Question: mmquant run failure
0
gravatar for caranlove
4 weeks ago by
caranlove0
caranlove0 wrote:

I am attempting to run mmquant and it keeps being killed after reading in the .gtf files. The script I am running is pasted below and the samples are all coordinate sorted bam files. Any ideas on why?

mmquant -a Reference.gtf -r 1.bam 2.bam 3.bam 4.bam 5.bam 6.bam 7.bam 8.bam 9.bam 10.bam 18.bam 19.bam -s FR -f BAM -t 13 -o GW_mmquant

An additional note: I have also added memory, allowing for 50gb and this did not seem to remedy the issue. Thanks!

mmquant rna-seq • 143 views
ADD COMMENTlink modified 4 weeks ago by h.mon27k • written 4 weeks ago by caranlove0

Can you post the error message, if there is one? Did you validate the GTF is correctly formatted, what is the available memory, what does the tool expect towards memory? Please add some details.

ADD REPLYlink written 4 weeks ago by ATpoint23k

Thank you for the response! The gtf file has been validated in other programs and appears to load in fine here. I allotted 4 cores and 20gb for the run as well as called -t13 as the program suggests. I am now getting the program to read in the gtf file and the bam files with:

mmquant -a reference.gtf -s FR -f BAM -r G1_cordsorted.bam G2_cordsorted.bam G3_cordsorted.bam G4_cordsorted.bam G5_cordsorted.bam G6_cordsorted.bam G7_cordsorted.bam G110_cordsorted.bam G111_cordsorted.bam G117_cordsorted.bam G118_cordsorted.bam G119_cordsorted.bam -t 13 -o G_mmquant

But it still fails before completion. The exact error message is:

Annotation file: reference.gtf
Read(s) file: G1_cordsorted.bam G2_cordsorted.bam G3_cordsorted.bam G4_cordsorted.bam G5_cordsorted.bam G6_cordsorted.bam G7_cordsorted.bam G110_cordsorted.bam G111_cordsorted.bam G117_cordsorted.bam G118_cordsorted.bam G119_cordsorted.bam
Sample names: G1_cordsorted G2_cordsorted G3_cordsorted G4_cordsorted G5_cordsorted G6_cordsorted G7_cordsorted G110_cordsorted G111_cordsorted G117_cordsorted G118_cordsorted G119_cordsorted
Output file: G_mmquant (0x11b5e10)
Stats file:  (0x11b62e0)
Overlap: -1
Overlap function: 1
Reading GTF file
    1,792,115 lines read, done.  36,945 genes found.
Reading BAM file G2_cordsorted.bam
Reading BAM file G4_cordsorted.bam
Reading BAM file G6_cordsorted.bam
Reading BAM file G5_cordsorted.bam
Reading BAM file G3_cordsorted.bam
Reading BAM file G1_cordsorted.bam
Reading BAM file G7_cordsorted.bam
Reading BAM file G110_cordsorted.bam
Reading BAM file G111_cordsorted.bam
Reading BAM file G118_cordsorted.bam
Reading BAM file G117_cordsorted.bam
Reading BAM file G119_cordsorted.bam
/var/spool/torque/mom_priv/jobs/1505550.sapelo2.SC: line 12: 27935 Killed                  mmquant -a reference.gtf -s FR -f BAM -r G1_cordsorted.bam G2_cordsorted.bam G3_cordsorted.bam G4_cordsorted.bam G5_cordsorted.bam G6_cordsorted.bam G7_cordsorted.bam G110_cordsorted.bam G111_cordsorted.bam G117_cordsorted.bam G118_cordsorted.bam G119_cordsorted.bam -t 13 -o G_mmquant
ADD REPLYlink modified 4 weeks ago by h.mon27k • written 4 weeks ago by caranlove0

Are you running out of a resource (e.g. clock time, memory)? If you are using a job scheduler can you check scheduler log files for the job?

ADD REPLYlink written 4 weeks ago by genomax71k

Thank you for the suggestion! But the job run says I am using less than 1gb and only 3-7min of the 24 hrs allotted.

ADD REPLYlink written 4 weeks ago by caranlove0

That is fine. But what else is there in the job log? Is there any indication why the job is getting killed?

ADD REPLYlink written 4 weeks ago by genomax71k
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