Error on tutorial HASH(0x2574100))

[bioinfo-dirty-jobs]

I try to do this tutorial using conda enviroment.
I have this error:

n.pre_blast_filter -E 0.001 --genome_lib_dir /home/centos/illumina/TEST_FUSION/STAR-Fusion-Tutorial/ctat_genome_lib_build_dir
Error: cannot locate /home/centos/illumina/TEST_FUSION/STAR-Fusion-Tutorial/ctat_genome_lib_build_dir/blast_pairs.idx at /home/centos/miniconda3/envs/tutorial_fusion/lib/STAR-Fusion/FusionFilter/util/blast_filter.pl line 87.
Error, cmd /home/centos/miniconda3/envs/tutorial_fusion/lib/STAR-Fusion/FusionFilter/util/blast_filter.pl --fusion_preds /home/centos/illumina/TEST_FUSION/STAR-Fusion-Tutorial/STAR-Fusion_outdir/star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter -E 0.001 --genome_lib_dir /home/centos/illumina/TEST_FUSION/STAR-Fusion-Tutorial/ctat_genome_lib_build_dir died with ret 512 at /home/centos/miniconda3/envs/tutorial_fusion/lib/STAR-Fusion/util/../FusionFilter/blast_and_promiscuity_filter.pl line 161.
Error, cmd:
/home/centos/miniconda3/envs/tutorial_fusion/lib/STAR-Fusion/util/../FusionFilter/blast_and_promiscuity_filter.pl --out_prefix /home/centos/illumina/TEST_FUSION/STAR-Fusion-Tutorial/STAR-Fusion_outdir/star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion -E 0.001 --max_promiscuity 3 --fusion_preds /home/centos/illumina/TEST_FUSION/STAR-Fusion-Tutorial/STAR-Fusion_outdir/star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /home/centos/illumina/TEST_FUSION/STAR-Fusion-Tutorial/ctat_genome_lib_build_dir 
 died with ret (512) at /home/centos/miniconda3/envs/tutorial_fusion/lib/STAR-Fusion/util/../PerlLib/Process_cmd.pm line 19, <$fh> line 32.
	Process_cmd::process_cmd("/home/centos/miniconda3/envs/tutorial_fusion/lib/STAR-Fusion/"...) called at /home/centos/miniconda3/envs/tutorial_fusion/lib/STAR-Fusion/util/STAR-Fusion.filter line 240
Error, cmd: /home/centos/miniconda3/envs/tutorial_fusion/lib/STAR-Fusion/util/STAR-Fusion.filter  --fusion_preds /home/centos/illumina/TEST_FUSION/STAR-Fusion-Tutorial/STAR-Fusion_outdir/star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo  -E 0.001  --tmpdir /tmp  --min_junction_reads 1  --min_sum_frags 2  --require_LDAS 1  --max_promiscuity 3  --min_novel_junction_support 3  --min_alt_pct_junction 10  --aggregate_novel_junction_dist 5  --genome_lib_dir /home/centos/illumina/TEST_FUSION/STAR-Fusion-Tutorial/ctat_genome_lib_build_dir  --out_prefix /home/centos/illumina/TEST_FUSION/STAR-Fusion-Tutorial/STAR-Fusion_outdir/star-fusion.preliminary/star-fusion died with ret 512 at /home/centos/miniconda3/envs/tutorial_fusion/lib/STAR-Fusion/PerlLib/Pipeliner.pm line 79.
	Pipeliner::run(Pipeliner=HASH(0x2574100)) called at /home/centos/miniconda3/envs/tutorial_fusion/lib/STAR-Fusion/STAR-Fusion line 394

[brianjohnhaas]

Hi The tutorial only works with the latest software release, and bioconda hasn't been updated yet afaik. best, ~b

