Not enough memory for BAM sorting #122
Comments
|
Hi,
I see the issue. Are you running this via docker or singularity, or do you
have it running natively?
best,
~b
…On Sat, Dec 10, 2022 at 5:37 AM taot2007 ***@***.***> wrote:
Hi, Brian, I am running the CTAT-mutations (v3.2.0) pipeline, the library
version is StarFv1.10. I used the commamd:
$ nohup time ~/src/CTAT-Mutations-v3.2.0/ctat_mutations --cpu 15
--genome_lib_dir
~/Share/CTAT_resource_lib/GRCh38_GENECODE_v38/build/ctat_genome_lib_build_dir/
--left ~/data/1609_R1_val_1.fq.gz
--right ~/data/1609_R2_val_2.fq.gz
--sample_id 1609
--output ~/data/CTATmutations/1609/ >
~/data/CTATmutations/ctat_mutations.nohup.out 2>&1 &
While most of the samples went well, a few samples showed the error
information as below:
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
EXITING because of fatal ERROR: not enough memory for BAM sorting:
SOLUTION: re-run STAR with at least --limitBAMsortRAM 35644206690
Dec 10 17:07:21 ...... FATAL ERROR, exiting
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
It looks very clear that the memory for BAM was set too low. Is there
anyway to get this solved? Thanks so much!
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The Broad Institute
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Hi Brian，
I ran it natively.
Thanks,
Ting
From: Brian Haas ***@***.***>
Sent: Saturday, December 10, 2022 10:15 PM
To: NCIP/ctat-mutations ***@***.***>
Cc: taot2007 ***@***.***>; Author ***@***.***>
Subject: Re: [NCIP/ctat-mutations] Not enough memory for BAM sorting (Issue #122)
Hi,
I see the issue. Are you running this via docker or singularity, or do you
have it running natively?
best,
~b
…On Sat, Dec 10, 2022 at 5:37 AM taot2007 ***@***.***<mailto:***@***.***>> wrote:
Hi, Brian, I am running the CTAT-mutations (v3.2.0) pipeline, the library
version is StarFv1.10. I used the commamd:
$ nohup time ~/src/CTAT-Mutations-v3.2.0/ctat_mutations --cpu 15
--genome_lib_dir
~/Share/CTAT_resource_lib/GRCh38_GENECODE_v38/build/ctat_genome_lib_build_dir/
--left ~/data/1609_R1_val_1.fq.gz
--right ~/data/1609_R2_val_2.fq.gz
--sample_id 1609
--output ~/data/CTATmutations/1609/ >
~/data/CTATmutations/ctat_mutations.nohup.out 2>&1 &
While most of the samples went well, a few samples showed the error
information as below:
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
EXITING because of fatal ERROR: not enough memory for BAM sorting:
SOLUTION: re-run STAR with at least --limitBAMsortRAM 35644206690
Dec 10 17:07:21 ...... FATAL ERROR, exiting
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
It looks very clear that the memory for BAM was set too low. Is there
anyway to get this solved? Thanks so much!
—
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<#122>, or unsubscribe
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ok - I updated the devel branch on github so it now includes the
parameter --star_limitBAMsortRAM, so you can set the value that STAR
recommends or something larger.
Would you be able to pull the devel branch and give it another go?
best,
~brian
…On Sat, Dec 10, 2022 at 9:34 AM taot2007 ***@***.***> wrote:
Hi Brian，
I ran it natively.
Thanks,
Ting
From: Brian Haas ***@***.***>
Sent: Saturday, December 10, 2022 10:15 PM
To: NCIP/ctat-mutations ***@***.***>
Cc: taot2007 ***@***.***>; Author ***@***.***>
Subject: Re: [NCIP/ctat-mutations] Not enough memory for BAM sorting
(Issue #122)
Hi,
I see the issue. Are you running this via docker or singularity, or do you
have it running natively?
best,
~b
On Sat, Dec 10, 2022 at 5:37 AM taot2007 ***@***.***<mailto:***@***.***>>
wrote:
> Hi, Brian, I am running the CTAT-mutations (v3.2.0) pipeline, the
library
> version is StarFv1.10. I used the commamd:
>
> $ nohup time ~/src/CTAT-Mutations-v3.2.0/ctat_mutations --cpu 15
> --genome_lib_dir
>
~/Share/CTAT_resource_lib/GRCh38_GENECODE_v38/build/ctat_genome_lib_build_dir/
> --left ~/data/1609_R1_val_1.fq.gz
> --right ~/data/1609_R2_val_2.fq.gz
> --sample_id 1609
> --output ~/data/CTATmutations/1609/ >
> ~/data/CTATmutations/ctat_mutations.nohup.out 2>&1 &
>
> While most of the samples went well, a few samples showed the error
> information as below:
>
> XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> EXITING because of fatal ERROR: not enough memory for BAM sorting:
> SOLUTION: re-run STAR with at least --limitBAMsortRAM 35644206690
> Dec 10 17:07:21 ...... FATAL ERROR, exiting
> XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
>
> It looks very clear that the memory for BAM was set too low. Is there
> anyway to get this solved? Thanks so much!
