alevin: missing quants.mat.gz or core dump #992
Description
Is the bug primarily related to salmon (bulk mode) or alevin (single-cell mode)?
alevin
Describe the bug
In the tests run for the alevin Galaxy tool we observe a failing tests.
Essentially we run:
salmon index -i ./index --kmerLen '31' --gencode --threads 10 --transcripts 'input_index.fasta'
salmon alevin --libType ISR --index ./index --mates1 ./mate1.fastq --mates2 ./mate2.fastq -o ./output -p "$SLOTS" --indropV2 --w1 'ATCAT' --tgMap ./alevinmap.tsv --keepCBFraction '1.0' --dumpFeatures --dumpMtx --maxNumBarcodes '100000' --freqThreshold '5'
Where
input_index.fastais https://github.com/bgruening/galaxytools/blob/master/tools/salmon/test-data/minitranscript.fa- and the mate pair is unzipped versions of https://github.com/bgruening/galaxytools/blob/master/tools/salmon/test-data/fastqs/moreminifastq1.fastq.gz https://github.com/bgruening/galaxytools/blob/master/tools/salmon/test-data/fastqs/moreminifastq2.fastq.gz
- alevinmap.tsv is https://github.com/bgruening/galaxytools/blob/master/tools/salmon/test-data/minitxp.tsv
We see the following error
Version Info: This is the most recent version of salmon.
[2025-10-28 12:53:23.388] [alevinLog] [warning] Force Cells to 1 fraction of All possible CB.This is not recommended way to run the pipeline,and it might slow the pipeline
Logs will be written to ./output/logs
[2025-10-28 12:53:23.405] [jointLog] [info] setting maxHashResizeThreads to 3
[2025-10-28 12:53:23.405] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored.
[2025-10-28 12:53:23.405] [jointLog] [info] The --mimicBT2, --mimicStrictBT2 and --hardFilter flags imply mapping validation (--validateMappings). Enabling mapping validation.
[2025-10-28 12:53:23.405] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2025-10-28 12:53:23.405] [jointLog] [info] The use of range-factorized equivalence classes does not make sense in conjunction with --hardFilter. Disabling range-factorized equivalence classes.
[2025-10-28 12:53:23.405] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2025-10-28 12:53:23.405] [jointLog] [info] Using default value of 0.87 for minScoreFraction in Alevin
Using default value of 0.6 for consensusSlack in Alevin
### alevin (dscRNA-seq quantification) v1.10.1
### [ program ] => salmon
### [ command ] => alevin
### [ libType ] => { ISR }
### [ index ] => { ./index }
### [ mates1 ] => { ./mate1.fastq }
### [ mates2 ] => { ./mate2.fastq }
### [ output ] => { ./output }
### [ threads ] => { 3 }
### [ indropV2 ] => { }
### [ w1 ] => { ATCAT }
### [ tgMap ] => { ./alevinmap.tsv }
### [ keepCBFraction ] => { 1.0 }
### [ dumpFeatures ] => { }
### [ dumpMtx ] => { }
### [ maxNumBarcodes ] => { 100000 }
### [ freqThreshold ] => { 5 }
[2025-10-28 12:53:23.405] [alevinLog] [info] Found 322 transcripts(+0 decoys, +0 short and +0 duplicate names in the index)
[2025-10-28 12:53:23.405] [alevinLog] [info] Filled with 322 txp to gene entries
[2025-10-28 12:53:23.405] [alevinLog] [info] Found all transcripts to gene mappings
[2025-10-28 12:53:23.413] [alevinLog] [info] Processing barcodes files (if Present)
[2025-10-28 12:53:23.454] [alevinLog] [info] Done barcode density calculation.
[2025-10-28 12:53:23.454] [alevinLog] [info] # Barcodes Used: 1 / 125000.
[2025-10-28 12:53:23.454] [alevinLog] [info] Forcing to use 1 cells
[2025-10-28 12:53:23.475] [alevinLog] [info] Throwing 31 barcodes with < 5 reads
[2025-10-28 12:53:23.495] [alevinLog] [info] Total 1(has 31 low confidence) barcodes
[2025-10-28 12:53:23.515] [alevinLog] [info] Done True Barcode Sampling
[2025-10-28 12:53:23.516] [alevinLog] [info] Total 0.0008% reads will be thrown away because of noisy Cellular barcodes.
