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  • BWA weird thing

    HI guys

    I ran programs to generate .sam files, but find some weird things.
    432M ERR001275_1.recal.fastq.gz
    432M ERR001275_1.sai
    434M ERR001275_2.recal.fastq.gz
    437M ERR001275_2.sai
    8.0K ERR001275.sam

    421M ERR001276_1.recal.fastq.gz
    419M ERR001276_1.sai
    427M ERR001276_2.recal.fastq.gz
    423M ERR001276_2.sai
    4.4G ERR001276.sam

    compare 1275 and 1276, I suspect somehow .sam file generation for 1275 is crappy; is it because the .sam file itself is crappy, or anything wrong with the running?

    So I re-ran the program, but this time I use some easier command instead of copy-paste for many times, the script is like below:
    cd $HOME/scratch/bwa/

    job_number=$SGE_TASK_ID
    SAM_NAME=`head -"$job_number" master_list|tail -1`
    SAM_NAME_1=`head -"$job_number" master_list_1|tail -1`
    SAM_NAME_2=`head -"$job_number" master_list_2|tail -1`

    /share/bin/bwa sampe hg19_index "$SAM_NAME_1".sai "$SAM_NAME_2".sai "$SAM_NAME_1".recal.fastq.gz "$SAM_NAME_2".recal.fastq.gz > "$SAM_NAME".sam


    Is this script OK? But weird thing is, program output many core.* files of huge size......
    6.7G core.10401
    620K core.10480
    576K core.10779
    624K core.10791
    4.0G core.12127
    8.5G core.12139
    4.1G core.18199
    620K core.18221
    628K core.18227
    4.3G core.20054
    4.6G core.20066
    4.9G core.20078
    4.0G core.22390
    2.4G core.22402
    4.6G core.22482
    3.5G core.23568
    384M core.23580
    4.0G core.25848
    are these core files supposed to be .sam file?

    sorry to confuse you guys but I'm totally frustrated with this........

  • #2
    If you're getting core dumps, it means your program run is crashing, likely due to an invalid memory access causing a segmentation fault.

    Try analysing your core dumps with gdb if your system has it installed... this should provide a stack trace and give us a better idea of what is causing the error.

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