Open EsperanzaDai opened 1 month ago
Hi,
I think this somewhat rare issue should be resolved in the latest STAR software version, but that's not included in the current singularity or docker images. I can make a patch for it and see if that helps.... more soon.
On Wed, Jun 26, 2024 at 3:51 PM EsperanzaDai @.***> wrote:
I tried to run the example data provided in the git repo and got the following error. I am using the trinityfusion.v0.4.0.simg.
- Running CMD: /usr/local/bin/STAR --runThreadN 4 --genomeDir /mnt/ctat/ref_genome.fa.star.idx --outSAMtype BAM SortedByCoordinate --twopassMode None --alignSJDBoverhangMin 10 --genomeSuffixLengthMax 10000 --limitBAMsortRAM 47271261705 --alignInsertionFlush Right --alignMatesGapMax 100000 --alignIntronMax 100000 --outSAMattributes All --readFilesIn /mnt/procdir/example/reads_1.fq /mnt/procdir/example/reads_2.fq --genomeFastaFiles /mnt/procdir/example/fusion_results/trinity_fusion-UC_ctat-LR-fusion/FI/fi_workdir/finspector.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /mnt/procdir/example/fusion_results/trinity_fusion-UC_ctat-LR-fusion/FI/fi_workdir/finspector.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 Jun 26 15:45:06 ..... started STAR run Jun 26 15:45:06 ..... loading genome
EXITING because of FATAL ERROR: cannot insert sequence on the fly because of strand GstrandBit problem SOLUTION: please contact STAR author at https://groups.google.com/forum/#!forum/rna-star
Jun 26 15:45:32 ...... FATAL ERROR, exiting Error, cmd: /usr/local/bin/STAR --runThreadN 4 --genomeDir /mnt/ctat/ref_genome.fa.star.idx --outSAMtype BAM SortedByCoordinate --twopassMode None --alignSJDBoverhangMin 10 --genomeSuffixLengthMax 10000 --limitBAMsortRAM 47271261705 --alignInsertionFlush Right --alignMatesGapMax 100000 --alignIntronMax 100000 --outSAMattributes All --readFilesIn /mnt/procdir/example/reads_1.fq /mnt/procdir/example/reads_2.fq --genomeFastaFiles /mnt/procdir/example/fusion_results/trinity_fusion-UC_ctat-LR-fusion/FI/fi_workdir/finspector.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /mnt/procdir/example/fusion_results/trinity_fusion-UC_ctat-LR-fusion/FI/fi_workdir/finspector.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 died with ret 26880 No such file or directory at /usr/local/src/TrinityFusion/CTAT-LR-fusion/FusionInspector/util/../PerlLib/Pipeliner.pm line 167. Pipeliner::run(Pipeliner=HASH(0x55de07ac9d98)) called at /usr/local/src/TrinityFusion/CTAT-LR-fusion/FusionInspector/util/run_FI_STAR.pl line 322 Error: Command '/usr/local/src/TrinityFusion/CTAT-LR-fusion/FusionInspector/util/run_FI_STAR.pl --genome /mnt/ctat/ref_genome.fa --patch /mnt/procdir/example/fusion_results/trinity_fusion-UC_ctat-LR-fusion/FI/fi_workdir/finspector.fa --max_mate_dist 100000 -G /mnt/procdir/example/fusion_results/trinity_fusion-UC_ctat-LR-fusion/FI/fi_workdir/finspector.gtf --CPU 4 --out_prefix finspector.star --out_dir /mnt/procdir/example/fusion_results/trinity_fusion-UC_ctat-LR-fusion/FI/fi_workdir --reads "/mnt/procdir/example/reads_1.fq /mnt/procdir/example/reads_2.fq"' returned non-zero exit status 2., exit val: 2 Error, command: [ /usr/local/src/TrinityFusion/CTAT-LR-fusion/FusionInspector/util/run_FI_STAR.pl --genome /mnt/ctat/ref_genome.fa --patch /mnt/procdir/example/fusion_results/trinity_fusion-UC_ctat-LR-fusion/FI/fi_workdir/finspector.fa --max_mate_dist 100000 -G /mnt/procdir/example/fusion_results/trinity_fusion-UC_ctat-LR-fusion/FI/fi_workdir/finspector.gtf --CPU 4 --out_prefix finspector.star --out_dir /mnt/procdir/example/fusion_results/trinity_fusion-UC_ctat-LR-fusion/FI/fi_workdir --reads "/mnt/procdir/example/reads_1.fq /mnt/procdir/example/reads_2.fq" ] failed, stack trace: [ st: file:/usr/local/src/TrinityFusion/CTAT-LR-fusion/FusionInspector/PyLib/Pipeliner.py, lineno:86 st: file:/usr/local/src/TrinityFusion/CTAT-LR-fusion/FusionInspector/FusionInspector, lineno:813 st: file:/usr/local/src/TrinityFusion/CTAT-LR-fusion/FusionInspector/FusionInspector, lineno:1967 ] Traceback (most recent call last): File "/usr/local/src/TrinityFusion/CTAT-LR-fusion/FusionInspector/FusionInspector", line 1967, in FusionInspector().run() File "/usr/local/src/TrinityFusion/CTAT-LR-fusion/FusionInspector/FusionInspector", line 1541, in run pipeliner.run() File "/usr/local/src/TrinityFusion/CTAT-LR-fusion/FusionInspector/PyLib/Pipeliner.py", line 71, in run cmd.run(checkpoint_dir) File "/usr/local/src/TrinityFusion/CTAT-LR-fusion/FusionInspector/PyLib/Pipeliner.py", line 132, in run raise RuntimeError(errmsg) RuntimeError: Error, command: [ /usr/local/src/TrinityFusion/CTAT-LR-fusion/FusionInspector/util/run_FI_STAR.pl --genome /mnt/ctat/ref_genome.fa --patch /mnt/procdir/example/fusion_results/trinity_fusion-UC_ctat-LR-fusion/FI/fi_workdir/finspector.fa --max_mate_dist 100000 -G /mnt/procdir/example/fusion_results/trinity_fusion-UC_ctat-LR-fusion/FI/fi_workdir/finspector.gtf --CPU 4 --out_prefix finspector.star --out_dir /mnt/procdir/example/fusion_results/trinity_fusion-UC_ctat-LR-fusion/FI/fi_workdir --reads "/mnt/procdir/example/reads_1.fq /mnt/procdir/example/reads_2.fq" ] failed, stack trace: [ st: file:/usr/local/src/TrinityFusion/CTAT-LR-fusion/FusionInspector/PyLib/Pipeliner.py, lineno:86 st: file:/usr/local/src/TrinityFusion/CTAT-LR-fusion/FusionInspector/FusionInspector, lineno:813 st: file:/usr/local/src/TrinityFusion/CTAT-LR-fusion/FusionInspector/FusionInspector, lineno:1967 ] Error, cmd: /usr/local/src/TrinityFusion/CTAT-LR-fusion/FusionInspector/FusionInspector --fusions /mnt/procdir/example/fusion_results/trinity_fusion-UC_ctat-LR-fusion/fusion_intermediates_dir/chimeric_read_candidates.FI_listing --genome_lib_dir /mnt/ctat/ --FI_contigs_fa /mnt/procdir/example/fusion_results/trinity_fusion-UC_ctat-LR-fusion/fusion_intermediates_dir/LR-FI_targets.fa --FI_contigs_gtf /mnt/procdir/example/fusion_results/trinity_fusion-UC_ctat-LR-fusion/fusion_intermediates_dir/LR-FI_targets.gtf --left_fq /mnt/procdir/example/reads_1.fq --right_fq /mnt/procdir/example/reads_2.fq died with ret 256 No such file or directory at /usr/local/src/TrinityFusion/CTAT-LR-fusion/PerlLib/Pipeliner.pm line 181. Pipeliner::run(Pipeliner=HASH(0x55927b3006e0)) called at /usr/local/src/TrinityFusion/CTAT-LR-fusion/ctat-LR-fusion line 540 Error, cmd: /usr/local/src/TrinityFusion/CTAT-LR-fusion/ctat-LR-fusion -T trinity_discasm/discasm.Trinity.fasta --genome_lib_dir /mnt/ctat/ --left_fq /mnt/procdir/example/reads_1.fq --right_fq /mnt/procdir/example/reads_2.fq --CPU 4 --min_J 1 --min_sumJS 2 --min_novel_junction_support 3 -o trinity_fusion-UC_ctat-LR-fusion died with ret 512 No such file or directory at /usr/local/src/TrinityFusion/PerlLib/Pipeliner.pm line 186. Pipeliner::run(Pipeliner=HASH(0x56430f87e688)) called at /usr/local/src/TrinityFusion/TrinityFusion line 283
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Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas http://broad.mit.edu/~bhaas
Thank you so much!
just need to do a bit of testing and will be ready shortly
On Wed, Jun 26, 2024 at 4:56 PM EsperanzaDai @.***> wrote:
Thank you so much!