>
> —
> Reply to this email directly, view it on GitHub
> <#122>, or unsubscribe
> <
https://github.com/notifications/unsubscribe-auth/ABZRKXZCHCA2XY3D4OALYCLWMRMNZANCNFSM6AAAAAAS2GBEUY>
> .
> You are receiving this because you are subscribed to this thread.Message
> ID: ***@***.***<mailto:***@***.***>>
>
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--
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The Broad Institute
http://broadinstitute.org/~bhaas <http://broad.mit.edu/~bhaas>
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#122 (comment)>,
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It worked perfectly! Thanks so much!
|
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Thanks! Great to hear!
…On Sun, Dec 11, 2022 at 9:39 PM taot2007 ***@***.***> wrote:
It worked perfectly! Thanks so much!
ok - I updated the devel branch on github so it now includes the parameter
--star_limitBAMsortRAM, so you can set the value that STAR recommends or
something larger. Would you be able to pull the devel branch and give it
another go? best, ~brian
… <#m_-6267748613545710298_>
On Sat, Dec 10, 2022 at 9:34 AM taot2007 *@*.*> wrote: Hi Brian， I ran it
natively. Thanks, Ting From: Brian Haas @.*> Sent: Saturday, December 10,
2022 10:15 PM To: NCIP/ctat-mutations *@*.*> Cc: taot2007 @.*>; Author *@*
.*> Subject: Re: [NCIP/ctat-mutations] Not enough memory for BAM sorting
(Issue #122 <#122>) Hi, I see
the issue. Are you running this via docker or singularity, or do you have
it running natively? best, ~b On Sat, Dec 10, 2022 at 5:37 AM taot2007 @.*
mailto:***@***.*** <***@***.***>> wrote: > Hi, Brian, I am running the
CTAT-mutations (v3.2.0) pipeline, the library > version is StarFv1.10. I
used the commamd: > > $ nohup time
~/src/CTAT-Mutations-v3.2.0/ctat_mutations --cpu 15 > --genome_lib_dir >
~/Share/CTAT_resource_lib/GRCh38_GENECODE_v38/build/ctat_genome_lib_build_dir/
> --left ~/data/1609_R1_val_1.fq.gz > --right ~/data/1609_R2_val_2.fq.gz >
--sample_id 1609 > --output ~/data/CTATmutations/1609/ > >
~/data/CTATmutations/ctat_mutations.nohup.out 2>&1 & > > While most of the
samples went well, a few samples showed the error > information as below: >
> XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX >
EXITING because of fatal ERROR: not enough memory for BAM sorting: >
SOLUTION: re-run STAR with at least --limitBAMsortRAM 35644206690 > Dec 10
17:07:21 ...... FATAL ERROR, exiting >
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX > > It
looks very clear that the memory for BAM was set too low. Is there > anyway
to get this solved? Thanks so much! > > — > Reply to this email directly,
view it on GitHub > <#122
<#122>>, or unsubscribe > <
https://github.com/notifications/unsubscribe-auth/ABZRKXZCHCA2XY3D4OALYCLWMRMNZANCNFSM6AAAAAAS2GBEUY>
> . > You are receiving this because you are subscribed to this
thread.Message > ID: *@*.*mailto:***@***.*** <***@***.***>> > -- -- Brian
J. Haas The Broad Institute http://broadinstitute.org/~bhaas
<http://broadinstitute.org/~bhaas> http://broad.mit.edu/~bhaas
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GitHub< #122 (comment)
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Hi, Brian, I am running the CTAT-mutations (v3.2.0) pipeline, the library version is StarFv1.10. I used the commamd:
$ nohup time ~/src/CTAT-Mutations-v3.2.0/ctat_mutations --cpu 15
--genome_lib_dir ~/Share/CTAT_resource_lib/GRCh38_GENECODE_v38/build/ctat_genome_lib_build_dir/
--left ~/data/1609_R1_val_1.fq.gz
--right ~/data/1609_R2_val_2.fq.gz
--sample_id 1609
--output ~/data/CTATmutations/1609/ > ~/data/CTATmutations/ctat_mutations.nohup.out 2>&1 &
While most of the samples went well, a few samples showed the error information as below:
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
EXITING because of fatal ERROR: not enough memory for BAM sorting:
SOLUTION: re-run STAR with at least --limitBAMsortRAM 35644206690
Dec 10 17:07:21 ...... FATAL ERROR, exiting
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
It looks very clear that the memory for BAM was set too low. Is there anyway to get this solved? Thanks so much!
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