…

On Mon, Mar 19, 2018 at 8:08 AM, bioinfo-dirty-jobs < ***@***.***> wrote: I try to do this tutorial using conda enviroment. I have this error: n.pre_blast_filter -E 0.001 --genome_lib_dir /home/centos/illumina/TEST_FUSION/STAR-Fusion-Tutorial/ctat_genome_lib_build_dir Error: cannot locate /home/centos/illumina/TEST_FUSION/STAR-Fusion-Tutorial/ctat_genome_lib_build_dir/blast_pairs.idx at /home/centos/miniconda3/envs/tutorial_fusion/lib/STAR-Fusion/FusionFilter/util/blast_filter.pl line 87. Error, cmd /home/centos/miniconda3/envs/tutorial_fusion/lib/STAR-Fusion/FusionFilter/util/blast_filter.pl --fusion_preds /home/centos/illumina/TEST_FUSION/STAR-Fusion-Tutorial/STAR-Fusion_outdir/star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter -E 0.001 --genome_lib_dir /home/centos/illumina/TEST_FUSION/STAR-Fusion-Tutorial/ctat_genome_lib_build_dir died with ret 512 at /home/centos/miniconda3/envs/tutorial_fusion/lib/STAR-Fusion/util/../FusionFilter/blast_and_promiscuity_filter.pl line 161. Error, cmd: /home/centos/miniconda3/envs/tutorial_fusion/lib/STAR-Fusion/util/../FusionFilter/blast_and_promiscuity_filter.pl --out_prefix /home/centos/illumina/TEST_FUSION/STAR-Fusion-Tutorial/STAR-Fusion_outdir/star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion -E 0.001 --max_promiscuity 3 --fusion_preds /home/centos/illumina/TEST_FUSION/STAR-Fusion-Tutorial/STAR-Fusion_outdir/star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /home/centos/illumina/TEST_FUSION/STAR-Fusion-Tutorial/ctat_genome_lib_build_dir died with ret (512) at /home/centos/miniconda3/envs/tutorial_fusion/lib/STAR-Fusion/util/../PerlLib/Process_cmd.pm line 19, <$fh> line 32. Process_cmd::process_cmd("/home/centos/miniconda3/envs/tutorial_fusion/lib/STAR-Fusion/"...) called at /home/centos/miniconda3/envs/tutorial_fusion/lib/STAR-Fusion/util/STAR-Fusion.filter line 240 Error, cmd: /home/centos/miniconda3/envs/tutorial_fusion/lib/STAR-Fusion/util/STAR-Fusion.filter --fusion_preds /home/centos/illumina/TEST_FUSION/STAR-Fusion-Tutorial/STAR-Fusion_outdir/star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo -E 0.001 --tmpdir /tmp --min_junction_reads 1 --min_sum_frags 2 --require_LDAS 1 --max_promiscuity 3 --min_novel_junction_support 3 --min_alt_pct_junction 10 --aggregate_novel_junction_dist 5 --genome_lib_dir /home/centos/illumina/TEST_FUSION/STAR-Fusion-Tutorial/ctat_genome_lib_build_dir --out_prefix /home/centos/illumina/TEST_FUSION/STAR-Fusion-Tutorial/STAR-Fusion_outdir/star-fusion.preliminary/star-fusion died with ret 512 at /home/centos/miniconda3/envs/tutorial_fusion/lib/STAR-Fusion/PerlLib/Pipeliner.pm line 79. Pipeliner::run(Pipeliner=HASH(0x2574100)) called at /home/centos/miniconda3/envs/tutorial_fusion/lib/STAR-Fusion/STAR-Fusion line 394 — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#1>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AHMVX1Ppjz4H4i2kcc9LyzUka0zQ7vBEks5tf5-qgaJpZM4SwC5i> .

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

[bioinfo-dirty-jobs]

I try to use the last version from github:
Here you have the error:

