No such file or directory at /usr/local/src/STAR-Fusion/PerlLib/Pipeliner.pm line 181

[mapostolides]

The Docker container tutorial isn't working for me. I successfully ran:

docker run --rm -it -v pwd :/data trinityctat/ctatfusion:latest bash

Once the container was pulled, I successfully ran...

${STAR_FUSION_HOME}/FusionFilter/prep_genome_lib.pl \ --genome_fa minigenome.fa \ --gtf minigenome.gtf \ --fusion_annot_lib CTAT_HumanFusionLib.mini.dat.gz

...with no errors. However, when running the following command...

${STAR_FUSION_HOME}/STAR-Fusion \ --left_fq rnaseq_1.fastq.gz \ --right_fq rnaseq_2.fastq.gz \ --genome_lib_dir ctat_genome_lib_build_dir

...I ran into an error which I'm not sure how to resolve.

root@50aaf3eb3bd1:/data# ${STAR_FUSION_HOME}/STAR-Fusion --left_fq rnaseq_1.fastq.gz --right_fq rnaseq_2.fastq.gz --genome_lib_dir ctat_genome_lib_build_dir 
${STAR_FUSION_HOME}/STAR-Fusion --left_fq rnaseq_1.fastq.gz --right_fq rnaseq_2.fastq.gz --genome_lib_dir ctat_genome_lib_build_dir 
* Running CMD: /usr/local/bin/STAR --genomeDir /data/ctat_genome_lib_build_dir/ref_genome.fa.star.idx  --outReadsUnmapped None  --chimSegmentMin 12  --chimJunctionOverhangMin 12  --chimOutJunctionFormat 1  --alignSJDBoverhangMin 10  --alignMatesGapMax 100000  --alignIntronMax 100000  --alignSJstitchMismatchNmax 5 -1 5 5  --runThreadN 4 --outSAMstrandField intronMotif  --outSAMunmapped Within  --outSAMtype BAM Unsorted  --readFilesIn /data/rnaseq_1.fastq.gz /data/rnaseq_2.fastq.gz  --outSAMattrRGline ID:GRPundef  --chimMultimapScoreRange 10 --chimMultimapNmax 10 --chimNonchimScoreDropMin 10  --peOverlapNbasesMin 12 --peOverlapMMp 0.1  --genomeLoad NoSharedMemory  --twopassMode Basic  --readFilesCommand 'gunzip -c' 
Nov 23 20:37:50 ..... started STAR run
Nov 23 20:37:50 ..... loading genome
Nov 23 20:37:59 ..... started 1st pass mapping
Nov 23 20:40:06 ..... finished 1st pass mapping
Nov 23 20:40:06 ..... inserting junctions into the genome indices
Killed
Error, cmd: /usr/local/bin/STAR --genomeDir /data/ctat_genome_lib_build_dir/ref_genome.fa.star.idx  --outReadsUnmapped None  --chimSegmentMin 12  --chimJunctionOverhangMin 12  --chimOutJunctionFormat 1  --alignSJDBoverhangMin 10  --alignMatesGapMax 100000  --alignIntronMax 100000  --alignSJstitchMismatchNmax 5 -1 5 5  --runThreadN 4 --outSAMstrandField intronMotif  --outSAMunmapped Within  --outSAMtype BAM Unsorted  --readFilesIn /data/rnaseq_1.fastq.gz /data/rnaseq_2.fastq.gz  --outSAMattrRGline ID:GRPundef  --chimMultimapScoreRange 10 --chimMultimapNmax 10 --chimNonchimScoreDropMin 10  --peOverlapNbasesMin 12 --peOverlapMMp 0.1  --genomeLoad NoSharedMemory  --twopassMode Basic  --readFilesCommand 'gunzip -c'  died with ret 35072 No such file or directory at /usr/local/src/STAR-Fusion/PerlLib/Pipeliner.pm line 181.
	Pipeliner::run(Pipeliner=HASH(0x1572cd0)) called at /usr/local/src/STAR-Fusion/STAR-Fusion line 862
	main::run_STAR(Pipeliner=HASH(0x1572cd0), "/data/rnaseq_1.fastq.gz", "/data/rnaseq_2.fastq.gz", "") called at /usr/local/src/STAR-Fusion/STAR-Fusion line 509

I went to the file /usr/local/src/STAR-Fusion/PerlLib/Pipeliner.pm inside the Docker container, and that exact file was, in fact, there. I'm not sure exactly what the reason for the above error might be, since I followed the instructions exactly.

