Inquiry

[小林賢子]

Dear STAR-Fusion team (Dr. Brian J. Haas)

I installed Docker container and reference data resources.

However I cannot run STAR-Fusion.

Below is the command and Error message.

Is the the path to directories wrong? (the contents of the directory is shown at the bottom)

Would you please tell me how to solve that.

Tetsuko Kobayashi (in JAPAN)

<Command>

user@localhost:~/STAR-Fusion$ docker run -v `pwd`:/data --rm trinityctat/starfusion STAR-Fusion --left_fq /home/user/STAR-Fusion/YT_1.fastq.gz --right_fq /home/user/STAR-Fusion/YT_2.fastq.gz --genome_lib_dir /home/user/STAR-Fusion/GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir -O /data/StarFusionOut --FusionInspector validate --examine_coding_effect --denovo_reconstruct

<Error message>

Error, cannot locate genome_lib_dir: /home/user/STAR-Fusion/GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir at /usr/local/src/STAR-Fusion/STAR-Fusion line 507.

<The contents of the directory>

user@localhost:~/STAR-Fusion$ ls
2.7.10a.tar.gz                                              STAR-2.7.10a.tar.gz              YT_1.fastq
GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play           STAR-Fusion                      YT_1.fastq.gz
GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play.tar.gz    STAR-Fusion-v1.11.0              YT_2.fastq
GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play.tar.gz.1  STAR-Fusion-v1.11.0.FULL.tar.gz  YT_2.fastq.gz
STAR-2.7.10a                                                StarFusionOut                    releases

[Brian Haas]

Hi,

From the docker command, it appears the current working directory is being mounted at /data

If the ctat genome lib is there, then you'll need to refer to it by a path that starts with /data accordingly.

hope this helps!

~b

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

 

[小林賢子]

Dear Dr. Brian J. Haas

Thank you very much for your guide.

I have tried it according to your advice like below.

user@localhost:~/STAR-Fusion$ docker run -v `pwd`:/data --rm trinityctat/starfusion

user@localhost:~/STAR-Fusion$ STAR-Fusion --left_fq /data/YT_1.fastq.gz --right_fq /data/YT_2.fastq.gz --genome_lib_dir /data/ctat_genome_lib_build_dir -O /data/StarFusionOut --FusionInspector validate --examine_coding_effect --denovo_reconstruct

STAR-Fusion: コマンドが見つかりません (cannot find the command "STAR-Fusion")

Error message says "cannot find the command 'STAR-Fusion' "

I looked up Docker information, it show like below.

user@localhost:~/STAR-Fusion$ docker ps -a
CONTAINER ID   IMAGE                    COMMAND       CREATED        STATUS                    PORTS     NAMES
334218e0add3   trinityctat/starfusion   "/bin/bash"   47 hours ago   Exited (0) 47 hours ago             upbeat_kilby

So, Docker says that the COMMAND is "/bin/bash". However, this was also invalid.

 Would you please tell me where and what is the correct command for running STAR-Fusion when using Docker image trinityctat/starfusion?

Tetsuko Kobayashi (JAPAN)

2022年8月12日金曜日 5:44:04 UTC+9 bh...@broadinstitute.org:

[Brian Haas]

Hi,

It looks like you're running 2 separate commands here instead of one command.  Include the STAR-Fusion command in initial the call to docker, as you did in your earlier attempt first posted.

To view this discussion on the web visit https://groups.google.com/d/msgid/star-fusion/c608c250-0657-4f2d-a7bd-d4d18456ddecn%40googlegroups.com.

[小林賢子]

Dear Dr. Brian J. Haas

Thank you very much for your teaching.

However, I have not overcome the problems yet.

Would you please check the grammar and the contents in relating directories?