CMD: /home/centos/illumina/TEST_FUSION/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /home/centos/illumina/TEST_FUSION/STAR-Fusion-Tutorial/rnaseq_1.fastq.gz /home/centos/illumina/TEST_FUSION/STAR-Fusion-Tutorial/STAR-Fusion_outdir/FusionInspector-validate/finspector.fusion_predictions.final.abridged > /home/centos/illumina/TEST_FUSION/STAR-Fusion-Tutorial/STAR-Fusion_outdir/FusionInspector-validate/finspector.fusion_predictions.final.abridged.FFPM already processed. Skipping.
Running: /home/centos/illumina/TEST_FUSION/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /home/centos/illumina/TEST_FUSION/STAR-Fusion-Tutorial/STAR-Fusion_outdir/FusionInspector-validate --json_outfile /home/centos/illumina/TEST_FUSION/STAR-Fusion-Tutorial/STAR-Fusion_outdir/FusionInspector-validate/finspector.fusion_inspector_web.json --file_prefix finspector
  File "/home/centos/illumina/TEST_FUSION/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py", line 156
    print C_ARG_INCLUDE_TRINITY + " was given but one of the following files are expected to exist and did not:" + " or ".join([ C_STR_INCLUDE_TRINITY_BED, C_STR_INCLUDE_TRINITY_BED_GZ ])
                              ^
SyntaxError: invalid syntax
Traceback (most recent call last):
  File "/home/centos/illumina/TEST_FUSION/STAR-Fusion/FusionInspector/FusionInspector", line 931, in <module>
    FusionInspector().run()
  File "/home/centos/illumina/TEST_FUSION/STAR-Fusion/FusionInspector/FusionInspector", line 727, in run
    pipeliner.run()
  File "/home/centos/illumina/TEST_FUSION/STAR-Fusion/FusionInspector/PyLib/Pipeliner.py", line 53, in run
    run_cmd(cmd.get_cmd())
  File "/home/centos/illumina/TEST_FUSION/STAR-Fusion/FusionInspector/PyLib/Pipeliner.py", line 17, in run_cmd
    subprocess.check_call(cmd, shell=True)
  File "/home/centos/miniconda3/envs/tutorial_fusion/lib/python3.6/subprocess.py", line 291, in check_call
    raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '/home/centos/illumina/TEST_FUSION/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /home/centos/illumina/TEST_FUSION/STAR-Fusion-Tutorial/STAR-Fusion_outdir/FusionInspector-validate --json_outfile /home/centos/illumina/TEST_FUSION/STAR-Fusion-Tutorial/STAR-Fusion_outdir/FusionInspector-validate/finspector.fusion_inspector_web.json --file_prefix finspector' returned non-zero exit status 1.
Error, cmd: /home/centos/illumina/TEST_FUSION/STAR-Fusion/FusionInspector/FusionInspector --fusions star-fusion.fusion_predictions.abridged.tsv  --out_prefix finspector  --min_junction_reads 1  --min_novel_junction_support 3  --min_spanning_frags_only 5  --prep_for_IGV  --max_promiscuity 10  --out_dir /home/centos/illumina/TEST_FUSION/STAR-Fusion-Tutorial/STAR-Fusion_outdir/FusionInspector-validate  --genome_lib_dir /home/centos/illumina/TEST_FUSION/STAR-Fusion-Tutorial/ctat_genome_lib_build_dir  --CPU 4  --left_fq /home/centos/illumina/TEST_FUSION/STAR-Fusion-Tutorial/rnaseq_1.fastq.gz --right_fq /home/centos/illumina/TEST_FUSION/STAR-Fusion-Tutorial/rnaseq_2.fastq.gz  --annotate  died with ret 256 No such file or directory at /home/centos/illumina/TEST_FUSION/STAR-Fusion/PerlLib/Pipeliner.pm line 178.
	Pipeliner::run(Pipeliner=HASH(0x10123c0)) called at /home/centos/illumina/TEST_FUSION/STAR-Fusion//STAR-Fusion line 734

[brianjohnhaas]

It could be a python version issue. I think for most of what's been done here, python v2.7 was used. I'll have to run some tests with python3 and update accordingly.

