Segmentation fault (core dumped) in bulk mode

[linyiD001]

Is the bug primarily related to salmon (bulk mode) or alevin (single-cell mode)?
bulk mode

Describe the bug
A clear and concise description of what the bug is.
Running salmon quant in 276 samples on HPC, most of them run smoothly while 7 samples end with "Segmentation fault (core dumped)"

To Reproduce
Steps and data to reproduce the behavior:
run salmon quant in 276 samples on HPC, 7 failed with "Segmentation fault (core dumped)". But by changing the p from 16 to 64, 2 of them won't be stopped by this error.

Specifically, please provide at least the following information:

• Which version of salmon was used? v1.10.2
• How was salmon installed (compiled, downloaded executable, through bioconda)? bioconda
• Which reference (e.g. transcriptome) was used? GRCh38 transcripts from gencode v44
• Which read files were used? paired-end bulk RNA seq file in fastq.gz format
• Which which program options were used?
  …/miniconda3/envs/salmon1/bin/salmon quant -i …/share/references/gencode/salmon_index --libType A
  -1 $read1
  -2 $read2
  -p 16
  --validateMappings
  --gcBias
  --seqBias
  --recoverOrphans
  --rangeFactorizationBins 4
  --output $outdir

Expected behavior
A clear and concise description of what you expected to happen.
Salmon quant to produce quant.sf file.

Screenshots
If applicable, add screenshots or terminal output to help explain your problem.

Version Info Exception: server did not respond before timeout
### salmon (selective-alignment-based) v1.10.2
### [ program ] => salmon 
### [ command ] => quant 
### [ index ] => { /share/references/gencode/salmon_index }
### [ libType ] => { A }
### [ mates1 ] => { RNA_1.fastq.gz }
### [ mates2 ] => { RNA_2.fastq.gz }
### [ threads ] => { 16 }
### [ validateMappings ] => { }
### [ gcBias ] => { }
### [ seqBias ] => { }
### [ recoverOrphans ] => { }
### [ rangeFactorizationBins ] => { 4 }
### [ output ] => { salmon.standard/sample }
Logs will be written to salmon.standard/sample/logs
[2024-11-01 05:13:59.563] [jointLog] [info] setting maxHashResizeThreads to 16
[2024-11-01 05:13:59.563] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2024-11-01 05:13:59.563] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2024-11-01 05:13:59.563] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2024-11-01 05:13:59.563] [jointLog] [info] parsing read library format
[2024-11-01 05:13:59.563] [jointLog] [info] There is 1 library.
[2024-11-01 05:13:59.563] [jointLog] [info] Loading pufferfish index
[2024-11-01 05:13:59.563] [jointLog] [info] Loading dense pufferfish index.
-----------------------------------------
| Loading contig table | Time = 10.554 s
-----------------------------------------
size = 37302779
-----------------------------------------
| Loading contig offsets | Time = 91.707 ms
-----------------------------------------
-----------------------------------------
| Loading reference lengths | Time = 21.463 ms
-----------------------------------------
-----------------------------------------
| Loading mphf table | Time = 725.65 ms
-----------------------------------------
size = 3781971583
Number of ones: 37302778
Number of ones per inventory item: 512
Inventory entries filled: 72857
-----------------------------------------
| Loading contig boundaries | Time = 5.6684 s
-----------------------------------------
size = 3781971583
-----------------------------------------
| Loading sequence | Time = 688.13 ms
-----------------------------------------
size = 2662888243
-----------------------------------------
| Loading positions | Time = 4.9343 s
-----------------------------------------
size = 3536939191
-----------------------------------------
| Loading reference sequence | Time = 681.27 ms
-----------------------------------------
-----------------------------------------
| Loading reference accumulative lengths | Time = 21.142 ms
-----------------------------------------
[2024-11-01 05:14:22.991] [jointLog] [info] done
[2024-11-01 05:14:23.016] [jointLog] [info] Index contained 252,149 targets




