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ERROR when running FusionInspector #80

Closed InnoDing closed 4 months ago

InnoDing commented 4 months ago

Hi! The programme gives me an error when I run FusionInspector Here is my command: 

/mnt/inspurfs/home/weijk/anaconda3/envs/star-fusion/lib/STAR-Fusion/FusionInspector/FusionInspector --fusions /mnt/inspurfs/home/weijk/liuxinpeng/results/cr/Cr1cell-1/STAR-Fusion_outdir/star-fusion.fusion_predictions.abridged.tsv --out_prefix finspector --vis --include_Trinity --output_dir /mnt/inspurfs/home/weijk/liuxinpeng/results/Cr1cell-1/STAR-Fusion_outdir/FusionInspector-validate --genome_lib_dir /mnt/inspurfs/home/weijk/liuxinpeng/ciona1lib --CPU 4 --left_fq /mnt/inspurfs/home/weijk/Cr/Cr1cell-1/Cr1cell-1_1.fq.gz --right_fq /mnt/inspurfs/home/weijk/Cr/Cr1cell-1/Cr1cell-1_2.fq.gz

Here is the error information:

All commands completed successfully. :-)

succeeded(32), failed(2)   94.4444% completed.    

All commands completed successfully. :-)

succeeded(33), failed(2)   97.2222% completed.    

All commands completed successfully. :-)

succeeded(34), failed(2)   100% completed.    

We are sorry, commands in file: [FailedCommands] failed.  :-( 

Error, cmd: ParaFly -c trinity_GG.cmds -CPU 4 -v  died with ret 256 at /mnt/inspurfs/home/public/miniconda3/opt/trinity-2.1.1/Trinity line 2183.
Error: Command '/mnt/inspurfs/home/public/miniconda3/opt/trinity-2.1.1/Trinity --genome_guided_bam /mnt/inspurfs/home/weijk/liuxinpeng/results/Cr1cell-1/STAR-Fusion_outdir/FusionInspector-validate/finspector.consolidated.bam --max_memory 20G --genome_guided_max_intron 1000000 --CPU 4 --min_contig_length 100  --output /mnt/inspurfs/home/weijk/liuxinpeng/results/Cr1cell-1/STAR-Fusion_outdir/FusionInspector-validate/fi_workdir/trinity_GG' returned non-zero exit status 2., exit val: 2
Error, command: [ /mnt/inspurfs/home/public/miniconda3/opt/trinity-2.1.1/Trinity --genome_guided_bam /mnt/inspurfs/home/weijk/liuxinpeng/results/Cr1cell-1/STAR-Fusion_outdir/FusionInspector-validate/finspector.consolidated.bam --max_memory 20G --genome_guided_max_intron 1000000 --CPU 4 --min_contig_length 100  --output /mnt/inspurfs/home/weijk/liuxinpeng/results/Cr1cell-1/STAR-Fusion_outdir/FusionInspector-validate/fi_workdir/trinity_GG ] failed, stack trace: [ st: file:/mnt/inspurfs/home/weijk/anaconda3/envs/star-fusion/lib/STAR-Fusion/FusionInspector/PyLib/Pipeliner.py, lineno:86
st: file:/mnt/inspurfs/home/weijk/anaconda3/envs/star-fusion/lib/STAR-Fusion/FusionInspector/FusionInspector, lineno:1078
st: file:/mnt/inspurfs/home/weijk/anaconda3/envs/star-fusion/lib/STAR-Fusion/FusionInspector/FusionInspector, lineno:1942
 ] 
Traceback (most recent call last):
  File "/mnt/inspurfs/home/weijk/anaconda3/envs/star-fusion/lib/STAR-Fusion/FusionInspector/FusionInspector", line 1942, in <module>
    FusionInspector().run()
  File "/mnt/inspurfs/home/weijk/anaconda3/envs/star-fusion/lib/STAR-Fusion/FusionInspector/FusionInspector", line 1516, in run
    pipeliner.run()
  File "/mnt/inspurfs/home/weijk/anaconda3/envs/star-fusion/lib/STAR-Fusion/FusionInspector/PyLib/Pipeliner.py", line 71, in run
    cmd.run(checkpoint_dir)
  File "/mnt/inspurfs/home/weijk/anaconda3/envs/star-fusion/lib/STAR-Fusion/FusionInspector/PyLib/Pipeliner.py", line 132, in run
    raise RuntimeError(errmsg)
RuntimeError: Error, command: [ /mnt/inspurfs/home/public/miniconda3/opt/trinity-2.1.1/Trinity --genome_guided_bam /mnt/inspurfs/home/weijk/liuxinpeng/results/Cr1cell-1/STAR-Fusion_outdir/FusionInspector-validate/finspector.consolidated.bam --max_memory 20G --genome_guided_max_intron 1000000 --CPU 4 --min_contig_length 100  --output /mnt/inspurfs/home/weijk/liuxinpeng/results/Cr1cell-1/STAR-Fusion_outdir/FusionInspector-validate/fi_workdir/trinity_GG ] failed, stack trace: [ st: file:/mnt/inspurfs/home/weijk/anaconda3/envs/star-fusion/lib/STAR-Fusion/FusionInspector/PyLib/Pipeliner.py, lineno:86
st: file:/mnt/inspurfs/home/weijk/anaconda3/envs/star-fusion/lib/STAR-Fusion/FusionInspector/FusionInspector, lineno:1078
st: file:/mnt/inspurfs/home/weijk/anaconda3/envs/star-fusion/lib/STAR-Fusion/FusionInspector/FusionInspector, lineno:1942
 ]

