the folder structure, not configured correctly

[ChengguoShen]

1） I had successfully downloaed and installed in 12-1-2022, following

Linux Native Download precompiled ClinSV bundle for CentOS 6.8 x86_64

wget https://nci.space/clinsv/ClinSV_x86_64_v0.9.tar.gz tar zxf ClinSV_x86_64_v0.9.tar.gz clinsv_path=$PWD/clinsv

export PATH=$clinsv_path/bin:$PATH clinsv -r all -p $PWD/project_folder -i "$input_path/*.bam" -ref $refdata_path

actually running scrip [xxx@ln02 ~]$ clinsv -p $PWD/project_folder -i /cpdir/2021_11_JLS/yuanwl/project/WGS_lin_bam/10_pair/s180533/*.bam -s ./project_folder/sampleInfo.txt -ref /lustre/reference/hg19new ##############################################

ClinSV

##############################################

12/01/2022 17:25:20

clinsv dir: /lustre/home/xxx/clinsv

projectDir: /lustre/home/xxx/project_folder

sampleInfoFile: ./project_folder/sampleInfo.txt (read only)

name stem: project_folder

lumpyBatchSize: 15

genome reference: /lustre/reference/hg19new

run steps: all

number input bams: 1

Read Sample Info from ./project_folder/sampleInfo.txt

use: s180533L_normal_bqsr

use: s180533Tda_tumor_bqsr

use: s180533Tx_tumor_bqsr

3 samples to process

If not, please exit make a copy of sampleInfo.txt, modify it and rerun with -s sampleInfo_mod.txt pointing to the new sample info file.

Generate the commands and scripts

bigwig

lumpy

cnvnator

annotate

prioritize

qc

Run jobs

executing: sh /lustre/home/xxx/project_folder/alignments/s180533L_normal_bqsr/bw/sh/bigwig.createWigs.s180533L_normal_bqsr.sh &> /lustre/home/xxx/project_folder/alignments/s180533L_normal_bqsr/bw/sh/bigwig.createWigs.s180533L_normal_bqsr.e ...

finished after (hh:mm:ss): 00:00:00

exist status: 512

***** error exist status != 0 (512), please check /lustre/home/shencg/project_folder/alignments/s180533L_normal_bqsr/bw/sh/bigwig.createWigs.s180533L_normal_bqsr.e for more information

2) check error message [shencg@ln02 ~]$ cat /lustre/home/shencg/project_folder/alignments/s180533L_normal_bqsr/bw/sh/bigwig.createWigs.s180533L_normal_bqsr.e

• export PATH=/lustre/home/shencg/clinsv/bin:/lustre/home/shencg/clinsv/bin:/lustre/home/shencg/clinsvexport/bin:/usr/local/maui/sbin:/usr/local/maui/bin:/opt/tsce/share/bin:/opt/tsce/share/sbin:/opt/tsce/share/jdk1.6.0_10/bin:/opt/tsce/share/jdk1.6.0_10/jre/bin:/usr/lib64/qt-3.3/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:.:/usr/local/lib:/lustre/home/shencg/.local/bin:/lustre/home/shencg/bin
• PATH=/lustre/home/shencg/clinsv/bin:/lustre/home/shencg/clinsv/bin:/lustre/home/shencg/clinsvexport/bin:/usr/local/maui/sbin:/usr/local/maui/bin:/opt/tsce/share/bin:/opt/tsce/share/sbin:/opt/tsce/share/jdk1.6.0_10/bin:/opt/tsce/share/jdk1.6.0_10/jre/bin:/usr/lib64/qt-3.3/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:.:/usr/local/lib:/lustre/home/shencg/.local/bin:/lustre/home/shencg/bin
• cd /lustre/home/shencg/project_folder/alignments/s180533L_normal_bqsr/bw/
• sort -k2,2nr /lustre/reference/hg19new/genome/human_g1k_v37_decoy.fasta.fai
• awk '{print $1":1-"$2}'
• xargs -P 15 -t '-i{}' perl /lustre/home/shencg/clinsv/clinSV/scripts/bam2wig.pl 1 q0 '{}' /lustre/home/shencg/project_folder/alignments/s180533L_normal_bqsr/bw/tmp/s180533L_normal_bqsr.q0 /lustre/reference/hg19new/genome/human_g1k_v37_decoy.fasta /lustre/home/shencg/project_folder/alignments/s180533L_normal_bqsr/s180533L_normal_bqsr.bam sort: cannot read: /lustre/reference/hg19new/genome/human_g1k_v37_decoy.fasta.fai: No such file or directory

