KCCG /ClinSV issue with hg38

Question

[Ishak]

Dear Biostars

I work on KCCG /ClinSV here to extract the structural wgs with hg38

I run this code as shown

 clinsv -r all -p $PWD/project_folder -i "$input_path/NA12878_b38.bam" -ref $refdata_path -s sampleinfo_mod.txt

I get this result

##############################################
####                ClinSV                ####
##############################################
# 06/08/2021 15:33:40

# clinsv dir: /home/gnks/Desktop/Temp_yusuf_baran/clincv38_v2/clinsv
# projectDir: /home/gnks/Desktop/Temp_yusuf_baran/clincv38_v2/project_folder
# sampleInfoFile: sampleinfo_mod.txt (read only)
# name stem: project_folder
# lumpyBatchSize: 5
# genome reference: /home/gnks/Desktop/Temp_yusuf_baran/clincv38_v2/clinsv/refdata-b38
# run steps: all
# number input bams: 1

# Read Sample Info from sampleinfo_mod.txt
# use: FR05812606   H7LH3CCXX_6 /home/gnks/Desktop/Temp_yusuf_baran/clincv38_v2/NA12878_b38.bam 
# 1 samples to process
# If not, please exit and modify sampleinfo_mod.txt. 

###### Generate the commands and scripts ######

# bigwig

# lumpy

# cnvnator

# annotate

# prioritize

# qc

###### Run jobs ######

 ### executing: sh /home/gnks/Desktop/Temp_yusuf_baran/clincv38_v2/project_folder/alignments/FR05812606/bw/sh/bigwig.createWigs.FR05812606.sh &> /home/gnks/Desktop/Temp_yusuf_baran/clincv38_v2/project_folder/alignments/FR05812606/bw/sh/bigwig.createWigs.FR05812606.e  ...  

 ### finished after (hh:mm:ss): 00:00:00
 ### exist status: 0

/home/gnks/Desktop/Temp_yusuf_baran/clincv38_v2/project_folder/alignments/FR05812606/bw/sh/bigwig.createWigs.FR05812606.sh: 1: set: Illegal option -o pipefail
 ### executing: sh /home/gnks/Desktop/Temp_yusuf_baran/clincv38_v2/project_folder/alignments/FR05812606/bw/sh/bigwig.q0.FR05812606.sh &> /home/gnks/Desktop/Temp_yusuf_baran/clincv38_v2/project_folder/alignments/FR05812606/bw/sh/bigwig.q0.FR05812606.e  ...  

 ### finished after (hh:mm:ss): 00:00:00
 ### exist status: 0

 ### executing: sh /home/gnks/Desktop/Temp_yusuf_baran/clincv38_v2/project_folder/alignments/FR05812606/bw/sh/bigwig.q20.FR05812606.sh &> /home/gnks/Desktop/Temp_yusuf_baran/clincv38_v2/project_folder/alignments/FR05812606/bw/sh/bigwig.q20.FR05812606.e  ...  

/home/gnks/Desktop/Temp_yusuf_baran/clincv38_v2/project_folder/alignments/FR05812606/bw/sh/bigwig.q0.FR05812606.sh: 1: set: Illegal option -o pipefail
 ### finished after (hh:mm:ss): 00:00:00
 ### exist status: 0

 ### executing: sh /home/gnks/Desktop/Temp_yusuf_baran/clincv38_v2/project_folder/alignments/FR05812606/bw/sh/bigwig.mq.FR05812606.sh &> /home/gnks/Desktop/Temp_yusuf_baran/clincv38_v2/project_folder/alignments/FR05812606/bw/sh/bigwig.mq.FR05812606.e  ...  

/home/gnks/Desktop/Temp_yusuf_baran/clincv38_v2/project_folder/alignments/FR05812606/bw/sh/bigwig.q20.FR05812606.sh: 1: set: Illegal option -o pipefail
 ### finished after (hh:mm:ss): 00:00:00
 ### exist status: 0

 ### executing: sh /home/gnks/Desktop/Temp_yusuf_baran/clincv38_v2/project_folder/SVs/FR05812606/lumpy/sh/lumpy.preproc.FR05812606.sh &> /home/gnks/Desktop/Temp_yusuf_baran/clincv38_v2/project_folder/SVs/FR05812606/lumpy/sh/lumpy.preproc.FR05812606.e  ...  

/home/gnks/Desktop/Temp_yusuf_baran/clincv38_v2/project_folder/alignments/FR05812606/bw/sh/bigwig.mq.FR05812606.sh: 1: set: Illegal option -o pipefail
 ### finished after (hh:mm:ss): 00:00:00
 ### exist status: 0

/home/gnks/Desktop/Temp_yusuf_baran/clincv38_v2/project_folder/SVs/FR05812606/lumpy/sh/lumpy.preproc.FR05812606.sh: 1: set: Illegal option -o pipefail
 ### executing: sh /home/gnks/Desktop/Temp_yusuf_baran/clincv38_v2/project_folder/SVs/joined/lumpy/sh/lumpy.caller.joined.sh &> /home/gnks/Desktop/Temp_yusuf_baran/clincv38_v2/project_folder/SVs/joined/lumpy/sh/lumpy.caller.joined.e  ...  

