BWA alignment generating errors
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3.7 years ago
MAPK ★ 2.1k

I am trying to align interleaved fastq files (multiple runs) for SRA data I have downloaded. These fastq files are splitted by Read groups. I was able to use this exact command for other projects downloaded from SRA, but I am not sure why I am getting these errors for this project. Can someone please help me figure out the issue? It says Parse error at line 81135274 truncated file, but I tried downloading this file multiple times and get the same error. Please note that the character ^ is not the cause of this error because we label our samples as ${SAMPLE_NAME}^${DNA_BARCODE}^${PROJECT}.

[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RR
[M::mem_process_seqs] Processed 1600000 reads in 490.700 CPU sec, 30.573 real sec
[M::process] 0 single-end sequences; 1600000 paired-end sequences
Command terminated by signal 9
        Command being timed: "bwa mem -t 16 -R @RG\tID:2893343716\tPL:illumina\tPU:D2991ACXX.1\tLB:A-LOAD-LD001248-BL-NCR-04AD7584-lig1-lib1b\tPI:0\tDS:paired end\tDT:2013-07-31T19:00:00-0500\tSM:A-LOAD-LD001248\tCN:WUGSC -M -p /tmp//Homo_sapiens_assembly38.fasta /tmp//A-LOAD-LD001248^SRR1012371^phs000572_201612.2893343716.fq.gz"
        User time (seconds): 37857.30
        System time (seconds): 252.21
        Percent of CPU this job got: 1586%
        Elapsed (wall clock) time (h:mm:ss or m:ss): 40:01.55
        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): 25718172
        Average resident set size (kbytes): 0
        Major (requiring I/O) page faults: 0
        Minor (reclaiming a frame) page faults: 98842329
        Voluntary context switches: 8503560
        Involuntary context switches: 673761
        Swaps: 0
        File system inputs: 7339456
        File system outputs: 0
        Socket messages sent: 0
        Socket messages received: 0
        Signals delivered: 0
        Page size (bytes): 4096
        Exit status: 0
[W::sam_read1] Parse error at line 81135274
samtools sort: truncated file. Aborting
Command exited with non-zero status 1
        Command being timed: "samtools sort -@ 16 -m 2G -o /phs000572_201612/A-LOAD-LD001248^SRR1012371^phs000572_201612/A-LOAD-LD001248^SRR1012371^phs000572_201612.2893343716.aln.srt.bam -T /gscmnt/gc2645/wgs/tmp/1709608.R54EtPrTRxCR2NUi/tmp.FVJ4slAmPU/"
        User time (seconds): 115.04
        System time (seconds): 18.55
        Percent of CPU this job got: 5%
        Elapsed (wall clock) time (h:mm:ss or m:ss): 40:01.66
        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): 25011988
        Average resident set size (kbytes): 0
        Major (requiring I/O) page faults: 0
        Minor (reclaiming a frame) page faults: 33516
        Voluntary context switches: 111500
        Involuntary context switches: 46742
        Swaps: 0
        File system inputs: 0
        File system outputs: 0
        Socket messages sent: 0
        Socket messages received: 0
        Signals delivered: 0
        Page size (bytes): 4096
        Exit status: 1
[20201025_223104] bwa+samtools finished, exit codes: 137 1, step time 0h40m1s
drwx--S--- 2 an lab 512 Oct 25 21:49 tmp.FVJ4slAmPU
[20201025_223104] Run failed at bwa+samtools step, exit code: 1
Leftover files may be in /gscmnt/gc2645/wgs/tmp/1709608.R54EtPrTRxCR2NUi
Cleaning up /gscmnt/gc2645/wgs/tmp/1709608.R54EtPrTRxCR2NUi/tmp.FVJ4slAmPU
removed directory '/gscmnt/gc2645/wgs/tmp/1709608.R54EtPrTRxCR2NUi/tmp.FVJ4slAmPU'
rmdir: removing directory, '/gscmnt/gc2645/wgs/tmp/1709608.R54EtPrTRxCR2NUi'
Cleaning up cached files in /tmp/
BWA alignment • 1.3k views
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3
Entering edit mode

Command terminated by signal 9

you bwa command was killed by the server. https://stackoverflow.com/questions/16338884

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1
Entering edit mode

The samtools error is a consequence of a bwa problem. Did you check memory usage? Do you really have the files at /tmp which is the memory? That is not really a good idea. Put it somewhere on the file system. The memory is not for storage.

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