Question: BWA for Illumina
gravatar for thaisenayane
13 months ago by
thaisenayane10 wrote:

Hello, I'm starting to use Galaxy, and I'm trying to generate vcf and BAM files from my Fastq (paired end). I'm trying to align with BWA, I used BWA for Illumina to map the fastq files of one patient, I chose the hg19 canonical as reference, and trimmed both fastq files (FastQ trimmer by column) before the alignment. However the alignment never stop running, I waited 2 days in the weekend and after this I deleted. On Monday I started to running with my Lab's internet (which is faster then mine, but still a little slow), the alignment is still running for more the 24 hours... Is it normal to take all this time? I'm using my notebook (Dell, 4GB, i3). I already tried to refresh the history, but the status never change.

I appreciate the help,


alignment exome wes humam bwa • 474 views
ADD COMMENTlink modified 13 months ago by Jennifer Hillman Jackson25k • written 13 months ago by thaisenayane10
gravatar for Jennifer Hillman Jackson
13 months ago by
United States
Jennifer Hillman Jackson25k wrote:


I am assuming that by "running" you mean the job is in the yellow executing state, not the gray queued state. Please clarify if that is not the case. Jobs can sometimes queue for up to 24 hrs and execute for 48 hrs at Galaxy Main and even then sometimes exceed resources (memory or the walltime - aka runtime).

Long-running jobs can be often linked to inputs (size/format/quality), tool settings, and how many other jobs you have queued/executing. Check the content and format of the input fastq data. Also, check that all inputs are based on the same reference genome (example: reference genome and reference annotation - when both are used - must be a match for the build and chromosome identifier format).

Finally, we strongly suggest that you use the updated BWA or BWA-MEM tool. BWA for Illumina is an earlier version and consider deprecated. Give one of these others a try for comparison. If you do this at, you'll be able to contact us and ask for feedback about the "check" items above. Comment back to this post. Be sure to save all inputs and intermediate jobs undeleted. Deleting jobs while queued or executing, then restarting (without changes), will not get a job to run "quicker" - it just puts it back at the end of the queue.

Thanks! Jen, Galaxy team

ADD COMMENTlink written 13 months ago by Jennifer Hillman Jackson25k

Thank you, I'll try BWA or BWA-MEM.

ADD REPLYlink written 13 months ago by thaisenayane10
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