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

[Clouate]

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!