fastq-SE segmentation error

[YiqianGu]

Hi team,

Thanks for you great tools.
I was running SAW_7.1 then encountered fastq-SE segmentation error. I have attached the scripts I ran and the errors.
Please kindly let me know if you need anything else to troubleshoot.

Best,
Yiqian

Scripts I ran:

#/bin/bash
ulimit -n 10240
ulimit -v 33170449147
NUMBA_CACHE_DIR=./

dataDir=/dir/to/fq
outDir=/dir/to/outdir
files=$(ls $dataDir/*.fq.gz | paste -sd ',' -)
export SINGULARITY_BIND=$dataDir,$outDir

bash stereoPipeline_v7.1.sh
-sif /u/home/g/guyiqian/SAW_7.1.sif
-splitCount 16
-maskFile /dir/XXX.barcodeToPos.h5
-fq1 $files
-speciesName xxx
-tissueType skin
-refIndex /ref/hg38_ensembl_stereoseq
-annotationFile /ref/Homo_sapiens.GRCh38.111.gtf
-rRNAremove N
-threads 8
-outDir $outDir
-doCellBin Y

Error:
--- Error: [2024-6-14 13:47:40] SAW-A10102: There is a bug in fastq-SE segmentation.
bcSTAR: ReadsParse.cpp:383: ThreadProcess(IOparam*, IOThread*)::<lambda(ThreadProcess(IOparam*, IOThread*)::FQbuf*, char*)>: Assertion `false' failed.
/usr/local/bin/mapping: line 1: 7845 Aborted /opt/saw_st_software/pipeline/mapping/bcSTAR $*
INFO: Cleaning up image...
Command exited with non-zero status 134
Command being timed: "singularity exec /u/home/g/guyiqian/SAW_7.1.sif mapping --outSAMattributes spatial --outSAMtype BAM SortedByCoordinate --genomeDir /u/scratch/g/guyiqian/ref/hg38_ensembl_stereoseq --runThreadN 8 --outFileNamePrefix /u/scratch/g/guyiqian/analysis/V24010079-B03209F113/00.mapping/03.B03209F113.Q4. --sysShell /bin/bash --stParaFile /u/scratch/g/guyiqian/analysis/V24010079-B03209F113/00.mapping/03.B03209F113.Q4.bcPara --readNameSeparator " " --limitBAMsortRAM 63168332971 --limitOutSJcollapsed 10000000 --limitIObufferSize=280000000 --outBAMsortingBinsN 50 --outSAMmultNmax 1"
User time (seconds): 2513.00
System time (seconds): 164.30
Percent of CPU this job got: 686%
Elapsed (wall clock) time (h:mm:ss or m:ss): 6:29.90
Average shared text size (kbytes): 0
Average unshared data size (kbytes): 0
Average stack size (kbytes): 0
Average total size (kbytes): 0
Maximum resident set size (kbytes): 51315776
Average resident set size (kbytes): 0
Major (requiring I/O) page faults: 0
Minor (reclaiming a frame) page faults: 69168789
Voluntary context switches: 530030
Involuntary context switches: 76640
Swaps: 0
File system inputs: 7248680
File system outputs: 73693912
Socket messages sent: 0
Socket messages received: 0
Signals delivered: 0
Page size (bytes): 4096
Exit status: 134

[KentLE]

Hi, this is generally because the fq file was not read correctly. It seems that the error occurred when mapping *_3.fq.gz. You could check whether the path of *_3.fq.gz was correctly recorded in 00.mapping/03.fastq.list, check the completeness of the fq file, and confirm that it did not use a soft link.

[YiqianGu]

Thanks! That helps!