Any help would be much appreciated!

Thanks,
Michael

[brianjohnhaas]

Hi, It probably ran out of memory. STAR can require a lot of RAM (40G) for running on the human genome.

…

On Fri, Nov 23, 2018 at 3:45 PM mapostolides ***@***.***> wrote: The Docker container tutorial isn't working for me. I successfully ran: docker run --rm -it -v pwd:/data trinityctat/ctatfusion:latest bash Once the container was pulled, I successfully ran... ${STAR_FUSION_HOME}/FusionFilter/prep_genome_lib.pl \ --genome_fa minigenome.fa \ --gtf minigenome.gtf \ --fusion_annot_lib CTAT_HumanFusionLib.mini.dat.gz ...with no errors. However, when running the following command... ${STAR_FUSION_HOME}/STAR-Fusion \ --left_fq rnaseq_1.fastq.gz \ --right_fq rnaseq_2.fastq.gz \ --genome_lib_dir ctat_genome_lib_build_dir ...I ran into an error which I'm not sure how to resolve. ***@***.***:/data# ${STAR_FUSION_HOME}/STAR-Fusion --left_fq rnaseq_1.fastq.gz --right_fq rnaseq_2.fastq.gz --genome_lib_dir ctat_genome_lib_build_dir ${STAR_FUSION_HOME}/STAR-Fusion --left_fq rnaseq_1.fastq.gz --right_fq rnaseq_2.fastq.gz --genome_lib_dir ctat_genome_lib_build_dir - Running CMD: /usr/local/bin/STAR --genomeDir /data/ctat_genome_lib_build_dir/ref_genome.fa.star.idx --outReadsUnmapped None --chimSegmentMin 12 --chimJunctionOverhangMin 12 --chimOutJunctionFormat 1 --alignSJDBoverhangMin 10 --alignMatesGapMax 100000 --alignIntronMax 100000 --alignSJstitchMismatchNmax 5 -1 5 5 --runThreadN 4 --outSAMstrandField intronMotif --outSAMunmapped Within --outSAMtype BAM Unsorted --readFilesIn /data/rnaseq_1.fastq.gz /data/rnaseq_2.fastq.gz --outSAMattrRGline ID:GRPundef --chimMultimapScoreRange 10 --chimMultimapNmax 10 --chimNonchimScoreDropMin 10 --peOverlapNbasesMin 12 --peOverlapMMp 0.1 --genomeLoad NoSharedMemory --twopassMode Basic --readFilesCommand 'gunzip -c' Nov 23 20:37:50 ..... started STAR run Nov 23 20:37:50 ..... loading genome Nov 23 20:37:59 ..... started 1st pass mapping Nov 23 20:40:06 ..... finished 1st pass mapping Nov 23 20:40:06 ..... inserting junctions into the genome indices Killed Error, cmd: /usr/local/bin/STAR --genomeDir /data/ctat_genome_lib_build_dir/ref_genome.fa.star.idx --outReadsUnmapped None --chimSegmentMin 12 --chimJunctionOverhangMin 12 --chimOutJunctionFormat 1 --alignSJDBoverhangMin 10 --alignMatesGapMax 100000 --alignIntronMax 100000 --alignSJstitchMismatchNmax 5 -1 5 5 --runThreadN 4 --outSAMstrandField intronMotif --outSAMunmapped Within --outSAMtype BAM Unsorted --readFilesIn /data/rnaseq_1.fastq.gz /data/rnaseq_2.fastq.gz --outSAMattrRGline ID:GRPundef --chimMultimapScoreRange 10 --chimMultimapNmax 10 --chimNonchimScoreDropMin 10 --peOverlapNbasesMin 12 --peOverlapMMp 0.1 --genomeLoad NoSharedMemory --twopassMode Basic --readFilesCommand 'gunzip -c' died with ret 35072 No such file or directory at /usr/local/src/STAR-Fusion/PerlLib/Pipeliner.pm line 181. Pipeliner::run(Pipeliner=HASH(0x1572cd0)) called at /usr/local/src/STAR-Fusion/STAR-Fusion line 862 main::run_STAR(Pipeliner=HASH(0x1572cd0), "/data/rnaseq_1.fastq.gz", "/data/rnaseq_2.fastq.gz", "") called at /usr/local/src/STAR-Fusion/STAR-Fusion line 509` I went to the directory /usr/local/src/STAR-Fusion/PerlLib/Pipeliner.pm inside the Docker container, and that exact file was, in fact, there. I'm not sure exactly what the reason for the above error might be, since I followed the instructions exactly. Any help would be much appreciated! Thanks, Michael — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#3>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AHMVX3Ta4OCv3g9B6YRXJO-1dD6UuITVks5uyF6FgaJpZM4YxG5m> .

