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zhou-lab / biscuit

BISulfite-seq CUI Toolkit
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segfaults & floating point exceptions with -p and/or -c #11

Closed ttriche closed 7 years ago

ttriche commented 7 years ago

Program: BISCUIT (BISulfite-seq CUI Toolkit) Version: 0.2.0.20161222

$ biscuit align hg38.fa -t16 -p -c POETIC-11_R1.fastq POETIC-11_R2.fastq > output.bam
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 1059604 sequences (160000204 bp)...
[M::process] 1059604 single-end sequences; 0 paired-end sequences
Floating point exception
$ biscuit align hg38.fa -t16 -c POETIC-11_R1.fastq POETIC-11_R2.fastq > output.bam
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 1059604 sequences (160000204 bp)...
Floating point exception
$ biscuit align hg38.fa -t16 -p POETIC-11_R1.fastq POETIC-11_R2.fastq > output.bam
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[W::main_align] when '-p' is in use, the second query file is ignored.
[M::process] read 1059604 sequences (160000204 bp)...
[M::process] 1059604 single-end sequences; 0 paired-end sequences
[M::process] read 1059604 sequences (160000204 bp)...
[M::mem_process_seqs] Processed 1059604 reads in 3742.793 CPU sec, 235.158 real 
sec
[M::process] 1059604 single-end sequences; 0 paired-end sequences
[M::process] read 1059604 sequences (160000204 bp)...
[M::mem_process_seqs] Processed 1059604 reads in 3649.333 CPU sec, 228.816 real 
sec
[M::process] 1059604 single-end sequences; 0 paired-end sequences
[M::process] read 1059604 sequences (160000204 bp)...
[M::mem_process_seqs] Processed 1059604 reads in 3642.387 CPU sec, 232.409 real sec
Segmentation fault
$ biscuit align hg38.fa -p -c POETIC-11_R1.fastq POETIC-11_R2.fastq > output.bam
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 66226 sequences (10000126 bp)...
[M::process] 66226 single-end sequences; 0 paired-end sequences
Floating point exception
$ biscuit align hg38.fa -c POETIC-11_R1.fastq POETIC-11_R2.fastq > output.bam
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 66226 sequences (10000126 bp)...
Floating point exception

WGBS runs from a HiSeq X

ttriche commented 7 years ago

Misuse of arguments on my part! Closing.