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STAR-Fusion / STAR-Fusion-Tutorial

Tutorial for STAR-Fusion, FusionInspector, and de novo reconstruction of fusion transcripts using Trinity
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Error, cannot locate genome_lib_dir: /data/GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play.tar.gz at /usr/local/src/STAR-Fusion/STAR-Fusion line 508. #8

Open jdjdj0202 opened 11 months ago

jdjdj0202 commented 11 months ago

Hi, I tried to run STAR-Fusion using docker. I entered command lines as below on Mac terminal. Fastqfiles and GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play.tar.gz file are in the same directory. I don't know why this error happens.

docker run -v pwd:/data --rm --platform linux/amd64 trinityctat/starfusion \ STAR-Fusion \ --left_fq /data/ATL005_R1_fastq.gz \ --right_fq /data/ATL005_R2_fastq.gz \ --genome_lib_dir /data/GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play.tar.gz \ -O /data/StarFusionOut \ --FusionInspector validate \ --examine_coding_effect \ --denovo_reconstruct

Error, cannot locate genome_lib_dir: /data/GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play.tar.gz at /usr/local/src/STAR-Fusion/STAR-Fusion line 508.

Please help me. Thanks!!!!!

brianjohnhaas commented 11 months ago

Hi,

You'll need to first untar the

GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play.tar.gz

and then reference the base ctat genome lib directory via the --genome_lib_dir parameter.

best,

~b

On Thu, Oct 12, 2023 at 11:55 PM jdjdj0202 @.***> wrote:

Hi, I tried to run STAR-Fusion using docker. I entered command lines as below on Mac terminal. Fastqfiles and GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play.tar.gz file are in the same directory. I don't know why this error happens.

docker run -v pwd:/data --rm --platform linux/amd64 trinityctat/starfusion STAR-Fusion --left_fq /data/ATL005_R1_fastq.gz --right_fq /data/ATL005_R2_fastq.gz --genome_lib_dir /data/GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play.tar.gz -O /data/StarFusionOut --FusionInspector validate --examine_coding_effect --denovo_reconstruct

Error, cannot locate genome_lib_dir: /data/GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play.tar.gz at /usr/local/src/STAR-Fusion/STAR-Fusion line 508.

Please help me. Thanks!!!!!

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you are subscribed to this thread.Message ID: @.***>

--

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

jdjdj0202 commented 11 months ago

THanks. I unzipped the tar.gz file and tried again. However, the same error occurs. The file is located in 'data' directory which is the same as left_fq and right_fq files.

trial 1

docker run -v pwd:/data --rm --platform linux/amd64 trinityctat/starfusion \ STAR-Fusion \ --left_fq /data/ATL005_R1_fastq.gz \ --right_fq /data/ATL005_R2_fastq.gz \ --genome_lib_dir /data/GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play \ -O /data/StarFusionOut \ --FusionInspector validate \ --examine_coding_effect \ --denovo_reconstruct

--> ERROR Error, cannot locate genome_lib_dir: /data/GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play at /usr/local/src/STAR-Fusion/STAR-Fusion line 508.

trial 2

docker run -v pwd:/data --rm --platform linux/amd64 trinityctat/starfusion \ STAR-Fusion \ --left_fq /data/ATL005_R1_fastq.gz \ --right_fq /data/ATL005_R2_fastq.gz \ --genome_lib_dir /data/GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir \ -O /data/StarFusionOut \ --FusionInspector validate \ --examine_coding_effect \ --denovo_reconstruct

--> ERROR Error, cannot locate genome_lib_dir: /data/GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir at /usr/local/src/STAR-Fusion/STAR-Fusion line 508.

Please help me. Thanks a lot.

Sincerely, Dajeong Jeong

brianjohnhaas commented 11 months ago

Hi,

Can you try running:

docker run -v pwd:/data --rm --platform linux/amd64 trinityctat/starfusion ls -ltr /data

and

docker run -v pwd:/data --rm --platform linux/amd64 trinityctat/starfusion ls -ltr /data/GRCh38_gencode_v22CTAT lib_Mar012021.plug-n-play

and

docker run -v pwd:/data --rm --platform linux/amd64 trinityctat/starfusion ls -ltr /data/GRCh38_gencode_v22CTAT lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir

to see if it shows the various contents as you'd expect?

