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TrinityCTAT / ctat-mutations

Mutation detection using GATK4 best practices and latest RNA editing filters resources. Works with both Hg38 and Hg19
https://github.com/TrinityCTAT/ctat-mutations
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Not enough memory for BAM sorting #122

Open taot2007 opened 1 year ago

taot2007 commented 1 year ago

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!

brianjohnhaas commented 1 year ago

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!

— Reply to this email directly, view it on GitHub https://github.com/NCIP/ctat-mutations/issues/122, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABZRKXZCHCA2XY3D4OALYCLWMRMNZANCNFSM6AAAAAAS2GBEUY . You are receiving this because you are subscribed to this thread.Message ID: @.***>

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Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas http://broad.mit.edu/~bhaas

taot2007 commented 1 year ago

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 https://github.com/NCIP/ctat-mutations/issues/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://broad.mit.edu/~bhaas

— Reply to this email directly, view it on GitHubhttps://github.com/NCIP/ctat-mutations/issues/122#issuecomment-1345273924, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AI7FCPDHBD6OYDXG4PX2TLDWMSF65ANCNFSM6AAAAAAS2GBEUY. You are receiving this because you authored the thread.Message ID: @.**@.>>

brianjohnhaas commented 1 year ago

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 https://github.com/NCIP/ctat-mutations/issues/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://broad.mit.edu/~bhaas

— Reply to this email directly, view it on GitHub< https://github.com/NCIP/ctat-mutations/issues/122#issuecomment-1345273924>, or unsubscribe< https://github.com/notifications/unsubscribe-auth/AI7FCPDHBD6OYDXG4PX2TLDWMSF65ANCNFSM6AAAAAAS2GBEUY>.

You are receiving this because you authored the thread.Message ID: @.**@.>>

— Reply to this email directly, view it on GitHub https://github.com/NCIP/ctat-mutations/issues/122#issuecomment-1345277713, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABZRKX5RP3NW3IBIBJ6XPX3WMSIIFANCNFSM6AAAAAAS2GBEUY . You are receiving this because you commented.Message ID: @.***>

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Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas http://broad.mit.edu/~bhaas

taot2007 commented 1 year ago

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 … 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:@.>> > -- -- Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas http://broad.mit.edu/~bhaas — Reply to this email directly, view it on GitHub< #122 (comment)>, or unsubscribe< https://github.com/notifications/unsubscribe-auth/AI7FCPDHBD6OYDXG4PX2TLDWMSF65ANCNFSM6AAAAAAS2GBEUY>. You are receiving this because you authored the thread.Message ID: @.**@.>> — Reply to this email directly, view it on GitHub <#122 (comment)>, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABZRKX5RP3NW3IBIBJ6XPX3WMSIIFANCNFSM6AAAAAAS2GBEUY . You are receiving this because you commented.Message ID: @.***> -- -- Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas http://broad.mit.edu/~bhaas

brianjohnhaas commented 1 year ago

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 --starlimitBAMsortRAM, 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 https://github.com/NCIP/ctat-mutations/issues/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 https://github.com/NCIP/ctat-mutations/issues/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 http://broad.mit.edu/~bhaas — Reply to this email directly, view it on GitHub< #122 (comment) https://github.com/NCIP/ctat-mutations/issues/122#issuecomment-1345273924>, or unsubscribe< https://github.com/notifications/unsubscribe-auth/AI7FCPDHBD6OYDXG4PX2TLDWMSF65ANCNFSM6AAAAAAS2GBEUY> https://github.com/notifications/unsubscribe-auth/AI7FCPDHBD6OYDXG4PX2TLDWMSF65ANCNFSM6AAAAAAS2GBEUY%3E. You are receiving this because you authored the thread.Message ID: @.*@.>> — Reply to this email directly, view it on GitHub <#122 (comment) https://github.com/NCIP/ctat-mutations/issues/122#issuecomment-1345277713>, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABZRKX5RP3NW3IBIBJ6XPX3WMSIIFANCNFSM6AAAAAAS2GBEUY https://github.com/notifications/unsubscribe-auth/ABZRKX5RP3NW3IBIBJ6XPX3WMSIIFANCNFSM6AAAAAAS2GBEUY . You are receiving this because you commented.Message ID: @.> -- -- Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas http://broad.mit.edu/~bhaas

— Reply to this email directly, view it on GitHub https://github.com/NCIP/ctat-mutations/issues/122#issuecomment-1345784781, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABZRKX4CAXIXHCR43PBI6QDWM2F7XANCNFSM6AAAAAAS2GBEUY . You are receiving this because you commented.Message ID: @.***>

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Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas http://broad.mit.edu/~bhaas