Sincerely,

Tetsuko Kobayashi (JAPAN)

<One command, and error message>

user@localhost:~/STAR-Fusion$ docker run -v `pwd`:/data --rm trinityctat/starfusion STAR-Fusion --left_fq /data/YT_1.fastq.gz --right_fq /data/YT_2.fastq.gz --genome_lib_dir /data/ctat_genome_lib_build_dir -O /data/StarFusionOut --FusionInspector validate --examine_coding_effect --denovo_reconstruct

Error, cannot locate genome_lib_dir: /data/ctat_genome_lib_build_dir at /usr/local/src/STAR-Fusion/STAR-Fusion line 507.

<the contents in the current working directory>

user@localhost:~/STAR-Fusion$ ls
2.7.10a.tar.gz                                              STAR-2.7.10a         STAR-Fusion-v1.11.0.FULL.tar.gz  YT_2.fastq
GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play           STAR-2.7.10a.tar.gz  StarFusionOut                    YT_2.fastq.gz
GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play.tar.gz    STAR-Fusion          YT_1.fastq                       releases

GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play.tar.gz.1  STAR-Fusion-v1.11.0  YT_1.fastq.gz

<the content in the directory of ~/STAR-Fusion/GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play>

user@localhost:~/STAR-Fusion$ ls ~/STAR-Fusion/GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play
ctat_genome_lib_build_dir

2022年8月14日日曜日 20:15:25 UTC+9 bh...@broadinstitute.org:

[Brian Haas]

I think the issue has to do with how the ctat genome lib is being specified. 

In your command, you have:   --genome_lib_dir /data/ctat_genome_lib_build_dir

but I suspect it should be:

     --genome_lib_dir /data/GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir

based on your file organization

To view this discussion on the web visit https://groups.google.com/d/msgid/star-fusion/377296d8-a210-4254-bbdd-d0ad64b9b6fdn%40googlegroups.com.

[小林賢子]

Dear Dr. Brian J. Haas

Thank you very much for your teaching many times.

I have changed the argument for --genome_lib_dir according to your advice like below.

However, I have not yet solve the issue how the ctat genome lib is being specified.

Would you please tell me next strategy?

Tetsuko Kobayashi

user@localhost:~$ docker run -v `pwd`:/data --rm trinityctat/starfusion STAR-Fusion --left_fq /data/YT_1.fastq.gz --right_fq /data/YT_2.fastq.gz --genome_lib_dir /data/GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir -O /data/StarFusionOut --FusionInspector validate --examine_coding_effect --denovo_reconstruct
Error, cannot locate genome_lib_dir: /data/GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir at /usr/local/src/STAR-Fusion/STAR-Fusion line 507.

2022年8月15日月曜日 22:04:49 UTC+9 bh...@broadinstitute.org:

[Brian Haas]

I suppose there could be a problem with how your ctat genome lib exists there.

i see the name 'GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play' in your directory that you're mounting into the docker as /data

Is this a directory, and does it contain the ctat_genome_lib_build_dir/ subdirectory?

To view this discussion on the web visit https://groups.google.com/d/msgid/star-fusion/809df02c-a804-4c21-a04f-4aa009420effn%40googlegroups.com.

[小林賢子]

Dear Dr. Brian J. Haas

I am so so happy!!

Today, I again copied and pasted the same command as 17th August with a feeling of 'here goes nothing'.

Then, surprisingly, I'm not sure why, STAR-Fusion start running! and finally I got the fusion list!!

I can get many fusion lists now.

I would like to express my deep gratitude for your kindness.

Best wishes,  

Tetsuko Kobayashi

2022年8月17日水曜日 22:00:13 UTC+9 bh...@broadinstitute.org:

[Brian Haas]

Great to hear it's working for you now!

~b

To view this discussion on the web visit https://groups.google.com/d/msgid/star-fusion/93859324-5f20-40af-9651-f93c71017864n%40googlegroups.com.

[小林賢子]

Dear Dr. Brian J. Haas

Thank you so much for your help the other day.

Now I am trying executing another sample.

Below is the command that was copied and pasted from the other day's successful one and outputs for the command.

They look too short, but they show the following sentence in the middle.