On Sun, Oct 15, 2023 at 11:56 PM jdjdj0202 @.***> wrote:

THanks. I unzipped the tar.gz file and tried again. However, the same error occurs. The file is located in 'data' directory which is the same as left_fq and right_fq files.

trial 1

docker run -v pwd:/data --rm --platform linux/amd64 trinityctat/starfusion STAR-Fusion --left_fq /data/ATL005_R1_fastq.gz --right_fq /data/ATL005_R2_fastq.gz --genome_lib_dir /data/GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play -O /data/StarFusionOut --FusionInspector validate --examine_coding_effect --denovo_reconstruct

--> ERROR Error, cannot locate genome_lib_dir: /data/GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play at /usr/local/src/STAR-Fusion/STAR-Fusion line 508. trial 2

docker run -v pwd:/data --rm --platform linux/amd64 trinityctat/starfusion STAR-Fusion --left_fq /data/ATL005_R1_fastq.gz --right_fq /data/ATL005_R2_fastq.gz --genome_lib_dir /data/GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir

-O /data/StarFusionOut --FusionInspector validate --examine_coding_effect --denovo_reconstruct

--> ERROR Error, cannot locate genome_lib_dir: /data/GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir at /usr/local/src/STAR-Fusion/STAR-Fusion line 508.

Please help me. Thanks a lot.

Sincerely, Dajeong Jeong

— Reply to this email directly, view it on GitHub https://github.com/STAR-Fusion/STAR-Fusion-Tutorial/issues/8#issuecomment-1763686304, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABZRKX4A5UJM6I6NYHL2HDLX7SV7NAVCNFSM6AAAAAA56RBI76VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTONRTGY4DMMZQGQ . You are receiving this because you commented.Message ID: @.***>

--

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

jdjdj0202 commented 11 months ago

Hi, Thank you for your reply! I think the almost similar error occurs. Meanwhile, I found that the file size of "GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play" which I acquired after unzip the tar.gz file is very small. (31959209255 vs 96).

================================================ I tried:

docker run -v pwd:/data --rm --platform linux/amd64 trinityctat/starfusion ls -ltr /data

--> it showed

total 72 -rw-r--r-- 1 root root 10007 Oct 10 09:58 ChangeLog drwxr-xr-x 16 root root 512 Oct 10 09:58 Docker -rw-r--r-- 1 root root 1506 Oct 10 09:58 LICENSE -rw-r--r-- 1 root root 238 Oct 10 09:58 Makefile drwxr-xr-x 24 root root 768 Oct 10 09:58 PerlLib -rw-r--r-- 1 root root 379 Oct 10 09:58 README.md -rwxr-xr-x 1 root root 44028 Oct 10 09:58 STAR-Fusion drwxr-xr-x 7 root root 224 Oct 10 09:58 WDL drwxr-xr-x 3 root root 96 Oct 10 09:58 bioconda_recipe -rw-r--r-- 1 root root 406 Oct 10 09:58 notes drwxr-xr-x 9 root root 288 Oct 10 09:58 testing drwxr-xr-x 21 root root 672 Oct 10 09:58 util drwxr-xr-x 11 root root 352 Oct 10 09:58 FusionAnnotator drwxr-xr-x 15 root root 480 Oct 10 09:58 FusionFilter drwxr-xr-x 23 root root 736 Oct 10 09:58 FusionInspector drwxr-xr-x 5 root root 160 Oct 10 09:58 STAR-Fusion.github.io drwxr-xr-x 16 root root 512 Oct 10 09:58 STAR-Fusion.wiki drwxr-xr-x 13 root root 416 Oct 10 09:58 ctat-genome-lib-builder drwxr-xr-x 5 root root 160 Oct 10 10:07 plugins drwxr-xr-x 10 root root 320 Oct 16 03:49 data

