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[fputs] Broken pipe #18

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acgtun opened this issue Jul 21, 2015 · 9 comments
Closed

[fputs] Broken pipe #18

acgtun opened this issue Jul 21, 2015 · 9 comments

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@acgtun
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acgtun commented Jul 21, 2015

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

@brentp
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brentp commented Jul 21, 2015

can you send a small fastq to re-create?

@acgtun
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acgtun commented Jul 21, 2015

@SRR1171540.1 FCD14TWACXX:1:1101:1440:2156 length=90
GAGGTAGGAGAATTATTTGAATTTAGGAAGTGGAAGTTAGTGAGTCGAGATCGTGTTATTGTATTATAGTTTAGGCGATAGAGTAAGATT
+SRR1171540.1 FCD14TWACXX:1:1101:1440:2156 length=90
_bbecdcecggggiehiiifbghi_ghbghebfX^^^dfe^cfgeggegZ^ffee^b`g`febegdfbgfdhbdffddaaa_b]Y_b``c
@SRR1171540.2 FCD14TWACXX:1:1101:1399:2172 length=90
AGTGATATAGAGTTTTGGGTTATTTGTTTATGTAGTTTATTTATGTTTTTTGGTTTTTTTGGATTAAATTTTAAATTTATTATTTTTATT
+SRR1171540.2 FCD14TWACXX:1:1101:1399:2172 length=90
_bbececeeecgcfghiiibfbfhiibfgfhhh_f^effhihfhgfhiiiihdbghiiigec_dc_Z]bcdc`]`Z_bcccbceddc_cc
@SRR1171540.3 FCD14TWACXX:1:1101:1498:2200 length=90
GTTTTAATATTTTAATATTATTTTATTTTTTTTATTAATATAAGAAGGTAGGAATGTTTAGTTTTTGAGTTTAAGTTAAGTTATTGTATT
+SRR1171540.3 FCD14TWACXX:1:1101:1498:2200 length=90
bbbeeeeegeeggfffhhhfhfiifhiihiiiicghfdgbhhhfceeg^cbbW\be_egdbNV\bfd`d^dc]]Zbdbbbcccddcbbba
@SRR1171540.4 FCD14TWACXX:1:1101:1395:2217 length=90
AGTTTTTTAAGTAGTTGGGATTGTAGGTATGTGTATTATATTTGGTTAATATTTTAGTTTTTGTAGAAATAGGGTTTTTTTGTGTTGTTT
+SRR1171540.4 FCD14TWACXX:1:1101:1395:2217 length=90
_b_ceeeecage`ffghiiacdfd[egb_fgceb[bf]e_ffiiic`d_f`fdhhfe^efg`ffbe`e_dZbghH\^bcccccccccccc
@SRR1171540.5 FCD14TWACXX:1:1101:1351:2235 length=90
ATAGATTAGTAAAATATTATTTTAAGTGTTTTTTTATGTTTTAATTTGAATTTTTTTTTTGTTTTAATTGTAATAGTTATGGTAATTATT
+SRR1171540.5 FCD14TWACXX:1:1101:1351:2235 length=90
ab_eceeeggeccdgfhiihiiiddgbebefghhhXaffhhhfafghhdXceeegfggab]K\bc`T]bb`_GZRT]a``b`]`]`b]_b
@SRR1171540.6 FCD14TWACXX:1:1101:1735:2131 length=90
TATTTATAGTTTGTTATTTTTAGGGGATTAAGTTGGGAAGTTGAGTGGTTAATGATTGAGTTGTTTTAAATAGTTGGGTATTTAGTTAAT
+SRR1171540.6 FCD14TWACXX:1:1101:1735:2131 length=90
bbbeeeeegggggghiiiiiihhiiieghhigghgiibfg^egegacf^cebgfcehgabWaebfhff__cdb_`^bd^_acebbbb]Z_
@SRR1171540.7 FCD14TWACXX:1:1101:1605:2131 length=90
TTAAAAGTTATTATTTATTTTTTAGAAATTTTTGTATAAATTATTTTTTAATTTGTATGTGTTTAAAGTAGATATAAATGATTGTAAAAT
+SRR1171540.7 FCD14TWACXX:1:1101:1605:2131 length=90
_b_eeeecgfgggiiihiiiiiihihhhiiihiigfhfhhhihhhiiiiihihiigfhhghefhhfdcadccgfgeaggggeeeee_`bb
@SRR1171540.8 FCD14TWACXX:1:1101:1577:2173 length=90
ATTATGGGTTAGGTTTTGGATTTTAGAGGTGAAAGTTGGGAGTGGAGAATTGTATTTGTAAATTTTGTTTTTTGGTTTTTTTGAAAGAGT
+SRR1171540.8 FCD14TWACXX:1:1101:1577:2173 length=90
_bbeeeeecgaggeghfhiagghg_e_egPbb`]eY^eghZeO^c[ccZe`eWSae\b\_`Zedddfgfhgge`]acaccca]WYRYX`b
@SRR1171540.9 FCD14TWACXX:1:1101:1711:2174 length=90
TTTATAGGAGTTTTATTTTTTGGTATAAGTAAGGATGATATTGGGAGTATTTTTTAAAGTAGTATTTTTTTGAGGGAAAGTGATAGTAGG
+SRR1171540.9 FCD14TWACXX:1:1101:1711:2174 length=90
bbbeeeeccegcgihihihhefaebgedgafgfba^ccfafhiehdeN^[chhhib_`bddc\bdg_gdcbc^\^\FTXX]``b`bbc`b
@SRR1171540.10 FCD14TWACXX:1:1101:1639:2215 length=90
TTTATGTGGTAAATAAATTGGTTGTTTTGAATTTTGCTAATTTGGGAGGAGATGGGTTTTTTTGGGTTTTTTGTTTTAGTTATGGTTTGG
+SRR1171540.10 FCD14TWACXX:1:1101:1639:2215 length=90
abbeeecegegggiiihiiiihfhegiiifdgiiihhghfhihiiicfh^e^ccghWZ_cbgedbc\^_^aaa^b[bb^bb`cbcbcccc

@acgtun
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acgtun commented Jul 21, 2015

The above is the first 10 reads

@brentp
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brentp commented Jul 21, 2015

I don't get an error with those. Can you tell me the result of: bwa 2>&1 | head -5

@acgtun
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acgtun commented Jul 21, 2015

Program: bwa (alignment via Burrows-Wheeler transformation)
Version: 0.7.12-r1044
Contact: Heng Li lh3@sanger.ac.uk

@brentp
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brentp commented Jul 21, 2015

what reference are you using?

@acgtun
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acgtun commented Jul 21, 2015

UCSC hg19

@brentp
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brentp commented Jul 21, 2015

can you paste the full command that you are using and the full resulting error?
do you get an error with the 10 reads that you pasted?

@acgtun
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acgtun commented Jul 21, 2015

maybe the error was not in the first 10 reads

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