bam files conversion to fastq

Question: bam files conversion to fastq

3.6 years ago by

Portugal

anacrys7 • 0 wrote:

Hello,

I made the upload of a bam file from my computer into galaxy and I tried to convert it into a fastaq file using the Bam tools. However, the job status is "this job is waiting to run" for hours, though I've clicked on the refresh button for many times ... I can´t see any error report, but I don't think this is a regular situation. Is there any way I can solve this situation?

Thanks!

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modified 3.6 years ago by Jennifer Hillman Jackson ♦ 25k • written 3.6 years ago by anacrys7 • 0

3.6 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

A grey job indicates that a job is queued and waiting to run. Job states are described in our wiki here:
http://wiki.galaxyproject.org/Support#Dataset_status_and_how_jobs_execute

Jobs execute in the order submitted. Do you have other jobs queued/running? Is there room in your quota (check the bar over the History panel, or under "User->Preferences)? Is the input dataset OK (open it up and review)?

I just ran a BAM->SAM conversion queued for a few minutes, then ran, so the cluster itself is not overly busy right now. I checked your account and it looked like your last login was about 10 minutes before this question posted, so maybe the job was queued then? Or sometime before?

If this dataset loaded correctly, there are no other jobs queued, the account is under quota, and this particular job has been queued by itself for hours, then there is a problem. If it is still grey now, please let us know.

Best, Jen, Galaxy team

ADD COMMENT • link written 3.6 years ago by Jennifer Hillman Jackson ♦ 25k

Dear Jennifer, as a matter of fact when I opened the Galaxy page again, the job was done. It must have been stuck in the queue. But I have a couple of doubts about Fastq joiner, if may:

1) on the Fastq joiner instructions I see that the program will join the paired ends, but will exclude sequences that have lost their pair during quality check. Is there a way of keeping these lone sequences rather than ditching them? Other programs, like Fatsq Toolkit of Illumina Basespace, allow this...

2) the sequences joining scheme seems to simply concatenate /1 and /2 seqs as they are: shouldn't /2 seqs be reverted? shouldn't they be separated by an N in the middle in the final output?

Input formats Left-hand Read:

@HWI-EAS91_1_30788AAXX:7:21:1542:1758/1 GTCAATTGTACTGGTCAATACTAAAAGAATAGGATC +HWI-EAS91_1_30788AAXX:7:21:1542:1758/1 hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh

Right-hand Read:

@HWI-EAS91_1_30788AAXX:7:21:1542:1758/2 GCTCCTAGCATCTGGAGTCTCTATCACCTGAGCCCA +HWI-EAS91_1_30788AAXX:7:21:1542:1758/2 hhhhhhhhhhhhhhhhhhhhhhhh`hfhhVZSWehR

ADD REPLY • link written 3.6 years ago by anacrys7 • 0

Hi - I am glad the job completed. Would you mind posting these new issues as new questions? It is best to have one question per post. Thanks, Jen

ADD REPLY • link written 3.6 years ago by Jennifer Hillman Jackson ♦ 25k

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