And I can not find the 3 files :finspector.gmap_trinity_GG.fusions.fasta, finspector.gmap_trinity_GG.fusions.gff3, finspector.gmap_trinity_GG.fusions.gff3.bed.sorted.bed.gz

Thanks!

brianjohnhaas commented 4 months ago

Hi,

It looks like a couple of the Trinity jobs failed for some reason. If you find those failed Trinity commands, you could try running them directly to see what the issue is.

Otherwise, you can just drop the --include_Trinity parameter and it should wrap up with everything w/o the Trinity results.

best,

Brian

On Tue, Mar 5, 2024 at 3:29 AM InnoDing @.***> wrote:

Hi! The programme gives me an error when I run FusionInspector Here is my command:

/mnt/inspurfs/home/weijk/anaconda3/envs/star-fusion/lib/STAR-Fusion/FusionInspector/FusionInspector --fusions /mnt/inspurfs/home/weijk/liuxinpeng/results/cr/Cr1cell-1/STAR-Fusion_outdir/star-fusion.fusion_predictions.abridged.tsv --out_prefix finspector --vis --include_Trinity --output_dir /mnt/inspurfs/home/weijk/liuxinpeng/results/Cr1cell-1/STAR-Fusion_outdir/FusionInspector-validate --genome_lib_dir /mnt/inspurfs/home/weijk/liuxinpeng/ciona1lib --CPU 4 --left_fq /mnt/inspurfs/home/weijk/Cr/Cr1cell-1/Cr1cell-1_1.fq.gz --right_fq /mnt/inspurfs/home/weijk/Cr/Cr1cell-1/Cr1cell-1_2.fq.gz

Here is the error information:

All commands completed successfully. :-)

succeeded(32), failed(2) 94.4444% completed.

All commands completed successfully. :-)

succeeded(33), failed(2) 97.2222% completed.

All commands completed successfully. :-)

succeeded(34), failed(2) 100% completed.