[2024-11-01 05:14:24.607] [jointLog] [info] Number of decoys : 194
[2024-11-01 05:14:24.607] [jointLog] [info] First decoy index : 251,913 
[2024-11-01 05:14:29.425] [jointLog] [info] Automatically detected most likely library type as ISR

[A

[32mprocessed[31m 500,000 [32mfragments[0m
hits: 216,939, hits per frag:  0.43692[A

[32mprocessed[31m 1,000,000 [32mfragments[0m
hits: 435,436, hits per frag:  0.442697[A

[32mprocessed[31m 1,500,000 [32mfragments[0m
hits: 654,611, hits per frag:  0.438092[A

[32mprocessed[31m 2,000,000 [32mfragments[0m
hits: 857,321, hits per frag:  0.431748[A

[32mprocessed[31m 2,500,000 [32mfragments[0m
hits: 1,074,298, hits per frag:  0.432761[A

[32mprocessed[31m 3,000,000 [32mfragments[0m
hits: 1,284,332, hits per frag:  0.42818[A

[32mprocessed[31m 3,500,000 [32mfragments[0m
hits: 1,498,233, hits per frag:  0.429293[A

[32mprocessed[31m 4,000,000 [32mfragments[0m
hits: 1,711,798, hits per frag:  0.430057[A

[32mprocessed[31m 4,500,000 [32mfragments[0m
hits: 1,922,074, hits per frag:  0.428288[A

[32mprocessed[31m 5,000,000 [32mfragments[0m
hits: 2,141,874, hits per frag:  0.429173[A

[32mprocessed[31m 5,500,000 [32mfragments[0m
hits: 2,357,668, hits per frag:  0.429649[A

[32mprocessed[31m 6,000,000 [32mfragments[0m
hits: 2,572,712, hits per frag:  0.428869[A

[32mprocessed[31m 6,500,000 [32mfragments[0m
hits: 2,786,283, hits per frag:  0.429422[A

[32mprocessed[31m 7,000,000 [32mfragments[0m
hits: 2,999,448, hits per frag:  0.428769[A

[32mprocessed[31m 7,500,000 [32mfragments[0m
hits: 3,216,873, hits per frag:  0.429855[A

[32mprocessed[31m 8,000,002 [32mfragments[0m
hits: 3,429,351, hits per frag:  0.429607[A

[32mprocessed[31m 8,500,000 [32mfragments[0m
hits: 3,653,847, hits per frag:  0.430186[A

[32mprocessed[31m 9,000,000 [32mfragments[0m
hits: 3,865,545, hits per frag:  0.430114[A

[32mprocessed[31m 9,500,000 [32mfragments[0m
hits: 4,082,863, hits per frag:  0.429877[A

[32mprocessed[31m 10,000,000 [32mfragments[0m
hits: 4,296,158, hits per frag:  0.430151[A

[32mprocessed[31m 10,500,000 [32mfragments[0m
hits: 4,498,625, hits per frag:  0.428477[A

[32mprocessed[31m 11,000,000 [32mfragments[0m
hits: 4,708,743, hits per frag:  0.428498[A

[32mprocessed[31m 11,500,000 [32mfragments[0m
hits: 4,921,964, hits per frag:  0.428175[A

[32mprocessed[31m 12,000,000 [32mfragments[0m
hits: 5,133,578, hits per frag:  0.428577[A

[32mprocessed[31m 12,500,000 [32mfragments[0m
hits: 5,350,891, hits per frag:  0.428676[A

[32mprocessed[31m 13,000,000 [32mfragments[0m
hits: 5,567,705, hits per frag:  0.428405[A

[32mprocessed[31m 13,500,000 [32mfragments[0m
hits: 5,782,788, hits per frag:  0.428385[A

[32mprocessed[31m 14,000,000 [32mfragments[0m
hits: 6,002,319, hits per frag:  0.428934[A

[32mprocessed[31m 14,500,001 [32mfragments[0m
hits: 6,215,104, hits per frag:  0.428998[A