3) pls have a look at our ref hg 19 below [shencg@ln02 ~]$ ls -atl /lustre/reference/hg19new total 14644836 drwxrwxr-x 3 htwu htwu 4096 Mar 18 2021 . drwxrwxr-x 21 fsu bioinfo 4096 Aug 6 2020 .. drwxrwxr-x 2 htwu htwu 4096 May 10 2020 vcf -rw-rw-r-- 1 htwu htwu 3539 Jan 17 2020 hg19.fa.fai -rw-rw-r-- 1 htwu htwu 1568580688 Jan 14 2020 hg19.fa.sa -rw-rw-r-- 1 htwu htwu 8591 Jan 14 2020 hg19.fa.amb -rw-rw-r-- 1 htwu htwu 4040 Jan 14 2020 hg19.fa.ann -rw-rw-r-- 1 htwu htwu 784290318 Jan 14 2020 hg19.fa.pac -rw-rw-r-- 1 htwu htwu 3137161344 Jan 14 2020 hg19.fa.bwt -rw-r--r-- 1 htwu htwu 5490045949 Jan 13 2020 hg19.fa.img -rw-rw-r-- 1 htwu htwu 10166 Jan 13 2020 hg19.dict -rw-rw-r-- 1 htwu htwu 3199905909 Aug 22 2018 hg19.fa -rw-rw-r-- 1 htwu htwu 816241703 Mar 9 2009 hg19.2bit

4） I redownloaded human genome reference data GRCh37 decoy (hs37d5) in your paper in 13-1-2022, which is little difference from hg19

wget https://nci.space/clinsv/refdata-b37_v0.9.tar

check md5sum: 921ecb9b9649563a16e3a47f25954951

tar xf refdata-b37_v0.9.tar refdata_path=$PWD/clinsv/refdata-b37

5) the new runing scripts and error messages below

[shencg@ln02 ~]$ clinsv -p $PWD/project_folder -i /cpdir/2021_11_JLS/yuanwl/project/WGS_lin_bam/10_pair/s180533/*.bam -s ./project_folder/sampleInfo.txt -ref /lustre/home/shencg/clinsv/refdata-b37 ##############################################

ClinSV

##############################################

13/01/2022 12:51:09

clinsv dir: /lustre/home/shencg/clinsv

projectDir: /lustre/home/shencg/project_folder

sampleInfoFile: ./project_folder/sampleInfo.txt (read only)

name stem: project_folder

lumpyBatchSize: 15

genome reference: /lustre/home/shencg/clinsv/refdata-b37

run steps: all

number input bams: 1

Read Sample Info from ./project_folder/sampleInfo.txt

use: s180533L_normal_bqsr

use: s180533Tda_tumor_bqsr

use: s180533Tx_tumor_bqsr

3 samples to process

If not, please exit make a copy of sampleInfo.txt, modify it and rerun with -s sampleInfo_mod.txt pointing to the new sample info file.