We are sorry, commands in file: [FailedCommands] failed. :-(

Error, cmd: ParaFly -c trinity_GG.cmds -CPU 4 -v died with ret 256 at /mnt/inspurfs/home/public/miniconda3/opt/trinity-2.1.1/Trinity line 2183. Error: Command '/mnt/inspurfs/home/public/miniconda3/opt/trinity-2.1.1/Trinity --genome_guided_bam /mnt/inspurfs/home/weijk/liuxinpeng/results/Cr1cell-1/STAR-Fusion_outdir/FusionInspector-validate/finspector.consolidated.bam --max_memory 20G --genome_guided_max_intron 1000000 --CPU 4 --min_contig_length 100 --output /mnt/inspurfs/home/weijk/liuxinpeng/results/Cr1cell-1/STAR-Fusion_outdir/FusionInspector-validate/fi_workdir/trinity_GG' returned non-zero exit status 2., exit val: 2 Error, command: [ /mnt/inspurfs/home/public/miniconda3/opt/trinity-2.1.1/Trinity --genome_guided_bam /mnt/inspurfs/home/weijk/liuxinpeng/results/Cr1cell-1/STAR-Fusion_outdir/FusionInspector-validate/finspector.consolidated.bam --max_memory 20G --genome_guided_max_intron 1000000 --CPU 4 --min_contig_length 100 --output /mnt/inspurfs/home/weijk/liuxinpeng/results/Cr1cell-1/STAR-Fusion_outdir/FusionInspector-validate/fi_workdir/trinity_GG ] failed, stack trace: [ st: file:/mnt/inspurfs/home/weijk/anaconda3/envs/star-fusion/lib/STAR-Fusion/FusionInspector/PyLib/Pipeliner.py, lineno:86 st: file:/mnt/inspurfs/home/weijk/anaconda3/envs/star-fusion/lib/STAR-Fusion/FusionInspector/FusionInspector, lineno:1078 st: file:/mnt/inspurfs/home/weijk/anaconda3/envs/star-fusion/lib/STAR-Fusion/FusionInspector/FusionInspector, lineno:1942 ] Traceback (most recent call last): File "/mnt/inspurfs/home/weijk/anaconda3/envs/star-fusion/lib/STAR-Fusion/FusionInspector/FusionInspector", line 1942, in FusionInspector().run() File "/mnt/inspurfs/home/weijk/anaconda3/envs/star-fusion/lib/STAR-Fusion/FusionInspector/FusionInspector", line 1516, in run pipeliner.run() File "/mnt/inspurfs/home/weijk/anaconda3/envs/star-fusion/lib/STAR-Fusion/FusionInspector/PyLib/Pipeliner.py", line 71, in run cmd.run(checkpoint_dir) File "/mnt/inspurfs/home/weijk/anaconda3/envs/star-fusion/lib/STAR-Fusion/FusionInspector/PyLib/Pipeliner.py", line 132, in run raise RuntimeError(errmsg) RuntimeError: Error, command: [ /mnt/inspurfs/home/public/miniconda3/opt/trinity-2.1.1/Trinity --genome_guided_bam /mnt/inspurfs/home/weijk/liuxinpeng/results/Cr1cell-1/STAR-Fusion_outdir/FusionInspector-validate/finspector.consolidated.bam --max_memory 20G --genome_guided_max_intron 1000000 --CPU 4 --min_contig_length 100 --output /mnt/inspurfs/home/weijk/liuxinpeng/results/Cr1cell-1/STAR-Fusion_outdir/FusionInspector-validate/fi_workdir/trinity_GG ] failed, stack trace: [ st: file:/mnt/inspurfs/home/weijk/anaconda3/envs/star-fusion/lib/STAR-Fusion/FusionInspector/PyLib/Pipeliner.py, lineno:86 st: file:/mnt/inspurfs/home/weijk/anaconda3/envs/star-fusion/lib/STAR-Fusion/FusionInspector/FusionInspector, lineno:1078 st: file:/mnt/inspurfs/home/weijk/anaconda3/envs/star-fusion/lib/STAR-Fusion/FusionInspector/FusionInspector, lineno:1942 ]

And I can not find the 3 files :finspector.gmap_trinity_GG.fusions.fasta, finspector.gmap_trinity_GG.fusions.gff3, finspector.gmap_trinity_GG.fusions.gff3.bed.sorted.bed.gz

Thanks!

— Reply to this email directly, view it on GitHub https://github.com/FusionInspector/FusionInspector/issues/80, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABZRKX44D6L24PD6VXRYLVTYWV66DAVCNFSM6AAAAABEGVIA76VHI2DSMVQWIX3LMV43ASLTON2WKOZSGE3DQNRQGQ4TENY . You are receiving this because you are subscribed to this thread.Message ID: @.***>

--

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

InnoDing commented 4 months ago

Thanks! I tried to delete the fusion genes that failed. And I got the Trinity-GG.fasta file this time. However, it turns out that Trinity-GG.fasta does not cotain the reconstructed transcripts I want. Here is my command:

/mnt/inspurfs/home/weijk/anaconda3/envs/star-fusion/lib/STAR-Fusion/FusionInspector/FusionInspector --fusions /mnt/inspurfs/home/weijk/liuxinpeng/results/cr/Cr1cell-1/STAR-Fusion_outdir/star-fusion.fusion_predictions.abridged.tsv --genome_lib_dir /mnt/inspurfs/home/weijk/liuxinpeng/ciona1lib --left_fq /mnt/inspurfs/home/weijk/Cr/Cr1cell-1/Cr1cell-1_1.fq.gz --right_fq /mnt/inspurfs/home/weijk/Cr/Cr1cell-1/Cr1cell-1_2.fq.gz --output_dir /mnt/inspurfs/home/weijk/liuxinpeng/results/Cr1cell-1/ --out_prefix finspector --vis --include_Trinity

Error information:

All commands completed successfully. :-)

Wednesday, March 6, 2024: 15:57:47  CMD: find Dir_*  -name '*inity.fasta'  | /mnt/inspurfs/home/public/miniconda3/opt/trinity-2.1.1/util/support_scripts/GG_partitioned_trinity_aggregator.pl TRINITY_GG > Trinity-GG.fasta.tmp