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Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas http://broad.mit.edu/~bhaas
I've updated the version of STAR here to 2.11.b:
Hopefully this solves the problem. If it doesn't, we might need to rebuild the reference genome STAR index using that version of STAR.
best,
Brian
On Wed, Jun 26, 2024 at 7:49 PM Brian Haas @.***> wrote:
just need to do a bit of testing and will be ready shortly
On Wed, Jun 26, 2024 at 4:56 PM EsperanzaDai @.***> wrote:
Thank you so much!
— Reply to this email directly, view it on GitHub https://github.com/trinityrnaseq/TrinityFusion/issues/6#issuecomment-2192613448, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABZRKX5U25VKCB6A6Q3ZU4TZJMTH5AVCNFSM6AAAAABJ6RN7S2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCOJSGYYTGNBUHA . You are receiving this because you commented.Message ID: @.***>
--
Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas http://broad.mit.edu/~bhaas
Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas http://broad.mit.edu/~bhaas
Thank you so much! The new container with the new STAR version works!
Fantastic! Thx for the update
On Fri, Jun 28, 2024 at 1:37 PM EsperanzaDai @.***> wrote:
Thank you so much! The new container with the new STAR version works!
— Reply to this email directly, view it on GitHub https://github.com/trinityrnaseq/TrinityFusion/issues/6#issuecomment-2197379828, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABZRKX7CQEQFSAWNNZBCBM3ZJWNPDAVCNFSM6AAAAABJ6RN7S2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCOJXGM3TSOBSHA . You are receiving this because you commented.Message ID: @.***>
Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas http://broad.mit.edu/~bhaas
I tried to run the example data provided in the git repo and got the following error. I am using the trinityfusion.v0.4.0.simg.
EXITING because of FATAL ERROR: cannot insert sequence on the fly because of strand GstrandBit problem SOLUTION: please contact STAR author at https://groups.google.com/forum/#!forum/rna-star
Jun 26 15:45:32 ...... FATAL ERROR, exiting Error, cmd: /usr/local/bin/STAR --runThreadN 4 --genomeDir /mnt/ctat/ref_genome.fa.star.idx --outSAMtype BAM SortedByCoordinate --twopassMode None --alignSJDBoverhangMin 10 --genomeSuffixLengthMax 10000 --limitBAMsortRAM 47271261705 --alignInsertionFlush Right --alignMatesGapMax 100000 --alignIntronMax 100000 --outSAMattributes All --readFilesIn /mnt/procdir/example/reads_1.fq /mnt/procdir/example/reads_2.fq --genomeFastaFiles /mnt/procdir/example/fusion_results/trinity_fusion-UC_ctat-LR-fusion/FI/fi_workdir/finspector.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /mnt/procdir/example/fusion_results/trinity_fusion-UC_ctat-LR-fusion/FI/fi_workdir/finspector.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 died with ret 26880 No such file or directory at /usr/local/src/TrinityFusion/CTAT-LR-fusion/FusionInspector/util/../PerlLib/Pipeliner.pm line 167. Pipeliner::run(Pipeliner=HASH(0x55de07ac9d98)) called at /usr/local/src/TrinityFusion/CTAT-LR-fusion/FusionInspector/util/run_FI_STAR.pl line 322 Error: Command '/usr/local/src/TrinityFusion/CTAT-LR-fusion/FusionInspector/util/run_FI_STAR.pl --genome /mnt/ctat/ref_genome.fa --patch /mnt/procdir/example/fusion_results/trinity_fusion-UC_ctat-LR-fusion/FI/fi_workdir/finspector.fa --max_mate_dist 100000 -G /mnt/procdir/example/fusion_results/trinity_fusion-UC_ctat-LR-fusion/FI/fi_workdir/finspector.gtf --CPU 4 --out_prefix finspector.star --out_dir /mnt/procdir/example/fusion_results/trinity_fusion-UC_ctat-LR-fusion/FI/fi_workdir --reads "/mnt/procdir/example/reads_1.fq /mnt/procdir/example/reads_2.fq"' returned non-zero exit status 