Generate the commands and scripts

bigwig

lumpy

cnvnator

annotate

prioritize

qc

Run jobs

executing: sh /lustre/home/shencg/project_folder/alignments/s180533L_normal_bqsr/bw/sh/bigwig.createWigs.s180533L_normal_bqsr.sh &> /lustre/home/shencg/project_folder/alignments/s180533L_normal_bqsr/bw/sh/bigwig.createWigs.s180533L_normal_bqsr.e ...

finished after (hh:mm:ss): 00:00:01

exist status: 0

executing: sh /lustre/home/shencg/project_folder/alignments/s180533Tda_tumor_bqsr/bw/sh/bigwig.createWigs.s180533Tda_tumor_bqsr.sh &> /lustre/home/shencg/project_folder/alignments/s180533Tda_tumor_bqsr/bw/sh/bigwig.createWigs.s180533Tda_tumor_bqsr.e ...

finished after (hh:mm:ss): 00:00:01

exist status: 0

executing: sh /lustre/home/shencg/project_folder/alignments/s180533Tx_tumor_bqsr/bw/sh/bigwig.createWigs.s180533Tx_tumor_bqsr.sh &> /lustre/home/shencg/project_folder/alignments/s180533Tx_tumor_bqsr/bw/sh/bigwig.createWigs.s180533Tx_tumor_bqsr.e ...

finished after (hh:mm:ss): 00:00:00

exist status: 0

executing: sh /lustre/home/shencg/project_folder/alignments/s180533L_normal_bqsr/bw/sh/bigwig.q0.s180533L_normal_bqsr.sh &> /lustre/home/shencg/project_folder/alignments/s180533L_normal_bqsr/bw/sh/bigwig.q0.s180533L_normal_bqsr.e ...

finished after (hh:mm:ss): 00:00:00

exist status: 65280

***** error exist status != 0 (65280), please check /lustre/home/shencg/project_folder/alignments/s180533L_normal_bqsr/bw/sh/bigwig.q0.s180533L_normal_bqsr.e for more information 6) check the error message [xxx@ln02 ~]$ cat /lustre/home/xxx/project_folder/alignments/s180533L_normal_bqsr/bw/sh/bigwig.q0.s180533L_normal_bqsr.e

• export PATH=/lustre/home/xxx/clinsv/bin:/lustre/home/xxx/clinsv/bin:/lustre/home/xxx/clinsvexport/bin:/usr/local/maui/sbin:/usr/local/maui/bin:/opt/tsce/share/bin:/opt/tsce/share/sbin:/opt/tsce/share/jdk1.6.0_10/bin:/opt/tsce/share/jdk1.6.0_10/jre/bin:/usr/lib64/qt-3.3/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:.:/usr/local/lib:/lustre/home/shencg/.local/bin:/lustre/home/shencg/bin
• PATH=/lustre/home/xxx/clinsv/bin:/lustre/home/shencg/clinsv/bin:/lustre/home/shencg/clinsvexport/bin:/usr/local/maui/sbin:/usr/local/maui/bin:/opt/tsce/share/bin:/opt/tsce/share/sbin:/opt/tsce/share/jdk1.6.0_10/bin:/opt/tsce/share/jdk1.6.0_10/jre/bin:/usr/lib64/qt-3.3/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:.:/usr/local/lib:/lustre/home/shencg/.local/bin:/lustre/home/shencg/bin
• cd /lustre/home/xxx/project_folder/alignments/s180533L_normal_bqsr/bw/
• wigToBigWig /lustre/home/shencg/project_folder/alignments/s180533L_normal_bqsr/bw/tmp/s180533L_normal_bqsr.q0.wig /lustre/home/xxx/clinsv/refdata-b37/genome/human_g1k_v37_decoy.fasta.chrom.sizes /lustre/home/shencg/project_folder/alignments/s180533L_normal_bqsr/bw/s180533L_normal_bqsr.q0.bw /lustre/home/shencg/project_folder/alignments/s180533L_normal_bqsr/bw/tmp/s180533L_normal_bqsr.q0.wig is empty of data

7) sampleInfoamation.text

[xxx@ln02 project_folder]$ cat sampleInfo.txt s180533L_normal_bqsr s180533Tda_tumor_bqsr s180533Tx_tumor_bqsr