Finished. See Trinity-GG.fasta for reconstructed transcripts

Execution Time = 4.23 minutes. CMD: /mnt/inspurfs/home/public/miniconda3/opt/trinity-2.1.1/Trinity --genome_guided_bam /mnt/inspurfs/home/weijk/liuxinpeng/results/Cr1cell-1/finspector.consolidated.bam --max_memory 20G --genome_guided_max_intron 1000000 --CPU 4 --min_contig_length 100  --output /mnt/inspurfs/home/weijk/liuxinpeng/results/Cr1cell-1/fi_workdir/trinity_GG
Running: touch /mnt/inspurfs/home/weijk/liuxinpeng/results/Cr1cell-1/chckpts_dir/run_trinity.ok
Running: /mnt/inspurfs/home/public/miniconda3/opt/trinity-2.1.1/util/misc/process_GMAP_alignments_gff3_chimeras_ok.pl --genome /mnt/inspurfs/home/weijk/liuxinpeng/results/Cr1cell-1/fi_workdir/finspector.fa --transcripts /mnt/inspurfs/home/weijk/liuxinpeng/results/Cr1cell-1/fi_workdir/trinity_GG/Trinity-GG.fasta --no_chimera > /mnt/inspurfs/home/weijk/liuxinpeng/results/Cr1cell-1/fi_workdir/finspector.gmap_trinity_GG.gff3
CMD: gmap_build -D /mnt/inspurfs/home/weijk/liuxinpeng/results/Cr1cell-1/fi_workdir -T /mnt/inspurfs/home/weijk/liuxinpeng/results/Cr1cell-1/fi_workdir -d finspector.fa.gmap -k 13 /mnt/inspurfs/home/weijk/liuxinpeng/results/Cr1cell-1/fi_workdir/finspector.fa >&2
--local flag not specified, so building localdb by default
Writing files under /mnt/inspurfs/home/weijk/liuxinpeng/results/Cr1cell-1/fi_workdir
Not sorting chromosomes.  To sort chromosomes other ways, use the -s flag.
A transcript gtf, gff3, FASTA, or genes file was given, but no transcriptome name was provided with the -c flag at /mnt/inspurfs/home/weijk/anaconda3/envs/star-fusion/bin/gmap_build line 216.
Error, cmd: gmap_build -D /mnt/inspurfs/home/weijk/liuxinpeng/results/Cr1cell-1/fi_workdir -T /mnt/inspurfs/home/weijk/liuxinpeng/results/Cr1cell-1/fi_workdir -d finspector.fa.gmap -k 13 /mnt/inspurfs/home/weijk/liuxinpeng/results/Cr1cell-1/fi_workdir/finspector.fa >&2 died with ret (512) at /mnt/inspurfs/home/public/miniconda3/opt/trinity-2.1.1/util/misc/process_GMAP_alignments_gff3_chimeras_ok.pl line 108.
Error: Command '/mnt/inspurfs/home/public/miniconda3/opt/trinity-2.1.1/util/misc/process_GMAP_alignments_gff3_chimeras_ok.pl --genome /mnt/inspurfs/home/weijk/liuxinpeng/results/Cr1cell-1/fi_workdir/finspector.fa --transcripts /mnt/inspurfs/home/weijk/liuxinpeng/results/Cr1cell-1/fi_workdir/trinity_GG/Trinity-GG.fasta --no_chimera > /mnt/inspurfs/home/weijk/liuxinpeng/results/Cr1cell-1/fi_workdir/finspector.gmap_trinity_GG.gff3' returned non-zero exit status 2., exit val: 2
Error, command: [ /mnt/inspurfs/home/public/miniconda3/opt/trinity-2.1.1/util/misc/process_GMAP_alignments_gff3_chimeras_ok.pl --genome /mnt/inspurfs/home/weijk/liuxinpeng/results/Cr1cell-1/fi_workdir/finspector.fa --transcripts /mnt/inspurfs/home/weijk/liuxinpeng/results/Cr1cell-1/fi_workdir/trinity_GG/Trinity-GG.fasta --no_chimera > /mnt/inspurfs/home/weijk/liuxinpeng/results/Cr1cell-1/fi_workdir/finspector.gmap_trinity_GG.gff3 ] failed, stack trace: [ st: file:/mnt/inspurfs/home/weijk/anaconda3/envs/star-fusion/lib/STAR-Fusion/FusionInspector/PyLib/Pipeliner.py, lineno:86
st: file:/mnt/inspurfs/home/weijk/anaconda3/envs/star-fusion/lib/STAR-Fusion/FusionInspector/FusionInspector, lineno:1722
st: file:/mnt/inspurfs/home/weijk/anaconda3/envs/star-fusion/lib/STAR-Fusion/FusionInspector/FusionInspector, lineno:1081
st: file:/mnt/inspurfs/home/weijk/anaconda3/envs/star-fusion/lib/STAR-Fusion/FusionInspector/FusionInspector, lineno:1942
 ] 
Traceback (most recent call last):
  File "/mnt/inspurfs/home/weijk/anaconda3/envs/star-fusion/lib/STAR-Fusion/FusionInspector/FusionInspector", line 1942, in <module>
    FusionInspector().run()
  File "/mnt/inspurfs/home/weijk/anaconda3/envs/star-fusion/lib/STAR-Fusion/FusionInspector/FusionInspector", line 1516, in run
    pipeliner.run()
  File "/mnt/inspurfs/home/weijk/anaconda3/envs/star-fusion/lib/STAR-Fusion/FusionInspector/PyLib/Pipeliner.py", line 71, in run
    cmd.run(checkpoint_dir)
  File "/mnt/inspurfs/home/weijk/anaconda3/envs/star-fusion/lib/STAR-Fusion/FusionInspector/PyLib/Pipeliner.py", line 132, in run
    raise RuntimeError(errmsg)
RuntimeError: Error, command: [ /mnt/inspurfs/home/public/miniconda3/opt/trinity-2.1.1/util/misc/process_GMAP_alignments_gff3_chimeras_ok.pl --genome /mnt/inspurfs/home/weijk/liuxinpeng/results/Cr1cell-1/fi_workdir/finspector.fa --transcripts /mnt/inspurfs/home/weijk/liuxinpeng/results/Cr1cell-1/fi_workdir/trinity_GG/Trinity-GG.fasta --no_chimera > /mnt/inspurfs/home/weijk/liuxinpeng/results/Cr1cell-1/fi_workdir/finspector.gmap_trinity_GG.gff3 ] failed, stack trace: [ st: file:/mnt/inspurfs/home/weijk/anaconda3/envs/star-fusion/lib/STAR-Fusion/FusionInspector/PyLib/Pipeliner.py, lineno:86
st: file:/mnt/inspurfs/home/weijk/anaconda3/envs/star-fusion/lib/STAR-Fusion/FusionInspector/FusionInspector, lineno:1722
st: file:/mnt/inspurfs/home/weijk/anaconda3/envs/star-fusion/lib/STAR-Fusion/FusionInspector/FusionInspector, lineno:1081
st: file:/mnt/inspurfs/home/weijk/anaconda3/envs/star-fusion/lib/STAR-Fusion/FusionInspector/FusionInspector, lineno:1942
 ]