2., exit val: 2 Error, command: [ /usr/local/src/TrinityFusion/CTAT-LR-fusion/FusionInspector/util/run_FI_STAR.pl --genome /mnt/ctat/ref_genome.fa --patch /mnt/procdir/example/fusion_results/trinity_fusion-UC_ctat-LR-fusion/FI/fi_workdir/finspector.fa --max_mate_dist 100000 -G /mnt/procdir/example/fusion_results/trinity_fusion-UC_ctat-LR-fusion/FI/fi_workdir/finspector.gtf --CPU 4 --out_prefix finspector.star --out_dir /mnt/procdir/example/fusion_results/trinity_fusion-UC_ctat-LR-fusion/FI/fi_workdir --reads "/mnt/procdir/example/reads_1.fq /mnt/procdir/example/reads_2.fq" ] failed, stack trace: [ st: file:/usr/local/src/TrinityFusion/CTAT-LR-fusion/FusionInspector/PyLib/Pipeliner.py, lineno:86 st: file:/usr/local/src/TrinityFusion/CTAT-LR-fusion/FusionInspector/FusionInspector, lineno:813 st: file:/usr/local/src/TrinityFusion/CTAT-LR-fusion/FusionInspector/FusionInspector, lineno:1967 ] Traceback (most recent call last): File "/usr/local/src/TrinityFusion/CTAT-LR-fusion/FusionInspector/FusionInspector", line 1967, in
FusionInspector().run()
File "/usr/local/src/TrinityFusion/CTAT-LR-fusion/FusionInspector/FusionInspector", line 1541, in run
pipeliner.run()
File "/usr/local/src/TrinityFusion/CTAT-LR-fusion/FusionInspector/PyLib/Pipeliner.py", line 71, in run
cmd.run(checkpoint_dir)
File "/usr/local/src/TrinityFusion/CTAT-LR-fusion/FusionInspector/PyLib/Pipeliner.py", line 132, in run
raise RuntimeError(errmsg)
RuntimeError: Error, command: [ /usr/local/src/TrinityFusion/CTAT-LR-fusion/FusionInspector/util/run_FI_STAR.pl --genome /mnt/ctat/ref_genome.fa --patch /mnt/procdir/example/fusion_results/trinity_fusion-UC_ctat-LR-fusion/FI/fi_workdir/finspector.fa --max_mate_dist 100000 -G /mnt/procdir/example/fusion_results/trinity_fusion-UC_ctat-LR-fusion/FI/fi_workdir/finspector.gtf --CPU 4 --out_prefix finspector.star --out_dir /mnt/procdir/example/fusion_results/trinity_fusion-UC_ctat-LR-fusion/FI/fi_workdir --reads "/mnt/procdir/example/reads_1.fq /mnt/procdir/example/reads_2.fq" ] failed, stack trace: [ st: file:/usr/local/src/TrinityFusion/CTAT-LR-fusion/FusionInspector/PyLib/Pipeliner.py, lineno:86
st: file:/usr/local/src/TrinityFusion/CTAT-LR-fusion/FusionInspector/FusionInspector, lineno:813
st: file:/usr/local/src/TrinityFusion/CTAT-LR-fusion/FusionInspector/FusionInspector, lineno:1967
]
Error, cmd: /usr/local/src/TrinityFusion/CTAT-LR-fusion/FusionInspector/FusionInspector --fusions /mnt/procdir/example/fusion_results/trinity_fusion-UC_ctat-LR-fusion/fusion_intermediates_dir/chimeric_read_candidates.FI_listing --genome_lib_dir /mnt/ctat/ --FI_contigs_fa /mnt/procdir/example/fusion_results/trinity_fusion-UC_ctat-LR-fusion/fusion_intermediates_dir/LR-FI_targets.fa --FI_contigs_gtf /mnt/procdir/example/fusion_results/trinity_fusion-UC_ctat-LR-fusion/fusion_intermediates_dir/LR-FI_targets.gtf --left_fq /mnt/procdir/example/reads_1.fq --right_fq /mnt/procdir/example/reads_2.fq died with ret 256 No such file or directory at /usr/local/src/TrinityFusion/CTAT-LR-fusion/PerlLib/Pipeliner.pm line 181.
Pipeliner::run(Pipeliner=HASH(0x55927b3006e0)) called at /usr/local/src/TrinityFusion/CTAT-LR-fusion/ctat-LR-fusion line 540
Error, cmd: /usr/local/src/TrinityFusion/CTAT-LR-fusion/ctat-LR-fusion -T trinity_discasm/discasm.Trinity.fasta --genome_lib_dir /mnt/ctat/ --left_fq /mnt/procdir/example/reads_1.fq --right_fq /mnt/procdir/example/reads_2.fq --CPU 4 --min_J 1 --min_sumJS 2 --min_novel_junction_support 3 -o trinity_fusion-UC_ctat-LR-fusion died with ret 512 No such file or directory at /usr/local/src/TrinityFusion/PerlLib/Pipeliner.pm line 186.
Pipeliner::run(Pipeliner=HASH(0x56430f87e688)) called at /usr/local/src/TrinityFusion/TrinityFusion line 283