BWA weird thing

CNVboy · 06-16-2011, 07:33 PM

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........

dp05yk · 06-16-2011, 08:34 PM

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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06-16-2011, 07:33 PM	#1
CNVboy Member Location: boston Join Date: Jun 2011 Posts: 27	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........

06-16-2011, 08:34 PM	#2
dp05yk Member Location: Brock University Join Date: Dec 2010 Posts: 66	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.