Trinity-GG.fasta file:

>TRINITY_GG_1_c0_g1_i1 len=306 path=[592:0-56 593:57-80 594:81-305] [-1, 592, 593, 594, -2]
AATTTGAACTGTAGCTATGAACGTTTGACATTCGAAAATAAACGCAGGTGACCGATCAAG
TGACGTCAAAGAAGCGAATTTTTCTCGCGATAATATTGTTAATACAACTCGTGTCAGGTC
CAGTTTAATCCGGGAACTCTTTAGTGGCGAGTTTTTAACACCAAAAGTTCATTTTAATTT
CCAACCTATACTCTTTATATATATGTCTGTCATTCCAATATAAGTGCTACTACTTCGACC
CGAGCGCAAATATTTTTAGCAGACATTTAATGTTTACGTGGAAACCCTTTACGTCCAGCT
GCCACA
>TRINITY_GG_1_c2_g1_i1 len=106 path=[25877:0-41 25878:42-68 25879:69-105] [-1, 25877, 25878, 25879, -2]
CGCCACAGCGGAGCCATTCTTTTGCGCAATACAAATTGTCGTGAATGGTAGCACGATCAA
ATTACAACGGACTTATGCGGGGACTTCCGTATATGTTGACTCCCTT

But the star-fusion.fusion_predictions.abridged.tsv I provide is like this:

#FusionName JunctionReadCount   SpanningFragCount   est_J   est_S   SpliceType  LeftGene    LeftBreakpoint  RightGene   RightBreakpoint LargeAnchorSupport  FFPM    LeftBreakDinuc  LeftBreakEntropy    RightBreakDinuc RightBreakEntropy   annots
LOC108950094--LOC100181121  593 154 593.00  154.00  INCL_NON_REF_SPLICE LOC108950094    NC_020166.2:6436087:+   LOC100181121    NW_004190420.2:909988:- YES_LDAS    9.6566  GT  1.8892  AG  1.8295  ["INTERCHROMOSOMAL[NC_020166.2--NW_004190420.2]"]
LOC113474372--LOC100180284  167 147 167.00  147.00  INCL_NON_REF_SPLICE LOC113474372    NC_020172.2:5113274:-   LOC100180284    NW_004191496.1:9547:+   YES_LDAS    4.0591  GT  1.7819  AG  1.8323  ["INTERCHROMOSOMAL[NC_020172.2--NW_004191496.1]"]
LOC100181816--LOC100185740  117 73  117.00  73.00   INCL_NON_REF_SPLICE LOC100181816    NW_004190442.2:2593:-   LOC100185740    NW_004191428.1:1083:+   YES_LDAS    2.4562  GT  1.6895  AG  1.8295  ["INTERCHROMOSOMAL[NW_004190442.2--NW_004191428.1]"]
LOC100183329--LOC100177674  23  3   23.00   3.00    ONLY_REF_SPLICE LOC100183329    NW_004191539.1:17278:-  LOC100177674    NC_020177.2:2595491:-   YES_LDAS    0.3361  GT  1.5546  ag  2.0729  ["INTERCHROMOSOMAL[NW_004191539.1--NC_020177.2]"]

What have I got? How can I fix it?

Best,

Liu

brianjohnhaas commented 4 months ago

Hi,

The Trinity reconstructions don't always provide consistent support and but it will report when it does find evidence. If the software installation is continuing to give you issues, try using our singularity image: https://github.com/STAR-Fusion/STAR-Fusion/wiki#want-to-use-singularity

This will include the latest version of the software, which should use minimap2 instead of gmap too.

Hope this helps,

Brian

On Wed, Mar 6, 2024 at 3:19 AM InnoDing @.***> wrote:

Thanks! I tried to delete the fusion genes that failed. And I got the Trinity-GG.fasta file this time. However, it turns out that Trinity-GG.fasta does not cotain the reconstructed transcripts I want. Here is my command:

/mnt/inspurfs/home/weijk/anaconda3/envs/star-fusion/lib/STAR-Fusion/FusionInspector/FusionInspector --fusions /mnt/inspurfs/home/weijk/liuxinpeng/results/cr/Cr1cell-1/STAR-Fusion_outdir/star-fusion.fusion_predictions.abridged.tsv --genome_lib_dir /mnt/inspurfs/home/weijk/liuxinpeng/ciona1lib --left_fq /mnt/inspurfs/home/weijk/Cr/Cr1cell-1/Cr1cell-1_1.fq.gz --right_fq /mnt/inspurfs/home/weijk/Cr/Cr1cell-1/Cr1cell-1_2.fq.gz --output_dir /mnt/inspurfs/home/weijk/liuxinpeng/results/Cr1cell-1/ --out_prefix finspector --vis --include_Trinity

Error information:

All commands completed successfully. :-)

Wednesday, March 6, 2024: 15:57:47 CMD: find Dir_ -name 'inity.fasta' | /mnt/inspurfs/home/public/miniconda3/opt/trinity-2.1.1/util/support_scripts/GG_partitioned_trinity_aggregator.pl TRINITY_GG > Trinity-GG.fasta.tmp