=========================================================================================== and

docker run -v pwd:/data --rm --platform linux/amd64 \ trinityctat/starfusion ls -ltr /data/GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play

error message: ls: cannot access '/data/GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play': No such file or directory

and

docker run -v pwd:/data --rm --platform linux/amd64 \ trinityctat/starfusion ls -ltr /data/GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir

error message: ls: cannot access '/data/GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir': No such file or directory

###################################### unzip process ######################################

I entered: tar -zxvf GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play.tar.gz

Following messages appeared: x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/AnnotFilterRule.pm x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_genome.fa x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/chkpts/ x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/chkpts/ref_annot.gtf.ok x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/chkpts/cp_ref_annot_cdna.ok x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/__chkpts/makeblastdb.ok x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/chkpts/blast_pairs.idx.ok x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/chkpts/ref_annot.cdsplus.dfam_masked.fa.idx.ok x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/chkpts/_prot_info_db.ok x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/chkpts/_fusion_annot_lib.idx.ok x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/__chkpts/fusion_annot_lib.cp.ok x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/chkpts/trans.blast.dat.index.ok x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/chkpts/index_pfam_hits.ok x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/__chkpts/cp_pfam_dat.ok x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/chkpts/ref_genome.fa.ok x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/chkpts/trans.blast.dat.cp.ok x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/chkpts/validate_ctat_genome_lib.ok x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/chkpts/ref_annot.gtf.gene_spans.ok x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/chkpts/index_ref_annot_cdna.ok x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/chkpts/ref_annot.cdsplus.dfam_masked.fa.cp.ok x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/chkpts/ref_annot.gtf.mini.sortu.ok x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/chkpts/ref_genome_fai.ok x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/chkpts/cp_gene_blast_pairs.ok x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/__chkpts/annotfiltrule_cp.ok x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/pfam_domains.dbm x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_genome.fa.fai x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_annot.cdsplus.fa.idx x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_annot.cdna.fa.idx x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/blast_pairs.idx x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_annot.gtf.gene_spans x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_annot.cdna.fa x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_genome.fa.star.idx/ x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_genome.fa.star.idx/Log.out x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_genome.fa.star.idx/build.ok x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_genome.fa.star.idx/sjdbList.fromGTF.out.tab x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_genome.fa.star.idx/exonGeTrInfo.tab x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_genome.fa.star.idx/SAindex x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_genome.fa.star.idx/transcriptInfo.tab x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_genome.fa.star.idx/geneInfo.tab x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_genome.fa.star.idx/sjdbInfo.txt x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_genome.fa.star.idx/SA x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_genome.fa.star.idx/chrStart.txt x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_genome.fa.star.idx/chrName.txt x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_genome.fa.star.idx/chrLength.txt x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_genome.fa.star.idx/genomeParameters.txt x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_genome.fa.star.idx/sjdbList.out.tab x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_genome.fa.star.idx/Genome x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_genome.fa.star.idx/chrNameLength.txt x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_genome.fa.star.idx/exonInfo.tab x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_annot.pep x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/trans.blast.align_coords.align_coords.dat x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_annot.cdsplus.fa x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/trans.blast.align_coords.align_coords.dbm x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/PFAM.domtblout.dat.gz x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_annot.gtf x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/trans.blast.dat.gz x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_genome.fa.nsq x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_annot.cds x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_genome.fa.nhr x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/blast_pairs.dat.gz x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/fusion_annot_lib.idx x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_annot.prot_info.dbm x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_genome.fa.nin x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/fusion_annot_lib.gz

####################################################################################

Is it a problem during the unzip process?

Please help me. Thanks!!

brianjohnhaas commented 11 months ago

Let's try the following

Go to a working directory where you plan on running the analysis and generating the outputs from running the software.

Move the GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play directory there.

Put your input reads there as well.

Then, from within that directory, run the docker command.

All that should exist in that working directory are those specific things to start with:

We can take it from there.

best,

~b

On Tue, Oct 17, 2023 at 5:43 AM jdjdj0202 @.***> wrote:

Hi, Thank you for your reply! I think the almost similar error occurs. Meanwhile, I found that the file size of "GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play" which I acquired after unzip the tar.gz file is very small. (31959209255 vs 96).

