Error (exit status:256)

[tomlodz]

Hello,

I have a little problem with ClinSV. Both versions on dockers v0.9 and v1.0, after some time from the start of processing, the analysis stops with the following message:

finished after (hh:mm:ss): 00:00:00
exist status: 256

***** error exist status != 0 (256), please check /app/project_folder/SVs/joined/lumpy/sh/lumpy.caller.joined.e for more information

The lumpy.caller.joined.e file says that there is no bam file in the directory. This file should probably be generated during the analysis itself. Below is the content of the file:

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
    declare -A meanArr
    declare -A stdevArr
    declare -A readLArr
    ++ samtools view /app/project_folder/alignments/1.bam/1.bam.bam chr1:1000000-1100000
    ++ cut -f 10
    ++ awk '{ print length}'
    ++ sort -rn
    ++ awk '(NR==1){print}'
    [E::hts_open_format] fail to open file '/app/project_folder/alignments/1.bam/1.bam.bam'
    samtools view: failed to open "/app/project_folder/alignments/1.bam/1.bam.bam" for reading: No such file or directory
    readLArr[1.bam]=

Thanks in advance

[drmjc]

Hi, What was the command that you ran, and where are the BAM+BAI files? thanks

[tomlodz]

Command was as follows:

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

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

File structure was as follows because there was a error "refdata-bX not matching". That structure fix this error.

test
|   |contains your bam files *.bam
|   |contains your bai files *.bai
└───clinsv
|    |
|    └───refdata-b38
|    |     |
|    |     └───refdata-b38
|    |     |       | /all of refdata-b38's content/ 
|    
└───test_run

[OlenaMaiakovska]

I have the exactly same issue..

[tomlodz]

I tried to solve the problem and on the data from the Internet (NA12878_b38.bam) the analysis went without any problems. For me, it seems that the problem was that the line with the sample name and ID was missing in the header in the BAM file. Also the BAM files that were made on the standard HG38 reference sequence would not pass the analysis. BAM files must be mapped to the exact reference ClinSV uses. I made references from ref-data files from the fasta file.

Finally, one note that the bai file must have the extension X.bam.bai If it only has the X.bai extension, the program will not complete the analysis either.