Finished. See Trinity-GG.fasta for reconstructed transcripts

Execution Time = 4.23 minutes. CMD: /mnt/inspurfs/home/public/miniconda3/opt/trinity-2.1.1/Trinity --genome_guided_bam /mnt/inspurfs/home/weijk/liuxinpeng/results/Cr1cell-1/finspector.consolidated.bam --max_memory 20G --genome_guided_max_intron 1000000 --CPU 4 --min_contig_length 100 --output /mnt/inspurfs/home/weijk/liuxinpeng/results/Cr1cell-1/fi_workdir/trinity_GG Running: touch /mnt/inspurfs/home/weijk/liuxinpeng/results/Cr1cell-1/chckpts_dir/run_trinity.ok Running: /mnt/inspurfs/home/public/miniconda3/opt/trinity-2.1.1/util/misc/process_GMAP_alignments_gff3_chimeras_ok.pl --genome /mnt/inspurfs/home/weijk/liuxinpeng/results/Cr1cell-1/fi_workdir/finspector.fa --transcripts /mnt/inspurfs/home/weijk/liuxinpeng/results/Cr1cell-1/fi_workdir/trinity_GG/Trinity-GG.fasta --no_chimera > /mnt/inspurfs/home/weijk/liuxinpeng/results/Cr1cell-1/fi_workdir/finspector.gmap_trinity_GG.gff3 CMD: gmap_build -D /mnt/inspurfs/home/weijk/liuxinpeng/results/Cr1cell-1/fi_workdir -T /mnt/inspurfs/home/weijk/liuxinpeng/results/Cr1cell-1/fi_workdir -d finspector.fa.gmap -k 13 /mnt/inspurfs/home/weijk/liuxinpeng/results/Cr1cell-1/fi_workdir/finspector.fa >&2 --local flag not specified, so building localdb by default Writing files under /mnt/inspurfs/home/weijk/liuxinpeng/results/Cr1cell-1/fi_workdir Not sorting chromosomes. To sort chromosomes other ways, use the -s flag. A transcript gtf, gff3, FASTA, or genes file was given, but no transcriptome name was provided with the -c flag at /mnt/inspurfs/home/weijk/anaconda3/envs/star-fusion/bin/gmap_build line 216. Error, cmd: gmap_build -D /mnt/inspurfs/home/weijk/liuxinpeng/results/Cr1cell-1/fi_workdir -T /mnt/inspurfs/home/weijk/liuxinpeng/results/Cr1cell-1/fi_workdir -d finspector.fa.gmap -k 13 /mnt/inspurfs/home/weijk/liuxinpeng/results/Cr1cell-1/fi_workdir/finspector.fa >&2 died with ret (512) at /mnt/inspurfs/home/public/miniconda3/opt/trinity-2.1.1/util/misc/process_GMAP_alignments_gff3_chimeras_ok.pl line 108. Error: Command '/mnt/inspurfs/home/public/miniconda3/opt/trinity-2.1.1/util/misc/process_GMAP_alignments_gff3_chimeras_ok.pl --genome /mnt/inspurfs/home/weijk/liuxinpeng/results/Cr1cell-1/fi_workdir/finspector.fa --transcripts /mnt/inspurfs/home/weijk/liuxinpeng/results/Cr1cell-1/fi_workdir/trinity_GG/Trinity-GG.fasta --no_chimera > /mnt/inspurfs/home/weijk/liuxinpeng/results/Cr1cell-1/fi_workdir/finspector.gmap_trinity_GG.gff3' returned non-zero exit status 2., exit val: 2 Error, command: [ /mnt/inspurfs/home/public/miniconda3/opt/trinity-2.1.1/util/misc/process_GMAP_alignments_gff3_chimeras_ok.pl --genome /mnt/inspurfs/home/weijk/liuxinpeng/results/Cr1cell-1/fi_workdir/finspector.fa --transcripts /mnt/inspurfs/home/weijk/liuxinpeng/results/Cr1cell-1/fi_workdir/trinity_GG/Trinity-GG.fasta --no_chimera > /mnt/inspurfs/home/weijk/liuxinpeng/results/Cr1cell-1/fi_workdir/finspector.gmap_trinity_GG.gff3 ] failed, stack trace: [ st: file:/mnt/inspurfs/home/weijk/anaconda3/envs/star-fusion/lib/STAR-Fusion/FusionInspector/PyLib/Pipeliner.py, lineno:86 st: file:/mnt/inspurfs/home/weijk/anaconda3/envs/star-fusion/lib/STAR-Fusion/FusionInspector/FusionInspector, lineno:1722 st: file:/mnt/inspurfs/home/weijk/anaconda3/envs/star-fusion/lib/STAR-Fusion/FusionInspector/FusionInspector, lineno:1081 st: file:/mnt/inspurfs/home/weijk/anaconda3/envs/star-fusion/lib/STAR-Fusion/FusionInspector/FusionInspector, lineno:1942 ] Traceback (most recent call last): File "/mnt/inspurfs/home/weijk/anaconda3/envs/star-fusion/lib/STAR-Fusion/FusionInspector/FusionInspector", line 1942, in FusionInspector().run() File "/mnt/inspurfs/home/weijk/anaconda3/envs/star-fusion/lib/STAR-Fusion/FusionInspector/FusionInspector", line 1516, in run pipeliner.run() File "/mnt/inspurfs/home/weijk/anaconda3/envs/star-fusion/lib/STAR-Fusion/FusionInspector/PyLib/Pipeliner.py", line 71, in run cmd.run(checkpoint_dir) File "/mnt/inspurfs/home/weijk/anaconda3/envs/star-fusion/lib/STAR-Fusion/FusionInspector/PyLib/Pipeliner.py", line 132, in run raise RuntimeError(errmsg) RuntimeError: Error, command: [ /mnt/inspurfs/home/public/miniconda3/opt/trinity-2.1.1/util/misc/process_GMAP_alignments_gff3_chimeras_ok.pl --genome /mnt/inspurfs/home/weijk/liuxinpeng/results/Cr1cell-1/fi_workdir/finspector.fa --transcripts /mnt/inspurfs/home/weijk/liuxinpeng/results/Cr1cell-1/fi_workdir/trinity_GG/Trinity-GG.fasta --no_chimera > /mnt/inspurfs/home/weijk/liuxinpeng/results/Cr1cell-1/fi_workdir/finspector.gmap_trinity_GG.gff3 ] failed, stack trace: [ st: file:/mnt/inspurfs/home/weijk/anaconda3/envs/star-fusion/lib/STAR-Fusion/FusionInspector/PyLib/Pipeliner.py, lineno:86 st: file:/mnt/inspurfs/home/weijk/anaconda3/envs/star-fusion/lib/STAR-Fusion/FusionInspector/FusionInspector, lineno:1722 st: file:/mnt/inspurfs/home/weijk/anaconda3/envs/star-fusion/lib/STAR-Fusion/FusionInspector/FusionInspector, lineno:1081 st: file:/mnt/inspurfs/home/weijk/anaconda3/envs/star-fusion/lib/STAR-Fusion/FusionInspector/FusionInspector, lineno:1942 ]