[32mprocessed[31m 15,000,000 [32mfragments[0m
hits: 6,434,896, hits per frag:  0.429183[A

[32mprocessed[31m 15,500,000 [32mfragments[0m
hits: 6,641,883, hits per frag:  0.428788[A

[32mprocessed[31m 16,000,000 [32mfragments[0m
hits: 6,858,932, hits per frag:  0.428804[A

[32mprocessed[31m 16,500,000 [32mfragments[0m
hits: 7,073,161, hits per frag:  0.428873[A

[32mprocessed[31m 17,000,000 [32mfragments[0m
hits: 7,283,801, hits per frag:  0.42879[A

[32mprocessed[31m 17,500,000 [32mfragments[0m
hits: 7,496,074, hits per frag:  0.428453[A

[32mprocessed[31m 18,000,000 [32mfragments[0m
hits: 7,713,179, hits per frag:  0.428928[A

[32mprocessed[31m 18,500,000 [32mfragments[0m
hits: 7,932,572, hits per frag:  0.428923[A

[32mprocessed[31m 19,000,000 [32mfragments[0m
hits: 8,144,149, hits per frag:  0.428876[A

[32mprocessed[31m 19,500,000 [32mfragments[0m
hits: 8,369,226, hits per frag:  0.429225[A

[32mprocessed[31m 20,000,000 [32mfragments[0m
hits: 8,584,772, hits per frag:  0.429399[A

[32mprocessed[31m 20,500,000 [32mfragments[0m
hits: 8,800,288, hits per frag:  0.429726[A

[32mprocessed[31m 21,000,001 [32mfragments[0m
hits: 9,016,478, hits per frag:  0.429653[A

[32mprocessed[31m 21,500,000 [32mfragments[0m
hits: 9,229,756, hits per frag:  0.429727[A

[32mprocessed[31m 22,000,000 [32mfragments[0m
hits: 9,449,005, hits per frag:  0.429716[A

[32mprocessed[31m 22,500,001 [32mfragments[0m
hits: 9,665,567, hits per frag:  0.429693[A

[32mprocessed[31m 23,000,000 [32mfragments[0m
hits: 9,886,728, hits per frag:  0.430177[A

[32mprocessed[31m 23,500,000 [32mfragments[0m
hits: 10,104,758, hits per frag:  0.43008[A

[32mprocessed[31m 24,000,000 [32mfragments[0m
hits: 10,317,472, hits per frag:  0.4299[A

[32mprocessed[31m 24,500,000 [32mfragments[0m
hits: 10,534,359, hits per frag:  0.430157[A

[32mprocessed[31m 25,000,000 [32mfragments[0m
hits: 10,748,602, hits per frag:  0.430214[A

[32mprocessed[31m 25,500,000 [32mfragments[0m
hits: 10,958,978, hits per frag:  0.429905[A

[32mprocessed[31m 26,000,000 [32mfragments[0m
hits: 11,179,020, hits per frag:  0.430235[A

[32mprocessed[31m 26,500,000 [32mfragments[0m
hits: 11,394,635, hits per frag:  0.430031[A

[32mprocessed[31m 27,000,001 [32mfragments[0m
hits: 11,609,653, hits per frag:  0.43023[A

[32mprocessed[31m 27,500,000 [32mfragments[0m
hits: 11,825,601, hits per frag:  0.430128
salmon.standard/sample.standard.sh: line 20: 13916 Segmentation fault      (core dumped) ……/miniconda3/envs/salmon1/bin/salmon quant -i ……/share/references/gencode/salmon_index --libType A -1 $read1 -2 $read2 -p 16 --validateMappings --gcBias --seqBias --recoverOrphans --rangeFactorizationBins 4 --output $outdir

Desktop (please complete the following information):

• OS: [e.g. Ubuntu Linux, OSX] HPC
• Version [ If you are on OSX, the output of sw_vers. If you are on linux the output of uname -a and lsb_release -a]

Additional context
Add any other context about the problem here.