…

On Mon, Mar 19, 2018 at 10:12 AM, bioinfo-dirty-jobs < ***@***.***> wrote: I try to use the last version from github: Here you have the error: CMD: /home/centos/illumina/TEST_FUSION/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /home/centos/illumina/TEST_FUSION/STAR-Fusion-Tutorial/rnaseq_1.fastq.gz /home/centos/illumina/TEST_FUSION/STAR-Fusion-Tutorial/STAR-Fusion_outdir/FusionInspector-validate/finspector.fusion_predictions.final.abridged > /home/centos/illumina/TEST_FUSION/STAR-Fusion-Tutorial/STAR-Fusion_outdir/FusionInspector-validate/finspector.fusion_predictions.final.abridged.FFPM already processed. Skipping. Running: /home/centos/illumina/TEST_FUSION/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /home/centos/illumina/TEST_FUSION/STAR-Fusion-Tutorial/STAR-Fusion_outdir/FusionInspector-validate --json_outfile /home/centos/illumina/TEST_FUSION/STAR-Fusion-Tutorial/STAR-Fusion_outdir/FusionInspector-validate/finspector.fusion_inspector_web.json --file_prefix finspector File "/home/centos/illumina/TEST_FUSION/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py", line 156 print C_ARG_INCLUDE_TRINITY + " was given but one of the following files are expected to exist and did not:" + " or ".join([ C_STR_INCLUDE_TRINITY_BED, C_STR_INCLUDE_TRINITY_BED_GZ ]) ^ SyntaxError: invalid syntax Traceback (most recent call last): File "/home/centos/illumina/TEST_FUSION/STAR-Fusion/FusionInspector/FusionInspector", line 931, in <module> FusionInspector().run() File "/home/centos/illumina/TEST_FUSION/STAR-Fusion/FusionInspector/FusionInspector", line 727, in run pipeliner.run() File "/home/centos/illumina/TEST_FUSION/STAR-Fusion/FusionInspector/PyLib/Pipeliner.py", line 53, in run run_cmd(cmd.get_cmd()) File "/home/centos/illumina/TEST_FUSION/STAR-Fusion/FusionInspector/PyLib/Pipeliner.py", line 17, in run_cmd subprocess.check_call(cmd, shell=True) File "/home/centos/miniconda3/envs/tutorial_fusion/lib/python3.6/subprocess.py", line 291, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command '/home/centos/illumina/TEST_FUSION/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /home/centos/illumina/TEST_FUSION/STAR-Fusion-Tutorial/STAR-Fusion_outdir/FusionInspector-validate --json_outfile /home/centos/illumina/TEST_FUSION/STAR-Fusion-Tutorial/STAR-Fusion_outdir/FusionInspector-validate/finspector.fusion_inspector_web.json --file_prefix finspector' returned non-zero exit status 1. Error, cmd: /home/centos/illumina/TEST_FUSION/STAR-Fusion/FusionInspector/FusionInspector --fusions star-fusion.fusion_predictions.abridged.tsv --out_prefix finspector --min_junction_reads 1 --min_novel_junction_support 3 --min_spanning_frags_only 5 --prep_for_IGV --max_promiscuity 10 --out_dir /home/centos/illumina/TEST_FUSION/STAR-Fusion-Tutorial/STAR-Fusion_outdir/FusionInspector-validate --genome_lib_dir /home/centos/illumina/TEST_FUSION/STAR-Fusion-Tutorial/ctat_genome_lib_build_dir --CPU 4 --left_fq /home/centos/illumina/TEST_FUSION/STAR-Fusion-Tutorial/rnaseq_1.fastq.gz --right_fq /home/centos/illumina/TEST_FUSION/STAR-Fusion-Tutorial/rnaseq_2.fastq.gz --annotate died with ret 256 No such file or directory at /home/centos/illumina/TEST_FUSION/STAR-Fusion/PerlLib/Pipeliner.pm line 178. Pipeliner::run(Pipeliner=HASH(0x10123c0)) called at /home/centos/illumina/TEST_FUSION/STAR-Fusion//STAR-Fusion line 734 — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#1 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AHMVX3CWtShq5Me7ovADtznmhYThRRBQks5tf7ywgaJpZM4SwC5i> .

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

[Martaprf]

I have the follow error I don´t know why :
Running CMD: /opt/STAR-Fusion-v1.5.0/util/STAR-Fusion.map_chimeric_reads_to_genes --genome_lib_dir /home/mferreira/annotations/GRCh37_v19_CTAT_lib_Feb092018/ctat_genome_lib_build_dir -J Chimeric.out.junction > /home/mferreira/Goncalo_project/gene_fusion/fastq/star_fusion_outdir/star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt
IntervalTree.c: loadable library and perl binaries are mismatched (got handshake key 0xdb00080, needed 0xde00080)
Error, cmd: /opt/STAR-Fusion-v1.5.0/util/STAR-Fusion.map_chimeric_reads_to_genes --genome_lib_dir /home/mferreira/annotations/GRCh37_v19_CTAT_lib_Feb092018/ctat_genome_lib_build_dir -J Chimeric.out.junction > /home/mferreira/Goncalo_project/gene_fusion/fastq/star_fusion_outdir/star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt died with ret 256 No such file or directory at /opt/STAR-Fusion-v1.5.0/PerlLib/Pipeliner.pm line 181.
Pipeliner::run(Pipeliner=HASH(0x1c7e240)) called at /opt/STAR-Fusion-v1.5.0/STAR-Fusion line 676

Can you help me with as fixed this?

