SAW-A10102 There is a bug in fastq-PE segmentation.

Hi,

I'm trying to use SAW (v 6.1) in a sample that I downloaded from SRA, and most FASTQ files are mapped without any problem, however, some present the following error. I tried downloading the FASTQ file again, but I still got the same problem.

 ~~~ mapping - SRR21088098_1.fastq.gz ~~~
INFO:    Environment variable SINGULARITY_BIND is set, but APPTAINER_BIND is preferred
WARNING: While bind mounting '/staging/leuven/stg_00054/Projects/Stereoseq/Takis/raw:/staging/leuven/stg_00054/Projects/Stereoseq/Takis//raw': destination is already in the mount point list
WARNING: While bind mounting '/staging/leuven/stg_00054/Projects/Stereoseq/Takis/reference:/staging/leuven/stg_00054/Projects/Stereoseq/Takis//reference': destination is already in the mount point list
--- Error: [2023-10-11 21:42:2] SAW-A10102: There is a bug in fastq-PE segmentation.
bcSTAR: ReadsParse.cpp:458: ThreadProcess(IOparam*, IOThread*)::<lambda(ThreadProcess(IOparam*, IOThread*)::FQbuf*, char*, ThreadProcess(IOparam*, IOThread*)::FQbuf*, char*)>: Assertion `false' failed.
/usr/local/bin/mapping: line 1: 2792485 Aborted                 (core dumped) /opt/saw_v6.1.0_software/pipeline/mapping/bcSTAR $*
Command exited with non-zero status 134
    Command being timed: "singularity exec /staging/leuven/stg_00054/lucas/bin/singularity/SAW_6.1.sif mapping --outSAMattributes spatial --outSAMtype BAM SortedByCoordinate --genomeDir /staging/leuven/stg_00054/Projects/Stereoseq/Takis//reference/mouse_STAR_SJ100/ --runThreadN 10 --outFileNamePrefix /staging/leuven/stg_00054/Projects/Stereoseq/Takis/results//results/00.mapping/SRR21088098_1. --sysShell /bin/bash --stParaFile /staging/leuven/stg_00054/Projects/Stereoseq/Takis/results//results/00.mapping/SRR21088098_1.bcPara --readNameSeparator " " --limitBAMsortRAM 63168332971 --limitOutSJcollapsed 10000000 --limitIObufferSize=280000000 --outBAMsortingBinsN 50"
    User time (seconds): 11713.42
    System time (seconds): 186.46
    Percent of CPU this job got: 825%
    Elapsed (wall clock) time (h:mm:ss or m:ss): 24:01.35
    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): 65651848
    Average resident set size (kbytes): 0
    Major (requiring I/O) page faults: 69
    Minor (reclaiming a frame) page faults: 1817546
    Voluntary context switches: 43734
    Involuntary context switches: 111650
    Swaps: 0
    File system inputs: 1243368
    File system outputs: 147493376
    Socket messages sent: 0
    Socket messages received: 0
    Signals delivered: 0
    Page size (bytes): 4096
    Exit status: 134

In the log files, I couldn't find much, it just suddenly stopped mapping. But I can see that no *.barcodeReadsCount.txt was generated. Do you have any suggestions?

Thank you Lucas

STOmics / SAW

SAW-A10102 There is a bug in fastq-PE segmentation. #76