COMBINE-lab/salmon

Segmentation core dumped - Salmon quant

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rugilemat commented

Is the bug primarily related to salmon (bulk mode) or alevin (single-cell mode)?
Salmon
Describe the bug
419663 Segmentation fault (core dumped)
To Reproduce
Steps and data to reproduce the behavior:
Code ran:
salmon quant --ont -p 24 -t ${ref} -l U -a "007_D14_transcript.bam" "007_D1_transcript.bam" "014_D14_transcript.bam" "014_D1_transcript.bam" "069_D14_transcript.bam" "069_D1_transcript.bam" "127_D14_transcript.bam" "127_D1_transcript.bam" "36S_D14_transcript.bam" "36S_D1_transcript.bam" "SCTI_D14_transcript.bam" "SCTI_D1_transcript.bam" "SCTI_D1_2000ng_transcript.bam" "ioGLUT_D7_transcript.bam" "ioMGL_D10_transcript.bam" -o ${output}/transcripts_quant

Specifically, please provide at least the following information:

  • Which version of salmon was used? 1.10.2
  • How was salmon installed (compiled, downloaded executable, through bioconda)? module installed on HPC
  • Which reference (e.g. transcriptome) was used? gencode.v44.transcriptome (Human)
  • Which read files were used? bam
  • Which program options were used? salmon quant

Expected behavior
A clear and concise description of what you expected to happen.
Salmon quant to generate quant output.
Screenshots
If applicable, add screenshots or terminal output to help explain your problem.

Version Server Response: Not Found
# salmon (alignment-based) v1.10.2
# [ program ] => salmon 
# [ command ] => quant 
# [ ont ] => { }
# [ threads ] => { 24 }
# [ targets ] => { /scratch/users/k19022845/refgenome/gencode.v44.transcripts.fa }
# [ libType ] => { U }
# [ alignments ] => { 007_D14_transcript.bam 007_D1_transcript.bam 014_D14_transcript.bam 014_D1_transcript.bam 069_D14_transcript.bam 069_D1_transcript.bam 127_D14_transcript.bam 127_D1_transcript.bam 36S_D14_transcript.bam 36S_D1_transcript.bam SCTI_D14_transcript.bam SCTI_D1_transcript.bam SCTI_D1_2000ng_transcript.bam ioGLUT_D7_transcript.bam ioMGL_D10_transcript.bam }
# [ output ] => { /scratch/prj/ppn_microglia_mod/directrna/salmon/transcripts_quant }
Logs will be written to /scratch/prj/ppn_microglia_mod/directrna/salmon/transcripts_quant/logs
[2024-04-09 18:22:04.559] [jointLog] [info] setting maxHashResizeThreads to 24
[2024-04-09 18:22:04.559] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
Library format { type:single end, relative orientation:none, strandedness:unstranded }
[2024-04-09 18:22:04.563] [jointLog] [info] numQuantThreads = 18
parseThreads = 6
Checking that provided alignment files have consistent headers . . . done
Populating targets from aln = "007_D14_transcript.bam", fasta = "/scratch/users/k19022845/refgenome/gencode.v44.transcripts.fa" . . .done