Trinity-GG.fasta file:

TRINITY_GG_1_c0_g1_i1 len=306 path=[592:0-56 593:57-80 594:81-305] [-1, 592, 593, 594, -2] AATTTGAACTGTAGCTATGAACGTTTGACATTCGAAAATAAACGCAGGTGACCGATCAAG TGACGTCAAAGAAGCGAATTTTTCTCGCGATAATATTGTTAATACAACTCGTGTCAGGTC CAGTTTAATCCGGGAACTCTTTAGTGGCGAGTTTTTAACACCAAAAGTTCATTTTAATTT CCAACCTATACTCTTTATATATATGTCTGTCATTCCAATATAAGTGCTACTACTTCGACC CGAGCGCAAATATTTTTAGCAGACATTTAATGTTTACGTGGAAACCCTTTACGTCCAGCT GCCACA TRINITY_GG_1_c2_g1_i1 len=106 path=[25877:0-41 25878:42-68 25879:69-105] [-1, 25877, 25878, 25879, -2] CGCCACAGCGGAGCCATTCTTTTGCGCAATACAAATTGTCGTGAATGGTAGCACGATCAA ATTACAACGGACTTATGCGGGGACTTCCGTATATGTTGACTCCCTT

But the star-fusion.fusion_predictions.abridged.tsv I provide is like this:

FusionName JunctionReadCount SpanningFragCount est_J est_S SpliceType LeftGene LeftBreakpoint RightGene RightBreakpoint LargeAnchorSupport FFPM LeftBreakDinuc LeftBreakEntropy RightBreakDinuc RightBreakEntropy annots

LOC108950094--LOC100181121 593 154 593.00 154.00 INCL_NON_REF_SPLICE LOC108950094 NC_020166.2:6436087:+ LOC100181121 NW_004190420.2:909988:- YES_LDAS 9.6566 GT 1.8892 AG 1.8295 ["INTERCHROMOSOMAL[NC_020166.2--NW_004190420.2]"] LOC113474372--LOC100180284 167 147 167.00 147.00 INCL_NON_REF_SPLICE LOC113474372 NC_020172.2:5113274:- LOC100180284 NW_004191496.1:9547:+ YES_LDAS 4.0591 GT 1.7819 AG 1.8323 ["INTERCHROMOSOMAL[NC_020172.2--NW_004191496.1]"] LOC100181816--LOC100185740 117 73 117.00 73.00 INCL_NON_REF_SPLICE LOC100181816 NW_004190442.2:2593:- LOC100185740 NW_004191428.1:1083:+ YES_LDAS 2.4562 GT 1.6895 AG 1.8295 ["INTERCHROMOSOMAL[NW_004190442.2--NW_004191428.1]"] LOC100183329--LOC100177674 23 3 23.00 3.00 ONLY_REF_SPLICE LOC100183329 NW_004191539.1:17278:- LOC100177674 NC_020177.2:2595491:- YES_LDAS 0.3361 GT 1.5546 ag 2.0729 ["INTERCHROMOSOMAL[NW_004191539.1--NC_020177.2]"]

What have I got? How can I fix it?

Best,

Liu

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

InnoDing commented 4 months ago

Thanks