exist status: 512

[vicrocodile]

Hi! I'm new to bioinformatics so hope my procedure and questions are well explained. I tried to use the docker image for clinSV but I got a message pointing out that need to exit and make a new copy of sampleInfo.txt. I made a new file named sampleInfo_mod.txt, and so I used this code.

sudo docker run -v $refdata_path:/app/ref-data \
-v $project_folder:/app/project_folder  \
-v $input_path:/app/input  \
--entrypoint "perl" mrbradley2/clinsv:v1.0 /app/clinsv/bin/clinsv \
-r all \
-s sampleInfo_mod.txt \
-p /app/project_folder/ \
-i "/app/input/*.bam" \
-ref /app/ref-data/refdata-b38 

however i got a new error

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

 ### finished after (hh:mm:ss): 00:00:00
 ### exist status: 512

 ***** error exist status != 0 (512), please check /app/project_folder/alignments/Human-3700/bw/sh/bigwig.createWigs.Human-3700.e for more information

Looked up to /app/project_folder/alignments/Human-3700/bw/sh/bigwig.createWigs.Human-3700.e and got this:

+ export PATH=/app/clinsv/bin:/app/clinsv/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
+ PATH=/app/clinsv/bin:/app/clinsv/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
+ cd /app/project_folder/alignments/Human-3700/bw/
+ awk '$2>=100000 {print $1":1-"$2}' /app/ref-data/refdata-b38/genome/Homo_sapiens_assembly38.fasta.chrom.sizes
+ xargs -P 15 -t '-i{}' perl /app/clinsv/clinSV/scripts/bam2wig.pl -s 1 -q q0 -r '{}' -o /app/project_folder/alignments/Human-3700/bw/tmp/Human-3700.q0 -f /app/ref-data/refdata-b38/genome/Homo_sapiens_assembly38.fasta -b /app/project_folder/alignments/Human-3700/Human-3700.bam
awk: cannot open /app/ref-data/refdata-b38/genome/Homo_sapiens_assembly38.fasta.chrom.sizes (No such file or directory)

I did check the file the supposedly is missing but it seems to be ok. What should I do?

So i got a few questions besides this error

1. I only indicate de name files in sampleInfo_mod.txt so basically is a 2 line text file with the name of my files in each line. Is that the correct way?
2. I also was wondering if this error could be because I'm using long-reads?

Thanks.

[J-Bradlee]

I think your error has to do with the reference genome not being found, i.e the path "$refdata_path" is incorrect.

If your set up is like this:

Current working directory
|   |contains your bam files *.bam
|   |contains your bai files *.bai
└───clinsv
|    |
|    └───refdata-b38
|    |     |
|    |     └───refdata-b38
|    |     |       | /all of refdata-b38's content/ 
|    
└───test_run
      | this is where clinsv generates all its output

You should then have these path variables:

refdata_path=$PWD/clinsv/refdata-b38
input_path=$PWD
project_folder=$PWD/test_run

If you have set it up like above, ClinSV should automatically make the sampleInfo.txt file from your input bam files (in the example above, your current working directory).

[vicrocodile]

Still not working. Same exit status: 512.

[drmjc]

Hi, clinsv is not designed for long reads. Suggest you look into sniffles. All the best, Mark

On Tue, 2 Aug 2022, 2:43 am vicrocodile, @.***> wrote:

Still not working. Same exit status.

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