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[fputs] Broken pipe #18
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can you send a small fastq to re-create? |
|
The above is the first 10 reads |
I don't get an error with those. Can you tell me the result of: |
Program: bwa (alignment via Burrows-Wheeler transformation) |
what reference are you using? |
UCSC hg19 |
can you paste the full command that you are using and the full resulting error? |
maybe the error was not in the first 10 reads |
I got this several error when run BWA-METH.
/haifengc/panfs/bireads/SRR1171540_1_1000000.fastq NA'
writing to:
samtools view -bS - | samtools sort - bwa-meth
[M::bwa_idx_load_from_disk] read 0 ALT contigs
converting reads in /home/rcf-40/haifengc/panfs/bireads/SRR1171540_1_1000000.fastq,NA
WARNING: running bwameth in single-end mode
[M::process] read 666668 sequences (60000120 bp)...
[M::process] read 333332 sequences (29999880 bp)...
[M::mem_process_seqs] Processed 666668 reads in 316.005 CPU sec, 319.250 real sec
Traceback (most recent call last):
File "bwameth.py", line 601, in
main(sys.argv[1:])
File "bwameth.py", line 586, in main
set_as_failed=args.set_as_failed)
File "bwameth.py", line 259, in bwa_mem
as_bam(cmd, fa, prefix, calmd, set_as_failed)
File "bwameth.py", line 299, in as_bam
out.write(str(aln) + '\n')
IOError: [Errno 32] Broken pipe
[fputs] Broken pipe
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