 ### finished after (hh:mm:ss): 00:00:00
 ### exist status: 0

/home/gnks/Desktop/Temp_yusuf_baran/clincv38_v2/project_folder/SVs/joined/lumpy/sh/lumpy.caller.joined.sh: 1: set: Illegal option -o pipefail
 ### executing: sh /home/gnks/Desktop/Temp_yusuf_baran/clincv38_v2/project_folder/SVs/joined/lumpy/sh/lumpy.depth.joined.sh &> /home/gnks/Desktop/Temp_yusuf_baran/clincv38_v2/project_folder/SVs/joined/lumpy/sh/lumpy.depth.joined.e  ...  

 ### finished after (hh:mm:ss): 00:00:00
 ### exist status: 0

 ### executing: sh /home/gnks/Desktop/Temp_yusuf_baran/clincv38_v2/project_folder/SVs/FR05812606/cnvnator/sh/cnvnator.caller.FR05812606.sh &> /home/gnks/Desktop/Temp_yusuf_baran/clincv38_v2/project_folder/SVs/FR05812606/cnvnator/sh/cnvnator.caller.FR05812606.e  ...  

/home/gnks/Desktop/Temp_yusuf_baran/clincv38_v2/project_folder/SVs/joined/lumpy/sh/lumpy.depth.joined.sh: 1: set: Illegal option -o pipefail
 ### finished after (hh:mm:ss): 00:00:00
 ### exist status: 0

/home/gnks/Desktop/Temp_yusuf_baran/clincv38_v2/project_folder/SVs/FR05812606/cnvnator/sh/cnvnator.caller.FR05812606.sh: 2: /home/gnks/Desktop/Temp_yusuf_baran/clincv38_v2/project_folder/SVs/FR05812606/cnvnator/sh/cnvnator.caller.FR05812606.sh: source: not found
/home/gnks/Desktop/Temp_yusuf_baran/clincv38_v2/project_folder/SVs/FR05812606/cnvnator/sh/cnvnator.caller.FR05812606.sh: 3: set: Illegal option -o pipefail
 ### executing: sh /home/gnks/Desktop/Temp_yusuf_baran/clincv38_v2/project_folder/SVs/joined/sh/annotate.main.joined.sh &> /home/gnks/Desktop/Temp_yusuf_baran/clincv38_v2/project_folder/SVs/joined/sh/annotate.main.joined.e  ...  

 ### finished after (hh:mm:ss): 00:00:00
 ### exist status: 0

/home/gnks/Desktop/Temp_yusuf_baran/clincv38_v2/project_folder/SVs/joined/sh/annotate.main.joined.sh: 1: set: Illegal option -o pipefail
 ### executing: sh /home/gnks/Desktop/Temp_yusuf_baran/clincv38_v2/project_folder/SVs/joined/sh/prioritize.main.joined.sh &> /home/gnks/Desktop/Temp_yusuf_baran/clincv38_v2/project_folder/SVs/joined/sh/prioritize.main.joined.e  ...  

 ### finished after (hh:mm:ss): 00:00:00
 ### exist status: 0

/home/gnks/Desktop/Temp_yusuf_baran/clincv38_v2/project_folder/SVs/joined/sh/prioritize.main.joined.sh: 1: set: Illegal option -o pipefail
 ### executing: sh /home/gnks/Desktop/Temp_yusuf_baran/clincv38_v2/project_folder/SVs/qc/sh/qc.main.joined.sh &> /home/gnks/Desktop/Temp_yusuf_baran/clincv38_v2/project_folder/SVs/qc/sh/qc.main.joined.e  ...  

 ### finished after (hh:mm:ss): 00:00:00
 ### exist status: 0

# 06/08/2021 15:33:40 Project project_folder project_folder | Total jobs 11 | Remaining jobs 0 | Remaining steps bigwig,lumpy,cnvnator,annotate,prioritize,qc  11 | Total time: 0 min

# 06/08/2021 15:33:40 Project project_folder project_folder | Total jobs 11 | Remaining jobs 0 | Remaining steps   0 | Total time: 0 min

# Everything done! Exit

# writing igv session files...

and this too

lumpy variants not present: /home/gnks/Desktop/Temp_yusuf_baran/clincv38_v2/project_folder/SVs/joined/SV-CNV.FR05812606.igv.bed.gz
/home/gnks/Desktop/Temp_yusuf_baran/clincv38_v2/project_folder/SVs/qc/sh/qc.main.joined.sh: 1: set: Illegal option -o pipefail
Use of uninitialized value $_[0] in substitution (s///) at /usr/share/perl/5.26/File/Basename.pm line 180.
fileparse(): need a valid pathname at /home/gnks/Desktop/Temp_yusuf_baran/clincv38_v2/clinsv/bin/clinsv line 1001.

Could you please suggest any solution?

[Pierre Lindenbaum]

/home/gnks/Desktop/Temp_yusuf_baran/clincv38_v2/project_folder/SVs/qc/sh/qc.main.joined.sh: 1: set: Illegal option -o pipefail

the shell is sh , it should be bash

[Ishak]

could you explain more how can I do that?

[Ishak]

This line is output therefore I cant edit it