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pavelasquezv
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bdolin
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Joseph Hughes
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Pierre Lindenbaum
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Recent Replies
Comment: The STAR program does not work after the mapping
by
Pierre Lindenbaum
146k
but do you __use__ the cluster using qsub or sbatch ?
Comment: The STAR program does not work after the mapping
by
pavelasquezv
▴
20
I already got to see. I have only 3.2 Gb. I think that's really the problem. I'll talk to the manager. Thank you all very much for your col…
Comment: [main_samview] fail to read the header from sample.bam
by
Qboy
•
0
Hey, I have one question.
What does an empty flag mean after probes.bam
Thank you!
Comment: Getting sequence information by using atoms
by
Pierre Lindenbaum
146k
awk '($1=="ATOM") {print $6}' < in.cif | paste -s -d '-'
??
Comment: The STAR program does not work after the mapping
by
pavelasquezv
▴
20
I am sorry. I am working on a cluster of the University. But I do not have I don't have administrator permissions to increase my memory
Comment: The STAR program does not work after the mapping
by
pavelasquezv
▴
20
Yes Pierre, i am working on a cluster of the University. Pero no tengo permisos para aumentar mi memoria :(
Comment: The STAR program does not work after the mapping
by
pavelasquezv
▴
20
Yes, I think you are right because I ran the same code on my pc that has 32 ram and it was perfect. Yes, I am working with --runMode genome…
Comment: 0% adapter bases after demultiplexing 10x data and "undetermined" sample
by
GenoMax
117k
Read 1 should contain `cellbarcodes + UMI`. In addition your samples are indexed by using standard Illumina indeses. You can see those inde…
Comment: The STAR program does not work after the mapping
by
Pierre Lindenbaum
146k
are you working on a cluster ? if yes, do you _use_ it ?
Comment: The STAR program does not work after the mapping
by
GenoMax
117k
My suggestion still stands. How much memory do you have available? If you don't have enough RAM and the job keeps getting killed because of…
Comment: The STAR program does not work after the mapping
by
pavelasquezv
▴
20
pelase! many thanks for your reply and tips!
Comment: The STAR program does not work after the mapping
by
pavelasquezv
▴
20
I tried with 4, 6, 8, 10, 12, 30, 50 cores but it still gives the same error. Do you have any other suggestions?
Comment: The STAR program does not work after the mapping
by
GenoMax
117k
> The program finished without any error.
Nope. So the program fails within a couple of minutes. How much RAM are you allocating for this…
Comment: How to subset a GVCF using GATK SelectVariants
by
ttom
▴
210
Yes, the wrong file extension was the problem. It works with `subset_samples.args`
Thank you !!
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