VIRUSBREAKEND > failure identifying viral sequences

[josh11351]

Hello, I am attempting to utilize virusbreakend and have been running into an issue I have been unable to solve. Whenever I attempt to run the shell script I am returned with the following error: Thu Oct 12 11:52:52 EDT 2023: Failure running identifying viral sequences
Thu Oct 12 11:52:52 EDT 2023: Exit status 0 for print_failure "identifying viral sequences"
I have been unable to find a solution based on the error message given in the log files.

also here are some screenshots of my full terminal page as well as the log

Any help is greatly appreciated!

[nalcala]

Hi,
I am having the exact same error @josh11351 . Did you find a fix for it?
Thanks!
Nicolas

[nalcala]

Of note, this does not happen on all my cram files (75 worked for ~15 that ended with that error). It seems to be coming from this line https://github.com/PapenfussLab/gridss/blob/09900c48d6d0e899a155cbc185f3d8e7c511bf05/scripts/virusbreakend#L498C19-L498C31 , which pipes 3 processes (executing the bash file created in the folder that extracts unmapped reads, running kraken2, and running gridss.kraken.SubsetToTaxonomy) and then moves $file_readname.tmp $file_readname . The weird part is that I do see in the log a message " gridss.kraken.SubsetToTaxonomy done" and I see a file *readname.tmp created with readnames in it, but not moved to *readname, so I guess there is a an error at some point for one read somewhere in the pipe.

The timing file created mentions a non-zero status 141:

Command exited with non-zero status 141
        Command being timed: "cram_file/cram_file_virusbreakend.vcf.virusbreakend.working/cram_file_virusbreakend.vcf.cat_input_as_fastq.sh"
User time (seconds): 2053.57
        System time (seconds): 109.37
        Percent of CPU this job got: 3%
        Elapsed (wall clock) time (h:mm:ss or m:ss): 17:51:58
        Average shared text size (kbytes): 0
        Average unshared data size (kbytes): 0
        Average stack size (kbytes): 0
        Average total size (kbytes): 0
        Maximum resident set size (kbytes): 981872
        Average resident set size (kbytes): 0
        Major (requiring I/O) page faults: 94
        Minor (reclaiming a frame) page faults: 11053813
        Voluntary context switches: 2095681
        Involuntary context switches: 10789
        Swaps: 0
        File system inputs: 105310893
        File system outputs: 11
        Socket messages sent: 0
        Socket messages received: 0
        Signals delivered: 0
        Page size (bytes): 4096
        Exit status: 141

I will keep investigating, but if anyone has an idea, please share!