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.

[jdjdj0202]

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]

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]

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]

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_v22_CTAT_ lib_Mar012021.plug-n-play 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 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 <#8 (comment)>, 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]

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]

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: - the genome lib directory - your input reads. 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!! — Reply to this email directly, view it on GitHub <#8 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABZRKXZ3RMDUCZZ2PLLN373X7ZHNBAVCNFSM6AAAAAA56RBI76VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTONRWGA2TKNZYGA> . 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]

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

[brianjohnhaas]

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 — Reply to this email directly, view it on GitHub <#8 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABZRKX7ZOZFASWH2W2SOSNLX76OEFAVCNFSM6AAAAAA56RBI76VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTONRYGA2DMOJVGA> . 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]

Thank you for your reply.

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

[brianjohnhaas]

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 — Reply to this email directly, view it on GitHub <#8 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABZRKX2ZTZI7U3TPZO47CS3YAJMNXAVCNFSM6AAAAAA56RBI76VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTONZSGU2TCMBSGA> . 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]

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

Sincerely,
Dajeong

[brianjohnhaas]

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 — Reply to this email directly, view it on GitHub <#8 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABZRKX64WM54YXKGTJB5OB3YB57IVAVCNFSM6AAAAAA56RBI76VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTOOBUHEYDOMZTHE> . You are receiving this because you commented.Message ID: ***@***.***>

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