================================================ I tried:

docker run -v pwd:/data --rm --platform linux/amd64 trinityctat/starfusion ls -ltr /data

--> it showed

total 72 -rw-r--r-- 1 root root 10007 Oct 10 09:58 ChangeLog drwxr-xr-x 16 root root 512 Oct 10 09:58 Docker -rw-r--r-- 1 root root 1506 Oct 10 09:58 LICENSE -rw-r--r-- 1 root root 238 Oct 10 09:58 Makefile drwxr-xr-x 24 root root 768 Oct 10 09:58 PerlLib -rw-r--r-- 1 root root 379 Oct 10 09:58 README.md -rwxr-xr-x 1 root root 44028 Oct 10 09:58 STAR-Fusion drwxr-xr-x 7 root root 224 Oct 10 09:58 WDL drwxr-xr-x 3 root root 96 Oct 10 09:58 bioconda_recipe -rw-r--r-- 1 root root 406 Oct 10 09:58 notes drwxr-xr-x 9 root root 288 Oct 10 09:58 testing drwxr-xr-x 21 root root 672 Oct 10 09:58 util drwxr-xr-x 11 root root 352 Oct 10 09:58 FusionAnnotator drwxr-xr-x 15 root root 480 Oct 10 09:58 FusionFilter drwxr-xr-x 23 root root 736 Oct 10 09:58 FusionInspector drwxr-xr-x 5 root root 160 Oct 10 09:58 STAR-Fusion.github.io drwxr-xr-x 16 root root 512 Oct 10 09:58 STAR-Fusion.wiki drwxr-xr-x 13 root root 416 Oct 10 09:58 ctat-genome-lib-builder drwxr-xr-x 5 root root 160 Oct 10 10:07 plugins drwxr-xr-x 10 root root 320 Oct 16 03:49 data

=========================================================================================== and

docker run -v pwd:/data --rm --platform linux/amd64 trinityctat/starfusion ls -ltr /data/GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play error message: ls: cannot access '/data/GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play': No such file or directory

and

docker run -v pwd:/data --rm --platform linux/amd64 trinityctat/starfusion ls -ltr /data/GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir error message: ls: cannot access '/data/GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir': No such file or directory

###################################### unzip process ######################################

I entered: tar -zxvf GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play.tar.gz

Following messages appeared: x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/AnnotFilterRule.pm x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_genome.fa x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/chkpts/ x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/chkpts/ref_annot.gtf.ok x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/chkpts/cp_ref_annot_cdna.ok x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/__chkpts/makeblastdb.ok x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/chkpts/blast_pairs.idx.ok x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/chkpts/ref_annot.cdsplus.dfam_masked.fa.idx.ok x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/chkpts/_prot_info_db.ok x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/chkpts/_fusion_annot_lib.idx.ok x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/__chkpts/fusion_annot_lib.cp.ok x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/chkpts/trans.blast.dat.index.ok x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/chkpts/index_pfam_hits.ok x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/__chkpts/cp_pfam_dat.ok x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/chkpts/ref_genome.fa.ok x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/chkpts/trans.blast.dat.cp.ok x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/chkpts/validate_ctat_genome_lib.ok x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/chkpts/ref_annot.gtf.gene_spans.ok x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/chkpts/index_ref_annot_cdna.ok x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/chkpts/ref_annot.cdsplus.dfam_masked.fa.cp.ok x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/chkpts/ref_annot.gtf.mini.sortu.ok x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/chkpts/ref_genome_fai.ok x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/chkpts/cp_gene_blast_pairs.ok x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/__chkpts/annotfiltrule_cp.ok x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/pfam_domains.dbm x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_genome.fa.fai x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_annot.cdsplus.fa.idx x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_annot.cdna.fa.idx x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/blast_pairs.idx x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_annot.gtf.gene_spans x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_annot.cdna.fa x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_genome.fa.star.idx/ x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_genome.fa.star.idx/Log.out x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_genome.fa.star.idx/build.ok x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_genome.fa.star.idx/sjdbList.fromGTF.out.tab x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_genome.fa.star.idx/exonGeTrInfo.tab x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_genome.fa.star.idx/SAindex x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_genome.fa.star.idx/transcriptInfo.tab x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_genome.fa.star.idx/geneInfo.tab x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_genome.fa.star.idx/sjdbInfo.txt x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_genome.fa.star.idx/SA x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_genome.fa.star.idx/chrStart.txt x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_genome.fa.star.idx/chrName.txt x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_genome.fa.star.idx/chrLength.txt x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_genome.fa.star.idx/genomeParameters.txt x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_genome.fa.star.idx/sjdbList.out.tab x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_genome.fa.star.idx/Genome x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_genome.fa.star.idx/chrNameLength.txt x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_genome.fa.star.idx/exonInfo.tab x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_annot.pep x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/trans.blast.align_coords.align_coords.dat x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_annot.cdsplus.fa x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/trans.blast.align_coords.align_coords.dbm x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/PFAM.domtblout.dat.gz x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_annot.gtf x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/trans.blast.dat.gz x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_genome.fa.nsq x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_annot.cds x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_genome.fa.nhr x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/blast_pairs.dat.gz x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/fusion_annot_lib.idx x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_annot.prot_info.dbm x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_genome.fa.nin x GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/fusion_annot_lib.gz