[2025-10-28 12:53:23.516] [alevinLog] [info] Done populating Z matrix
[2025-10-28 12:53:23.516] [alevinLog] [warning] 0 Whitelisted Barcodes with 0 frequency
[2025-10-28 12:53:23.516] [alevinLog] [info] Total 0 CB got sequence corrected
[2025-10-28 12:53:23.516] [alevinLog] [info] Done indexing Barcodes
[2025-10-28 12:53:23.516] [alevinLog] [info] Total Unique barcodes found: 1
[2025-10-28 12:53:23.516] [alevinLog] [info] Used Barcodes except Whitelist: 0
-----------------------------------------
| Loading contig table | Time = 323.47 us
-----------------------------------------
size = 1412
-----------------------------------------
| Loading contig offsets | Time = 62.763 us
-----------------------------------------
-----------------------------------------
| Loading reference lengths | Time = 3.273 us
-----------------------------------------
-----------------------------------------
| Loading mphf table | Time = 80.356 us
-----------------------------------------
size = 235270
Number of ones: 1411
Number of ones per inventory item: 512
Inventory entries filled: 3
-----------------------------------------
| Loading contig boundaries | Time = 656.43 us
-----------------------------------------
size = 235270
-----------------------------------------
| Loading sequence | Time = 110.75 us
-----------------------------------------
size = 192940
-----------------------------------------
| Loading positions | Time = 347.93 us
-----------------------------------------
size = 570828
-----------------------------------------
| Loading reference sequence | Time = 159.47 us
-----------------------------------------
-----------------------------------------
| Loading reference accumulative lengths | Time = 3.598 us
-----------------------------------------
[2025-10-28 12:53:23.538] [jointLog] [info] There is 1 library.
[2025-10-28 12:53:23.538] [jointLog] [info] Loading pufferfish index
[2025-10-28 12:53:23.538] [jointLog] [info] Loading dense pufferfish index.
[2025-10-28 12:53:23.540] [jointLog] [info] done
[2025-10-28 12:53:23.538] [alevinLog] [info] Done with Barcode Processing; Moving to Quantify
[2025-10-28 12:53:23.538] [alevinLog] [info] parsing read library format
[2025-10-28 12:53:23.603] [jointLog] [info] Index contained 322 targets
[2025-10-28 12:53:23.603] [jointLog] [info] Number of decoys : 0
[2025-10-28 12:53:23.723] [jointLog] [info] Computed 0 rich equivalence classes for further processing
[2025-10-28 12:53:23.723] [jointLog] [info] Counted 0 total reads in the equivalence classes
[2025-10-28 12:53:23.723] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2025-10-28 12:53:23.723] [jointLog] [info] Mapping rate = 0%
[2025-10-28 12:53:23.723] [jointLog] [info] finished quantifyLibrary()
[2025-10-28 12:53:23.727] [alevinLog] [info] Starting optimizer
[2025-10-28 12:53:23.750] [alevinLog] [warning] mrna file not provided; using is 1 less feature for whitelisting
[2025-10-28 12:53:23.750] [alevinLog] [warning] rrna file not provided; using is 1 less feature for whitelisting
[2025-10-28 12:53:23.750] [alevinLog] [info] Total 0.00 UMI after deduplicating.
[2025-10-28 12:53:23.750] [alevinLog] [info] Total 0 BiDirected Edges.
[2025-10-28 12:53:23.750] [alevinLog] [info] Total 0 UniDirected Edges.
[2025-10-28 12:53:23.750] [alevinLog] [info] Clearing EqMap; Might take some time.
[2025-10-28 12:53:23.754] [alevinLog] [warning] Num Low confidence barcodes too less 31 < 200.Can't performing whitelisting; Skipping
[2025-10-28 12:53:23.754] [alevinLog] [info] Starting dumping cell v gene counts in mtx format
[2025-10-28 12:53:23.754] [alevinLog] [error] Can't import Binary file quants.mat.gz, it doesn't exist
If we drop --dumpMtx the output ends with:
[2025-10-28 12:54:55.427] [alevinLog] [info] Finished optimizer
Floating point exception (core dumped)
I'm not 100% sure - but I assume that the test we running in the past.
To Reproduce
See above
Desktop (please complete the following information):
- OS: Ubuntu Linux
- Version 24.04.1