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

[mapostolides]

Hi Brian, thanks for your reply!

Are you sure that's the reason? I am using the exact files provided in the tutorial, and it states in the tutorial that 4G of RAM should be sufficient for the specific files provided inside the Docker container. The computer I am using has 8G of RAM, which is more than enough according to the tutorial. Is it possible that there is some other issue with the Docker container? This tutorial seems really useful, and it would be great if I could use your tools!

Thanks,
Michael

[brianjohnhaas]

right, for the tutorial it shouldn't require much RAM. Are you using the ctat genome lib that goes with the tutorial, or are you using the larger one that's used in regular star-fusion runs? The tutorial has a tiny genome lib and shouldn't require much ram.

…

On Sat, Nov 24, 2018 at 11:45 AM mapostolides ***@***.***> wrote: Hi Brian, thanks for your reply! Are you sure that's the reason? I am using the exact files provided in the tutorial, and it states in the tutorial that 4G of RAM should be sufficient for the specific files provided inside the Docker container. The computer I am using has 8G of RAM, which is more than enough according to the tutorial. Is it possible that there is some other issue with the Docker container? This tutorial seems really useful, and it would be great if I could use your tools! Thanks, Michael — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#3 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AHMVX-cS8dg854j-ENf20wbyLuNbC0n1ks5uyXelgaJpZM4YxG5m> .

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

[brianjohnhaas]

Also, the limitation is that the ctat genome lib that goes with the tutorial is only useful for that tutorial, and not for general use.

…

On Sat, Nov 24, 2018 at 1:13 PM Brian Haas ***@***.***> wrote: right, for the tutorial it shouldn't require much RAM. Are you using the ctat genome lib that goes with the tutorial, or are you using the larger one that's used in regular star-fusion runs? The tutorial has a tiny genome lib and shouldn't require much ram. On Sat, Nov 24, 2018 at 11:45 AM mapostolides ***@***.***> wrote: > Hi Brian, thanks for your reply! > > Are you sure that's the reason? I am using the exact files provided in > the tutorial, and it states in the tutorial that 4G of RAM should be > sufficient for the specific files provided inside the Docker container. The > computer I am using has 8G of RAM, which is more than enough according to > the tutorial. Is it possible that there is some other issue with the Docker > container? This tutorial seems really useful, and it would be great if I > could use your tools! > > Thanks, > Michael > > — > You are receiving this because you commented. > Reply to this email directly, view it on GitHub > <#3 (comment)>, > or mute the thread > <https://github.com/notifications/unsubscribe-auth/AHMVX-cS8dg854j-ENf20wbyLuNbC0n1ks5uyXelgaJpZM4YxG5m> > . > -- -- Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas <http://broad.mit.edu/~bhaas>

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

[mapostolides]

I'm using the one that comes inside the Docker container. I'm pretty sure that's the ctat genome library that goes with the tutorial. Thanks!