####################################################################################

Is it a problem during the unzip process?

Please help me. Thanks!!

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jdjdj0202 commented 11 months ago

Thank you for your kind reply.

Input read files and chat_genome_lib_build_dr are in the same directory named 'data'.

STAR-Fusion directory includes this 'data' directory.

I ran the docker command at this 'data' directory with the following command line, which resulted in another type of error.

Is it a problem related to Pipeliner as the error says? How could I solve this?

==================================================================================== docker run -v pwd:/data --rm --platform linux/amd64 trinityctat/starfusion \ STAR-Fusion \ --left_fq /data/ATL005_R1_fastq.gz \ --right_fq /data/ATL005_R2_fastq.gz \ --genome_lib_dir /data/GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir -O /data/StarFusionOut \ --FusionInspector validate \ --examine_coding_effect \ --denovo_reconstruct

==================================================================================== The error message is as follows:

-ctat genome lib [/data/GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir] validates. CMD: mkdir -p /usr/local/src/STAR-Fusion_outdir CMD: mkdir -p /usr/local/src/STAR-Fusion_outdir/_starF_checkpoints CMD: mkdir -p /usr/local/src/STAR-Fusion_outdir/star-fusion.preliminary

====================================================================================

I'd really appreciate if you could help me. Thanks.

Sincerely, Dajeong

brianjohnhaas commented 11 months ago

Hi,

It looks like it ran out of memory. Try running it on a machine that has at least 40G RAM

best,

~b

On Wed, Oct 18, 2023 at 5:26 AM jdjdj0202 @.***> wrote:

Thank you for your kind reply.

Input read files and chat_genome_lib_build_dr are in the same directory named 'data'.

STAR-Fusion directory includes this 'data' directory.

I ran the docker command at this 'data' directory with the following command line, which resulted in another type of error.

Is it a problem related to Pipeliner as the error says? How could I solve this?

==================================================================================== docker run -v pwd:/data --rm --platform linux/amd64 trinityctat/starfusion STAR-Fusion --left_fq /data/ATL005_R1_fastq.gz --right_fq /data/ATL005_R2_fastq.gz --genome_lib_dir /data/GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir -O /data/StarFusionOut --FusionInspector validate --examine_coding_effect --denovo_reconstruct

==================================================================================== The error message is as follows:

-ctat genome lib [/data/GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir] validates. CMD: mkdir -p /usr/local/src/STAR-Fusion_outdir CMD: mkdir -p /usr/local/src/STAR-Fusion_outdir/_starF_checkpoints CMD: mkdir -p /usr/local/src/STAR-Fusion_outdir/star-fusion.preliminary