[brianjohnhaas]

Hi, Try running 'make clean && make' in the STAR-Fusion base directory and then try again. best, ~brian

…

On Wed, Jan 23, 2019 at 6:04 AM Martaprf ***@***.***> wrote: I have the follow error I don´t know why : Running CMD: /opt/STAR-Fusion-v1.5.0/util/STAR-Fusion.map_chimeric_reads_to_genes --genome_lib_dir /home/mferreira/annotations/GRCh37_v19_CTAT_lib_Feb092018/ctat_genome_lib_build_dir -J Chimeric.out.junction > /home/mferreira/Goncalo_project/gene_fusion/fastq/star_fusion_outdir/star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt IntervalTree.c: loadable library and perl binaries are mismatched (got handshake key 0xdb00080, needed 0xde00080) Error, cmd: /opt/STAR-Fusion-v1.5.0/util/STAR-Fusion.map_chimeric_reads_to_genes --genome_lib_dir /home/mferreira/annotations/GRCh37_v19_CTAT_lib_Feb092018/ctat_genome_lib_build_dir -J Chimeric.out.junction > /home/mferreira/Goncalo_project/gene_fusion/fastq/star_fusion_outdir/star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt died with ret 256 No such file or directory at /opt/STAR-Fusion-v1.5.0/PerlLib/Pipeliner.pm line 181. Pipeliner::run(Pipeliner=HASH(0x1c7e240)) called at /opt/STAR-Fusion-v1.5.0/STAR-Fusion line 676 Can you help me with as fixed this? — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#1 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AHMVXxXgrKhww3JSgdLTVTOtUFudD_foks5vGEGogaJpZM4SwC5i> .

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

[Martaprf]

Thanks, but now appears this one:

• Running CMD: /home/mferreira/programs/STAR-Fusion-v1.5.0/util/STAR-Fusion.handle_multimapping_reads -J /home/mferreira/Goncalo_project/gene_fusion/fastq/star_fusion_outdir/star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --genome_lib_dir /home/mferreira/annotations/GRCh37_v19_CTAT_lib_Feb092018/ctat_genome_lib_build_dir -M 50 --filt_file /home/mferreira/Goncalo_project/gene_fusion/fastq/star_fusion_outdir/star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.fail > /home/mferreira/Goncalo_project/gene_fusion/fastq/star_fusion_outdir/star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass
  perl: symbol lookup error: /home/mferreira/anaconda3/lib/site_perl/5.26.2/x86_64-linux-thread-multi/auto/DB_File/DB_File.so: undefined symbol: db_version
  Error, cmd: /home/mferreira/programs/STAR-Fusion-v1.5.0/util/STAR-Fusion.handle_multimapping_reads -J /home/mferreira/Goncalo_project/gene_fusion/fastq/star_fusion_outdir/star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --genome_lib_dir /home/mferreira/annotations/GRCh37_v19_CTAT_lib_Feb092018/ctat_genome_lib_build_dir -M 50 --filt_file /home/mferreira/Goncalo_project/gene_fusion/fastq/star_fusion_outdir/star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.fail > /home/mferreira/Goncalo_project/gene_fusion/fastq/star_fusion_outdir/star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass died with ret 32512 No such file or directory at /home/mferreira/programs/STAR-Fusion-v1.5.0/PerlLib/Pipeliner.pm line 181.
  Pipeliner::run(Pipeliner=HASH(0xe91370)) called at /home/mferreira/programs/STAR-Fusion-v1.5.0/STAR-Fusion line 676

Whats going on? :|

[brianjohnhaas]

It looks like your installation of the perl modulel DB_File might be out of date. Try re-installing this: https://perldoc.perl.org/DB_File.html and let's see if it works. Note, if you can use Docker, it might be easier to just use our Docker image and you won't have to bother with these other installation issues. best, ~b