* STAR-Fusion complete.  See output: /data/StarFusionOut/star-fusion.fusion_predictions.tsv (or .abridged.tsv version)

I checked the tsv file and found that it contained the other day's result, that is, the fusion list generated from the other day's sample (YT_1/YT_2.fastq.gz).

I wonder if the execution completed or not.

If not, what is the problem?

And if completed, where is the list generated from today's sample (WSU-DLCL2_1/WSU-DLCL2_2.fastq.gz).

I was wondering if you could advise for this issue?

Tetsuko Kobayshi

user@localhost:~/STAR-Fusion$ docker run -v `pwd`:/data --rm trinityctat/starfusion STAR-Fusion --left_fq /data/WSU-DLCL2_1.fastq.gz --right_fq /data/WSU-DLCL2_2.fastq.gz --genome_lib_dir /data/GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir -O /data/StarFusionOut --FusionInspector validate --examine_coding_effect --denovo_reconstruct
-ctat genome lib [/data/GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir] validates.
-- Skipping CMD: /usr/local/bin/STAR --genomeDir /data/GRCh38_gencode_v37_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/WSU-DLCL2_1.fastq.gz /data/WSU-DLCL2_2.fastq.gz  --outSAMattrRGline ID:GRPundef  --chimMultimapScoreRange 3  --chimScoreJunctionNonGTAG -4  --chimMultimapNmax 20  --chimNonchimScoreDropMin 10  --peOverlapNbasesMin 12 --peOverlapMMp 0.1  --genomeLoad NoSharedMemory  --twopassMode Basic  --readFilesCommand 'gunzip -c'  --quantMode GeneCounts, checkpoint [/data/StarFusionOut/_starF_checkpoints/run_star_aligner.ok] exists.
-sample contains 34472172 rnaseq fragments
-- Skipping CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes  --genome_lib_dir /data/GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir  -J Chimeric.out.junction  -O /data/StarFusionOut/star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4 , checkpoint [/data/StarFusionOut/_starF_checkpoints/star-fusion.map_chim_to_genes.ok] exists.
-- Skipping CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.handle_multimapping_reads  -J /data/StarFusionOut/star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt  --genome_lib_dir /data/GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir  --filt_file /data/StarFusionOut/star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.fail  -M 50  > /data/StarFusionOut/star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass , checkpoint [/data/StarFusionOut/_starF_checkpoints/star-fusion.handle_multimappers.ok] exists.
-- Skipping CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.predict  -J /data/StarFusionOut/star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass  -O /data/StarFusionOut/star-fusion.preliminary/star-fusion , checkpoint [/data/StarFusionOut/_starF_checkpoints/star-fusion.STAR-Fusion.predict.ok] exists.
-- Skipping CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.filter  --fusion_preds /data/StarFusionOut/star-fusion.preliminary/star-fusion.fusion_candidates.preliminary  -J Chimeric.out.junction  --tmpdir /tmp  --min_junction_reads 1  --min_sum_frags 2  --require_LDAS 1  --max_promiscuity 10  --min_pct_dom_promiscuity 20  --min_novel_junction_support 3  --min_alt_pct_junction 10  --aggregate_novel_junction_dist 5  --min_spanning_frags_only 5  --genome_lib_dir /data/GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir  --out_prefix /data/StarFusionOut/star-fusion.preliminary/star-fusion, checkpoint [/data/StarFusionOut/_starF_checkpoints/STAR-Fusion.filter.ok] exists.
-- Skipping CMD: /usr/local/src/STAR-Fusion/util/incorporate_FFPM_into_final_report.pl /data/StarFusionOut/star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered 34472172 > /data/StarFusionOut/star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered.FFPM, checkpoint [/data/StarFusionOut/_starF_checkpoints/FFPM.ok] exists.
-- Skipping CMD: /usr/local/src/STAR-Fusion/util/append_breakpoint_junction_info.pl /data/StarFusionOut/star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered.FFPM /data/GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir > /data/StarFusionOut/star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo, checkpoint [/data/StarFusionOut/_starF_checkpoints/predicted_fusions_with_splice_info.ok] exists.
-- Skipping CMD: /usr/local/src/STAR-Fusion/FusionAnnotator/FusionAnnotator --genome_lib_dir /data/GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir --annotate /data/StarFusionOut/star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo > /data/StarFusionOut/star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot, checkpoint [/data/StarFusionOut/_starF_checkpoints/fusion_annotator.ok] exists.
-- Skipping CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/filter_by_annotation_rules.pl --fusions /data/StarFusionOut/star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot --genome_lib_dir /data/GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir, checkpoint [/data/StarFusionOut/_starF_checkpoints/annot_filter.ok] exists.
-- Skipping CMD: /usr/local/src/STAR-Fusion/util/filter_likely_RT_artifacts.pl --fusions /data/StarFusionOut/star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass --genome_lib_dir /data/GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir, checkpoint [/data/StarFusionOut/_starF_checkpoints/RTartifact_filter.ok] exists.
-- Skipping CMD: /usr/local/src/STAR-Fusion/util/filter_by_min_FFPM.pl /data/StarFusionOut/star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass.RTartifact.pass 0.1, checkpoint [/data/StarFusionOut/_starF_checkpoints/FFPM_filter.ok] exists.
-- Skipping CMD: cp /data/StarFusionOut/star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass.RTartifact.pass.minFFPM.0.1.pass star-fusion.fusion_predictions.tsv, checkpoint [/data/StarFusionOut/_starF_checkpoints/cp_final.ok] exists.
-- Skipping CMD: /usr/local/src/STAR-Fusion/util/column_exclusions.pl star-fusion.fusion_predictions.tsv JunctionReads,SpanningFrags > star-fusion.fusion_predictions.abridged.tsv, checkpoint [/data/StarFusionOut/_starF_checkpoints/abridged_final] exists.
-- Skipping CMD: /usr/local/src/STAR-Fusion/FusionAnnotator/util/fusion_to_coding_region_effect.pl  --fusions star-fusion.fusion_predictions.abridged.tsv --genome_lib_dir /data/GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir > star-fusion.fusion_predictions.abridged.coding_effect.tsv, checkpoint [/data/StarFusionOut/_starF_checkpoints/coding_eff.ok] exists.


