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  • jylee
    replied
    Hi all,
    I am encountering same issue SIGNAL 9 (KILL). I wonder how you solved this issue.

    Anthony h,
    Could you describe more detail how you set -k <int> options?

    Leave a comment:


  • anthony_h
    replied
    Yes, it was running out of memory.

    Switched to using -k instead of -a and it completed.

    Leave a comment:


  • Richard Finney
    replied
    How much memory does you system have?

    System may kill processes if there is severe resource starvation; i.e. no memory available.

    Leave a comment:


  • ctseto
    replied
    What happens when you use --local --very-sensitive-local at the same time? I assume it picks one and keeps on going?

    Leave a comment:


  • davidblaney
    replied
    I was thinking a memory issue when I first read this. Have a look at the requirement on there website. Failing that drop them an email.

    Leave a comment:


  • anthony_h
    replied
    Also getting KILL

    I am also getting this when I turn on the -a option.

    Without -a my file of ~7M reads gets mapped against human genome hg19 successfully. With -a it bombs out even if I truncate to 200k reads. Maybe the process is using too much memory and the OS is killing it?

    Leave a comment:


  • GeneJockey
    started a topic Bowtie signal 9 (KILL) error

    Bowtie signal 9 (KILL) error

    I'm aligning a bunch of Illumina runs using Bowtie2 and I'm getting a frustrating error with only a few of the fastq files.

    I run them with the following command:

    bowtie2 -p 10 -x mm10_genome -1 SRR594396_1.fastq -2 SRR594396_2.fastq --local --very-sensitive-local --no-mixed --no-discordant | samtools view -uS - | samtools sort -m 10000000000 - SRR594393_genome

    Here are the outputs I get for a few fastq file pairs:

    SRR594399_genome
    [samopen] SAM header is present: 22 sequences.
    Parse error at line 111594048: missing colon in auxiliary data
    [bam_sort_core] merging from 2 files...

    SRR594400_genome
    [samopen] SAM header is present: 22 sequences.
    bowtie2-align died with signal 9 (KILL)
    [sam_read1] reference 'SRR59' is recognized as '*'.
    [main_samview] truncated file.
    [bam_sort_core] merging from 2 files...

    SRR594401_genome
    [samopen] SAM header is present: 22 sequences.
    Parse error at line 111266936: sequence and quality are inconsistent
    [bam_sort_core] merging from 2 files...

    SRR594396_genome
    [samopen] SAM header is present: 22 sequences.
    bowtie2-align died with signal 9 (KILL)
    Parse error at line 111938538: missing colon in auxiliary data
    [bam_sort_core] merging from 2 files...

    SRR594415_genome
    [samopen] SAM header is present: 22 sequences.
    bowtie2-align died with signal 9 (KILL)
    Parse error at line 112131890: missing colon in auxiliary data
    [bam_sort_core] merging from 2 files...

    SRR594417_genome
    [samopen] SAM header is present: 22 sequences.
    bowtie2-align died with signal 9 (KILL)
    Parse error at line 112044487: sequence and quality are inconsistent
    [bam_sort_core] merging from 2 files...

    I can't find anything about this KILL error and googling the parse errors isn't helping much. I think the parsing has something to do with bowtie failing and then the sam->bam operation subsequently failing on the last line.

    Can anyone help with this KILL business?

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