…

On Sat, Nov 24, 2018 at 1:14 PM Brian Haas ***@***.***> wrote: Also, the limitation is that the ctat genome lib that goes with the tutorial is only useful for that tutorial, and not for general use. On Sat, Nov 24, 2018 at 1:13 PM Brian Haas ***@***.***> wrote: > right, for the tutorial it shouldn't require much RAM. Are you using the > ctat genome lib that goes with the tutorial, or are you using the larger > one that's used in regular star-fusion runs? The tutorial has a tiny > genome lib and shouldn't require much ram. > > On Sat, Nov 24, 2018 at 11:45 AM mapostolides ***@***.***> > wrote: > >> Hi Brian, thanks for your reply! >> >> Are you sure that's the reason? I am using the exact files provided in >> the tutorial, and it states in the tutorial that 4G of RAM should be >> sufficient for the specific files provided inside the Docker container. The >> computer I am using has 8G of RAM, which is more than enough according to >> the tutorial. Is it possible that there is some other issue with the Docker >> container? This tutorial seems really useful, and it would be great if I >> could use your tools! >> >> Thanks, >> Michael >> >> — >> You are receiving this because you commented. >> Reply to this email directly, view it on GitHub >> < #3 (comment) >, >> or mute the thread >> < https://github.com/notifications/unsubscribe-auth/AHMVX-cS8dg854j-ENf20wbyLuNbC0n1ks5uyXelgaJpZM4YxG5m > >> . >> > > > -- > -- > Brian J. Haas > The Broad Institute > http://broadinstitute.org/~bhaas <http://broad.mit.edu/~bhaas> > > > -- -- Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas <http://broad.mit.edu/~bhaas> — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#3 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AmmOfqitJ5wBOc9yT5RG-UDGsAkawUM_ks5uyYx8gaJpZM4YxG5m> .

[brianjohnhaas]

sorry about that. We've used it before for workshops and it hasn't required much ram. Not sure why it's causing trouble here. If you can try it on a larger machine, let's see if it works there. On Mon, Nov 26, 2018 at 11:02 AM mapostolides <notifications@github.com> wrote:

…

I'm using the one that comes inside the Docker container. I'm pretty sure that's the ctat genome library that goes with the tutorial. Thanks! On Sat, Nov 24, 2018 at 1:14 PM Brian Haas ***@***.***> wrote: > Also, the limitation is that the ctat genome lib that goes with the > tutorial is only useful for that tutorial, and not for general use. > > On Sat, Nov 24, 2018 at 1:13 PM Brian Haas ***@***.***> > wrote: > > > right, for the tutorial it shouldn't require much RAM. Are you using the > > ctat genome lib that goes with the tutorial, or are you using the larger > > one that's used in regular star-fusion runs? The tutorial has a tiny > > genome lib and shouldn't require much ram. > > > > On Sat, Nov 24, 2018 at 11:45 AM mapostolides < ***@***.***> > > wrote: > > > >> Hi Brian, thanks for your reply! > >> > >> Are you sure that's the reason? I am using the exact files provided in > >> the tutorial, and it states in the tutorial that 4G of RAM should be > >> sufficient for the specific files provided inside the Docker container. > The > >> computer I am using has 8G of RAM, which is more than enough according > to > >> the tutorial. Is it possible that there is some other issue with the > Docker > >> container? This tutorial seems really useful, and it would be great if I > >> could use your tools! > >> > >> Thanks, > >> Michael > >> > >> — > >> You are receiving this because you commented. > >> Reply to this email directly, view it on GitHub > >> < > #3 (comment) > >, > >> or mute the thread > >> < > https://github.com/notifications/unsubscribe-auth/AHMVX-cS8dg854j-ENf20wbyLuNbC0n1ks5uyXelgaJpZM4YxG5m > > > >> . > >> > > > > > > -- > > -- > > Brian J. Haas > > The Broad Institute > > http://broadinstitute.org/~bhaas <http://broad.mit.edu/~bhaas> > > > > > > > > > -- > -- > Brian J. Haas > The Broad Institute > http://broadinstitute.org/~bhaas <http://broad.mit.edu/~bhaas> > > — > You are receiving this because you authored the thread. > Reply to this email directly, view it on GitHub > < #3 (comment) >, > or mute the thread > < https://github.com/notifications/unsubscribe-auth/AmmOfqitJ5wBOc9yT5RG-UDGsAkawUM_ks5uyYx8gaJpZM4YxG5m > > . > — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#3 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AHMVX1BgqP0vukQuOom2Y5kUMsSPpLj7ks5uzBCqgaJpZM4YxG5m> .

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

[ruizgo]

Great, it solved my problem.

[Daemon-ser]

Great, it solved my problem.

Same problem here, how do you solve it ?

[mapostolides]

It was a while ago that I did this, but I know that Docker containers are launched by default with 2G of RAM.
Could it be because Docker needs to give more memory to containers?

[Daemon-ser]

It was a while ago that I did this, but I know that Docker containers are launched by default with 2G of RAM.
Could it be because Docker needs to give more memory to containers?

Thanks a lot.