processed 0 reads in current round[2024-04-09 18:22:15.424] [jointLog] [info] replaced 4 non-ACGT nucleotides with random nucleotides
[2024-04-09 18:22:15.581] [jointLog] [warning] read 3f6dc3db-5e41-45df-bca2-b781f076857f (length 4039 - align length 3921) has no trained error model
[2024-04-09 18:22:15.581] [jointLog] [warning] read 3f6dc3db-5e41-45df-bca2-b781f076857f (length 4039) has no trained clipping model
[2024-04-09 18:22:15.581] [jointLog] [warning] read 3f6dc3db-5e41-45df-bca2-b781f076857f (length 4039) has no trained clipping model
[2024-04-09 18:22:15.581] [jointLog] [warning] read 3f6dc3db-5e41-45df-bca2-b781f076857f (length 4039 - align length 3921) has no trained error model
[2024-04-09 18:22:15.581] [jointLog] [warning] read 3f6dc3db-5e41-45df-bca2-b781f076857f (length 4039) has no trained clipping model
[2024-04-09 18:22:15.581] [jointLog] [warning] read 3f6dc3db-5e41-45df-bca2-b781f076857f (length 4039) has no trained clipping model
[2024-04-09 18:22:15.581] [jointLog] [warning] read 3f6dc3db-5e41-45df-bca2-b781f076857f (length 4039 - align length 3921) has no trained error model
[2024-04-09 18:22:15.581] [jointLog] [warning] read 3f6dc3db-5e41-45df-bca2-b781f076857f (length 4039) has no trained clipping model
[2024-04-09 18:22:15.581] [jointLog] [warning] read 3f6dc3db-5e41-45df-bca2-b781f076857f (length 4039) has no trained clipping model
[2024-04-09 18:22:15.581] [jointLog] [warning] read 3f6dc3db-5e41-45df-bca2-b781f076857f (length 4039 - align length 3921) has no trained error model
[2024-04-09 18:22:15.581] [jointLog] [warning] read 3f6dc3db-5e41-45df-bca2-b781f076857f (length 4039) has no trained clipping model
[2024-04-09 18:22:15.581] [jointLog] [warning] read 3f6dc3db-5e41-45df-bca2-b781f076857f (length 4039) has no trained clipping model
[2024-04-09 18:22:15.581] [jointLog] [warning] read 3f6dc3db-5e41-45df-bca2-b781f076857f (length 4039 - align length 3921) has no trained error model
[2024-04-09 18:22:15.581] [jointLog] [warning] read 3f6dc3db-5e41-45df-bca2-b781f076857f (length 4039) has no trained clipping model
[2024-04-09 18:22:15.581] [jointLog] [warning] read 3f6dc3db-5e41-45df-bca2-b781f076857f (length 4039) has no trained clipping model
[2024-04-09 18:22:15.581] [jointLog] [warning] read 3f6dc3db-5e41-45df-bca2-b781f076857f (length 4039 - align length 3905) has no trained error model
[2024-04-09 18:22:15.581] [jointLog] [warning] read 3f6dc3db-5e41-45df-bca2-b781f076857f (length 4039) has no trained clipping model
[2024-04-09 18:22:15.581] [jointLog] [warning] read 3f6dc3db-5e41-45df-bca2-b781f076857f (length 4039) has no trained clipping model
[2024-04-09 18:22:15.583] [jointLog] [warning] read 6205e5a5-8cf4-4f1e-b3cf-942e5fc8856e (length 3626 - align length 3527) has no trained error model
[2024-04-09 18:22:15.583] [jointLog] [warning] read 6205e5a5-8cf4-4f1e-b3cf-942e5fc8856e (length 3626) has no trained clipping model
[2024-04-09 18:22:15.583] [jointLog] [warning] read 6205e5a5-8cf4-4f1e-b3cf-942e5fc8856e (length 3626) has no trained clipping model
[2024-04-09 18:22:15.590] [jointLog] [warning] read e225febf-502e-48ac-bb5d-924d0c397a2c (length 8594 - align length 238) has no trained error model
[2024-04-09 18:22:15.590] [jointLog] [warning] read e225febf-502e-48ac-bb5d-924d0c397a2c (length 8594) has no trained clipping model
[2024-04-09 18:22:15.590] [jointLog] [warning] read e225febf-502e-48ac-bb5d-924d0c397a2c (length 8594) has no trained clipping model
[2024-04-09 18:22:15.590] [jointLog] [warning] read e225febf-502e-48ac-bb5d-924d0c397a2c (length 8594 - align length 238) has no trained error model
[2024-04-09 18:22:15.590] [jointLog] [warning] read e225febf-502e-48ac-bb5d-924d0c397a2c (length 8594) has no trained clipping model
[2024-04-09 18:22:15.590] [jointLog] [warning] read e225febf-502e-48ac-bb5d-924d0c397a2c (length 8594) has no trained clipping model
[2024-04-09 18:22:15.590] [jointLog] [warning] read e225febf-502e-48ac-bb5d-924d0c397a2c (length 8594 - align length 238) has no trained error model
[2024-04-09 18:22:15.590] [jointLog] [warning] read e225febf-502e-48ac-bb5d-924d0c397a2c (length 8594) has no trained clipping model
[2024-04-09 18:22:15.590] [jointLog] [warning] read e225febf-502e-48ac-bb5d-924d0c397a2c (length 8594) has no trained clipping model

above warning repeated multiple times for different reads

[2024-04-09 21:53:51.012] [jointLog] [warning] read b47a6511-ca44-423e-a429-29a490da1c1b (length 13320 - align length 13013) has no trained error model
[2024-04-09 21:53:51.013] [jointLog] [warning] read b47a6511-ca44-423e-a429-29a490da1c1b (length 13320 - align length 12932) has no trained error model
[2024-04-09 21:53:51.013] [jointLog] [warning] read b47a6511-ca44-423e-a429-29a490da1c1b (length 13320 - align length 12932) has no trained error model
/var/lib/slurm/slurmd/job14839922/slurm_script: line 27: 419663 Segmentation fault      (core dumped) salmon quant --ont -p 24 -t ${ref} -l U -a "007_D14_transcript.bam" "007_D1_transcript.bam" "014_D14_transcript.bam" "014_D1_transcript.bam" "069_D14_transcript.bam" "069_D1_transcript.bam" "127_D14_transcript.bam" "127_D1_transcript.bam" "36S_D14_transcript.bam" "36S_D1_transcript.bam" "SCTI_D14_transcript.bam" "SCTI_D1_transcript.bam" "SCTI_D1_2000ng_transcript.bam" "ioGLUT_D7_transcript.bam" "ioMGL_D10_transcript.bam" -o ${output}/transcripts_quant

Additional context
The bam files were generated from ONT direct RNA SQKRNA004 kit reads aligned with minimap2. I have previously trialled running the above command on a single bam file and it seemed to have worked.