  • Running CMD: /usr/local/bin/STAR --genomeDir /data/GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_genome.fa.star.idx --outReadsUnmapped None --chimSegmentMin 12 --chimJunctionOverhangMin 8 --chimOutJunctionFormat 1 --alignSJDBoverhangMin 10 --alignMatesGapMax 100000 --alignIntronMax 100000 --alignSJstitchMismatchNmax 5 -1 5 5 --runThreadN 4 --outSAMstrandField intronMotif --outSAMunmapped Within --alignInsertionFlush Right --alignSplicedMateMapLminOverLmate 0 --alignSplicedMateMapLmin 30 --outSAMtype BAM Unsorted --readFilesIn /data/ATL005_R1_fastq.gz /data/ATL005_R2_fastq.gz --outSAMattrRGline ID:GRPundef --chimMultimapScoreRange 3 --chimScoreJunctionNonGTAG -4 --chimMultimapNmax 20 --chimNonchimScoreDropMin 10 --peOverlapNbasesMin 12 --peOverlapMMp 0.1 --genomeLoad NoSharedMemory --twopassMode None --readFilesCommand 'gunzip -c' --quantMode GeneCounts Oct 18 09:11:38 ..... started STAR run Oct 18 09:11:38 ..... loading genome Killed Error, cmd: /usr/local/bin/STAR --genomeDir /data/GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_genome.fa.star.idx --outReadsUnmapped None --chimSegmentMin 12 --chimJunctionOverhangMin 8 --chimOutJunctionFormat 1 --alignSJDBoverhangMin 10 --alignMatesGapMax 100000 --alignIntronMax 100000 --alignSJstitchMismatchNmax 5 -1 5 5 --runThreadN 4 --outSAMstrandField intronMotif --outSAMunmapped Within --alignInsertionFlush Right --alignSplicedMateMapLminOverLmate 0 --alignSplicedMateMapLmin 30 --outSAMtype BAM Unsorted --readFilesIn /data/ATL005_R1_fastq.gz /data/ATL005_R2_fastq.gz --outSAMattrRGline ID:GRPundef --chimMultimapScoreRange 3 --chimScoreJunctionNonGTAG -4 --chimMultimapNmax 20 --chimNonchimScoreDropMin 10 --peOverlapNbasesMin 12 --peOverlapMMp 0.1 --genomeLoad NoSharedMemory --twopassMode None --readFilesCommand 'gunzip -c' --quantMode GeneCounts died with ret 35072 No such file or directory at /usr/local/src/STAR-Fusion/PerlLib/Pipeliner.pm line 181. Pipeliner::run(Pipeliner=HASH(0x40006a2b40)) called at /usr/local/src/STAR-Fusion/STAR-Fusion line 1038 main::run_STAR(Pipeliner=HASH(0x40006a2b40), "/data/ATL005_R1_fastq.gz", "/data/ATL005_R2_fastq.gz", "") called at /usr/local/src/STAR-Fusion/STAR-Fusion line 610 zsh: command not found: -O

====================================================================================

I'd really appreciate if you could help me. Thanks.

Sincerely, Dajeong

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jdjdj0202 commented 11 months ago

Thank you for your reply.

I am already using a MacBook with 64GB RAM. Q_Q

brianjohnhaas commented 11 months ago

That should be plenty of RAM then. If you're using docker on something other than linux, then maybe dig into the docker usage configuration (docker desktop preferences?) and see if there are limits set on the available resources given to it to make sure enough RAM can be allocated to the docker image.

For example, on my mac, I see this:

[image: image.png]

and it would definitely require modification for anything with high memory to run on it.

hope this helps,

~b

On Fri, Oct 20, 2023 at 7:15 AM jdjdj0202 @.***> wrote:

Thank you for your reply.

I am already using a laptop with 64GB RAM. Q_Q

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jdjdj0202 commented 10 months ago

It works well!! Thank you so much! I really appreciate your help. Have a good day. :)

Sincerely, Dajeong

brianjohnhaas commented 10 months ago

Great to hear! thanks for the update.

B

On Mon, Oct 30, 2023 at 6:35 AM jdjdj0202 @.***> wrote:

It works well!! Thank you so much! I really appreciate your help. Have a good day. :)

Sincerely, Dajeong

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