copy neutral deletion duplications...
# running add-depth-to-PE-SR-calls-v4.pl
# in VCF: clinsv0.9/output/DCM_V_AVermeer/small_16D11813/SVs/joined/lumpy/tmp/in.15.vcf
# out VCF: clinsv0.9/output/DCM_V_AVermeer/small_16D11813/SVs/joined/lumpy/tmp/in.15.out
# in SR control: clinsv0.9/clinsv/refdata-b37/control/brkp/SR.brkp.gz
# in PE control: clinsv0.9/clinsv/refdata-b37/control/brkp/PE.brkp.gz
create tabix vcf to extract the copy neutral deletion duplications...
open in the input VCF...
# running add-depth-to-PE-SR-calls-v4.pl
# in VCF: clinsv0.9/output/DCM_V_AVermeer/small_16D11813/SVs/joined/lumpy/tmp/in.6.vcf
# out VCF: clinsv0.9/output/DCM_V_AVermeer/small_16D11813/SVs/joined/lumpy/tmp/in.6.out
# in SR control: clinsv0.9/clinsv/refdata-b37/control/brkp/SR.brkp.gz
# in PE control: clinsv0.9/clinsv/refdata-b37/control/brkp/PE.brkp.gz
create tabix vcf to extract the copy neutral deletion duplications...
# in SR control: clinsv0.9/clinsv/refdata-b37/control/brkp/SR.brkp.gz
# in PE control: clinsv0.9/clinsv/refdata-b37/control/brkp/PE.brkp.gz
create tabix vcf to extract the copy neutral deletion duplications...
# running add-depth-to-PE-SR-calls-v4.pl
# in VCF: clinsv0.9/output/DCM_V_AVermeer/small_16D11813/SVs/joined/lumpy/tmp/in.11.vcf
# out VCF: clinsv0.9/output/DCM_V_AVermeer/small_16D11813/SVs/joined/lumpy/tmp/in.11.out
# in SR control: clinsv0.9/clinsv/refdata-b37/control/brkp/SR.brkp.gz
# in PE control: clinsv0.9/clinsv/refdata-b37/control/brkp/PE.brkp.gz
create tabix vcf to extract the copy neutral deletion duplications...
open in the input VCF...
open in the input VCF...
open in the input VCF...
open in the input VCF...
open in the input VCF...
open in the input VCF...
open in the input VCF...
open in the input VCF...
open in the input VCF...
open in the input VCF...
open in the input VCF...
samples in vcf: test2
open the bw files...
samples in vcf: test2
open the bw files...
samples in vcf: test2
open the bw files...
samples in vcf: test2
open the bw files...
samples in vcf: test2
open the bw files...
samples in vcf: test2
open the bw files...
samples in vcf: test2
open the bw files...
samples in vcf: test2
open the bw files...
samples in vcf: test2
open the bw files...
samples in vcf: test2
open the bw files...
samples in vcf: test2
open the bw files...
samples in vcf: test2
open the bw files...
# sample: test2, bw found
# sample: test2, bw found
# sample: test2, bw found
# sample: test2, bw found
# sample: test2, bw found
# sample: test2, bw found
# sample: test2, bw found
# sample: test2, bw found
# sample: test2, bw found
# sample: test2, bw found
# sample: test2, bw found
# sample: test2, bw found
determine the average coverage per sample acrosse >MQ50 regions...
determine the average coverage per sample acrosse >MQ50 regions...
determine the average coverage per sample acrosse >MQ50 regions...
determine the average coverage per sample acrosse >MQ50 regions...
determine the average coverage per sample acrosse >MQ50 regions...
determine the average coverage per sample acrosse >MQ50 regions...
determine the average coverage per sample acrosse >MQ50 regions...
determine the average coverage per sample acrosse >MQ50 regions...
determine the average coverage per sample acrosse >MQ50 regions...
determine the average coverage per sample acrosse >MQ50 regions...
determine the average coverage per sample acrosse >MQ50 regions...
determine the average coverage per sample acrosse >MQ50 regions...
Illegal division by zero at /opt/clinsv/clinSV/scripts/add-depth-to-PE-SR-calls.pl line 130.
Illegal division by zero at /opt/clinsv/clinSV/scripts/add-depth-to-PE-SR-calls.pl line 130.
Illegal division by zero at /opt/clinsv/clinSV/scripts/add-depth-to-PE-SR-calls.pl line 130.
Illegal division by zero at /opt/clinsv/clinSV/scripts/add-depth-to-PE-SR-calls.pl line 130.
Illegal division by zero at /opt/clinsv/clinSV/scripts/add-depth-to-PE-SR-calls.pl line 130.
Illegal division by zero at /opt/clinsv/clinSV/scripts/add-depth-to-PE-SR-calls.pl line 130.
Illegal division by zero at /opt/clinsv/clinSV/scripts/add-depth-to-PE-SR-calls.pl line 130.
Illegal division by zero at /opt/clinsv/clinSV/scripts/add-depth-to-PE-SR-calls.pl line 130.
Illegal division by zero at /opt/clinsv/clinSV/scripts/add-depth-to-PE-SR-calls.pl line 130.
Illegal division by zero at /opt/clinsv/clinSV/scripts/add-depth-to-PE-SR-calls.pl line 130.
Illegal division by zero at /opt/clinsv/clinSV/scripts/add-depth-to-PE-SR-calls.pl line 130.
Illegal division by zero at /opt/clinsv/clinSV/scripts/add-depth-to-PE-SR-calls.pl line 130.
xargs: perl: exited with status 255; aborting
xargs: perl: exited with status 255; aborting
drmjc commented 1 year ago

Hi, i'm guessing from your other thread you saw that we use -M rather than -Y? Does that solve this problem?

avanbeelen commented 1 year ago

Hi, I used -M this time, but I am still working on it. I'll update you on the progress. Thanks for your help, best regards, Aron

Op ma 13 mrt 2023 om 10:35 schreef Mark Cowley @.***>:

Hi, i'm guessing from your other thread you saw that we use -M rather than -Y? Does that solve this problem?

— Reply to this email directly, view it on GitHub https://github.com/KCCG/ClinSV/issues/51#issuecomment-1465799699, or unsubscribe https://github.com/notifications/unsubscribe-auth/AMUNBADDBQPA763N6OA4KV3W33S6HANCNFSM6AAAAAAVSGGROE . You are receiving this because you are subscribed to this thread.Message ID: @.***>