…

On Wed, Jan 23, 2019 at 10:03 AM Martaprf ***@***.***> wrote: Thanks, but now appears this one: - Running CMD: /home/mferreira/programs/STAR-Fusion-v1.5.0/util/STAR-Fusion.handle_multimapping_reads -J /home/mferreira/Goncalo_project/gene_fusion/fastq/star_fusion_outdir/star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --genome_lib_dir /home/mferreira/annotations/GRCh37_v19_CTAT_lib_Feb092018/ctat_genome_lib_build_dir -M 50 --filt_file /home/mferreira/Goncalo_project/gene_fusion/fastq/star_fusion_outdir/star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.fail > /home/mferreira/Goncalo_project/gene_fusion/fastq/star_fusion_outdir/star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass perl: symbol lookup error: /home/mferreira/anaconda3/lib/site_perl/5.26.2/x86_64-linux-thread-multi/auto/DB_File/DB_File.so: undefined symbol: db_version Error, cmd: /home/mferreira/programs/STAR-Fusion-v1.5.0/util/STAR-Fusion.handle_multimapping_reads -J /home/mferreira/Goncalo_project/gene_fusion/fastq/star_fusion_outdir/star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --genome_lib_dir /home/mferreira/annotations/GRCh37_v19_CTAT_lib_Feb092018/ctat_genome_lib_build_dir -M 50 --filt_file /home/mferreira/Goncalo_project/gene_fusion/fastq/star_fusion_outdir/star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.fail > /home/mferreira/Goncalo_project/gene_fusion/fastq/star_fusion_outdir/star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass died with ret 32512 No such file or directory at /home/mferreira/programs/STAR-Fusion-v1.5.0/PerlLib/Pipeliner.pm line 181. Pipeliner::run(Pipeliner=HASH(0xe91370)) called at /home/mferreira/programs/STAR-Fusion-v1.5.0/STAR-Fusion line 676 Whats going on? :| — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#1 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AHMVX-kWvh9t7cXpHx6y_OTzbUg-MVkIks5vGHnDgaJpZM4SwC5i> .

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

[Martaprf]

I can´t run the docker, and now appears the first error again :|

Error, cmd: /home/mferreira/programs/STAR-Fusion-v1.5.0/util/STAR-Fusion.handle_multimapping_reads -J /home/mferreira/Goncalo_project/gene_fusion/fastq/star_fusion_outdir/star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --genome_lib_dir /home/mferreira/annotations/GRCh37_v19_CTAT_lib_Feb092018/ctat_genome_lib_build_dir -M 50 --filt_file /home/mferreira/Goncalo_project/gene_fusion/fastq/star_fusion_outdir/star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.fail > /home/mferreira/Goncalo_project/gene_fusion/fastq/star_fusion_outdir/star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass died with ret 32512 No such file or directory at /home/mferreira/programs/STAR-Fusion-v1.5.0/PerlLib/Pipeliner.pm line 181.
Pipeliner::run(Pipeliner=HASH(0x1f953a0)) called at /home/mferreira/programs/STAR-Fusion-v1.5.0/STAR-Fusion line 676

Thanks for your help!

[brianjohnhaas]

hi, this looks like a different kind of error. I'd suggest rerunning in a clean workspace so it doesn't try to resume from an earlier failure. best, ~b

…

On Wed, Jan 23, 2019 at 12:43 PM Martaprf ***@***.***> wrote: I can´t run the docker, and now appears the first error again :| Error, cmd: /home/mferreira/programs/STAR-Fusion-v1.5.0/util/STAR-Fusion.handle_multimapping_reads -J /home/mferreira/Goncalo_project/gene_fusion/fastq/star_fusion_outdir/star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --genome_lib_dir /home/mferreira/annotations/GRCh37_v19_CTAT_lib_Feb092018/ctat_genome_lib_build_dir -M 50 --filt_file /home/mferreira/Goncalo_project/gene_fusion/fastq/star_fusion_outdir/star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.fail > /home/mferreira/Goncalo_project/gene_fusion/fastq/star_fusion_outdir/star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass died with ret 32512 No such file or directory at /home/mferreira/programs/STAR-Fusion-v1.5.0/PerlLib/Pipeliner.pm line 181. Pipeliner::run(Pipeliner=HASH(0x1f953a0)) called at /home/mferreira/programs/STAR-Fusion-v1.5.0/STAR-Fusion line 676 Thanks for your help! — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#1 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AHMVX-j7IJJO0uN_sZYlxredjjPDu1yAks5vGJ9YgaJpZM4SwC5i> .

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