    * STAR-Fusion complete.  See output: /data/StarFusionOut/star-fusion.fusion_predictions.tsv (or .abridged.tsv version)


-- Skipping CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionInspector --fusions star-fusion.fusion_predictions.abridged.coding_effect.tsv  --out_prefix finspector  --min_junction_reads 1  --min_novel_junction_support 3  --min_spanning_frags_only 5  --max_mate_dist 100000  --vis  --max_promiscuity 10  --output_dir /data/StarFusionOut/FusionInspector-validate  --genome_lib_dir /data/GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir  --CPU 4  --left_fq /data/WSU-DLCL2_1.fastq.gz --right_fq /data/WSU-DLCL2_2.fastq.gz  --include_Trinity  --annotate  --examine_coding_effect , checkpoint [_fi_validate_590.ok] exists.

2022年8月19日金曜日 21:17:04 UTC+9 bh...@broadinstitute.org:

[Brian Haas]

Hi,

I think it's using the output directory from the other sample and seeing all the checkpoints for the earlier completed steps.

Try running this new sample in a different directory, or setting the output directory to a new value.

best,

~brian

To view this discussion on the web visit https://groups.google.com/d/msgid/star-fusion/6ade2dfe-0b0f-43d4-be50-b753cf92f775n%40googlegroups.com.

[小林賢子]

Dear Dr. Brian J. Haas

Thanks so much again!

It has been solved by the latter advice, that is, "setting the output directory to a new value".

I am always so grateful to you for your prompt support.

Best regards,

Tetsuko Kobayashi

2022年8月25日木曜日 21:03:11 UTC+9 bh...@broadinstitute.org: