Signal 11 error at the end of kat gcp command

[shannonekj]

I am running kat gcp using Snakemake on a cluster and have run into a problem upon what seems to be the completion of the kat gcp command.

I am running:

rule kat_rawRead_gcp:
    params:
        rep_dir = rep_dir,
        kmer = expand('{kmer}', kmer=KMER),
        start = rep_dir + 'kat_' + prefix + '_k{kmer}_katGCP_raw_reads'
    input:
        R1 = flt_dir + 'filtered_' + prefix + '_R1_001.fastq.gz',
        R2 = flt_dir + 'filtered_' + prefix + '_R2_001.fastq.gz'
    output:
        rep_dir + 'kat_' + prefix + '_k{kmer}_katGCP_raw_reads.mx',
        rep_dir + 'kat_' + prefix + '_k{kmer}_katGCP_raw_reads.mx.png',
        rep_dir + 'kat_' + prefix + '_k{kmer}_katGCP_raw_reads.dist_analysis.json'
    conda: 'envs/kat.yml'
    threads: workflow.cores * 1
    shell: '''
        kat gcp \
        -o {params.start} \
        -m {wildcards.kmer} \
        -t {threads} \
        {input.R1} {input.R2}
        echo Completed kat gcp for kmer size: {wildcards.kmer}
        '''

When I look at my stdout file it appears as if everything has run normally and a tail of the file produces:

(base) sejoslin@farm:assembly_genome_Hypomesus-transpacificus$ tail slurm/DS_assembly.j20349396.out
Creating plots
--------------

Plotting K-mer frequency distributions ... done.  Saved to: None
Plotting GC distributions ... done. Saved to: None

KAT GCP completed.
Total runtime: 5665.6s

It seems like the computation freezes at this step and when I look at the stderr file I see the following:

Activating conda environment: /home/sejoslin/git_repos/assembly_genome_Hypomesus-transpacificus/.snakemake/conda/d80d223b
Error: signal 11:
Stack trace:
kat(+0x7da9b)[0x565447502a9b]
/lib/x86_64-linux-gnu/libc.so.6(+0x3ef20)[0x150ac6a86f20]
/lib/x86_64-linux-gnu/libc.so.6(+0x945bd)[0x150ac6adc5bd]
/lib/x86_64-linux-gnu/libc.so.6(+0x958f5)[0x150ac6add8f5]
/lib/x86_64-linux-gnu/libc.so.6(realloc+0x36b)[0x150ac6ae0f9b]
/home/sejoslin/git_repos/assembly_genome_Hypomesus-transpacificus/.snakemake/conda/d80d223b/bin/../lib/libpython3.7m.so.1.0(PyList_Append+0xb1)[0x150ac7501681]
/home/sejoslin/git_repos/assembly_genome_Hypomesus-transpacificus/.snakemake/conda/d80d223b/bin/../lib/libpython3.7m.so.1.0(PyImport_Cleanup+0x63c)[0x150ac753f57c]
/home/sejoslin/git_repos/assembly_genome_Hypomesus-transpacificus/.snakemake/conda/d80d223b/bin/../lib/libpython3.7m.so.1.0(Py_FinalizeEx+0x83)[0x150ac75640e3]
kat(+0x31bed)[0x5654474b6bed]
/lib/x86_64-linux-gnu/libc.so.6(+0x43041)[0x150ac6a8b041]

I am using kat V2.4.2 installed through conda.

[shannonekj]

Could this be an issue with dependencies when installing from conda?

[cement-head]

Got same error (installed from conda/bioconda)

$ kat -hist 

(KAT does it's thing, and finishes, but barfs before it writes the output) 

Bining kmers ...Error: signal 11:
Stack trace:
kat(+0x87beb)[0x5606c183ebeb]
/lib/x86_64-linux-gnu/libc.so.6(+0x3ef20)[0x7f711be80f20]
kat(+0x72525)[0x5606c1829525]
kat(+0x712e4)[0x5606c18282e4]
kat(+0x14c54f)[0x5606c190354f]
/lib/x86_64-linux-gnu/libpthread.so.0(+0x76db)[0x7f711d0b86db]
/lib/x86_64-linux-gnu/libc.so.6(clone+0x3f)[0x7f711bf6388f]

[shannonekj]

@cement-head I installed an earlier version of kat (v2.4.1) and it didn't produce the error. Not sure what is up with v2.4.2.

Hope this helps!

[AlcaArctica]

Same problem here. Also with kat hist. I am using version 2.4.2.