MosaikBuild ERROR: The mate1 read name did not match the mate2 read name. Resynchronization support needs to be implemented.

[GoogleCodeExporter]

What steps will reproduce the problem?
1.MosaikBuild  -q tier1.disc.1.fq -q2 tier1.disc.2.fq -out tier1.disc.1.fq.dat 
-st illumina

What is the expected output? What do you see instead?
------------------------------------------------------------------------------
MosaikBuild 1.0.1388                                                2010-02-01
Michael Stromberg                 Marth Lab, Boston College Biology Department
------------------------------------------------------------------------------

- setting read group ID to: ZCN3PA6LMT4
- setting sample name to: unknown
- setting sequencing technology to: illumina
- trimming leading and lagging N's. Mates with >4 interior N's will be deleted.

- parsing paired-end/mate-pair FASTQ files:
reads: 0 |ERROR: The mate1 read name did not match the mate2 read name. 
Resynchronization support needs to be implemented.

What version of the product are you using? On what operating system?
linux system.

Please provide any additional information below.

the input fastq files have read names that match. Not sure why it hangs 
mosaikbuild
==> tier1.disc.1.fq <==
@GA2MACHINE1:4:27:1548:747#0/1
TCTTTGTTATTTCCTGTGTTTGCTGCGGAAAACAATTTGGTTGTTCCTCACAGAATGAGCATTGGGTGAAAAATGA
+
a_^a`a_^^_^a``aaZa^_``a`a_a_X^Va`^\U^\Z_]_a\Z__^^^V^_UW]^^]a^VUZY_U`XXUW]Z]\
@GA2MACHINE1:4:86:535:1476#0/1
TGTAAAAAATTTCTTCGAACTGGATGACACAACCTATCAAGACCTCTGGGATACAGCAAAGGCAGTGCTAAGAGGA
+
a_^aaa_`aa_aZ`a_`\_Z^`^^Z_^Z^__^^X___^_^]^^X^W_]]_X^_]]\]^ZZZZZ][X_Z]ZX^]YZZ
@GA2MACHINE1:5:28:615:276#0/1
GCATGGTGGCGCATGCCTATAATCCCAGCTACTCGGGAAGCTGAGGCAGGAGAATCGCTTGAACCCAGGAGGCAGA

==> tier1.disc.2.fq <==
@GA2MACHINE1:4:27:1548:747#0/2
GCCTTTGCTGTATCCCAGAGGTCTTGATAGGTTGTGTCATCCAGTTCGAAGAAATTTTTTACATTTCCATCTTGAN
+
abbbbabbbTY]aa_bbbbbaVb`aba_`bYW[b`aab``aYI]W^bb]baXTaaaaaabaab_aa`a[b_aaBBB
@GA2MACHINE1:4:86:535:1476#0/2
TTCCCTGAGATGTGAACTTAGATTCGGTCTGTGCTCTTTCAGACTTTTTTTCGGAGGGGTTTTGGGCTACAGACTT
+
aaa__aaaaaVaRa_a_a^a`__aWaWMMR^W_N\V]_[VHWSWUS_`_FLOXOV]XVZXVTMTSTGQLRNYZQWW
@GA2MACHINE1:5:28:615:276#0/2
ATGATTTCTTTTCTTTCTTGTTTTTTTTTTTTTCTTTTTTTTTTTTTTCAGGGGGGTTTCCGCCTTTTCCCCTGGG

Original issue reported on code.google.com by abou...@gmail.com on 30 Jul 2010 at 6:20

[GoogleCodeExporter]

Sorry forgot to add that I ran this to obtain the fastq files 

samtools view -bF 0x2 <tier1.bam> | bamToFastq -bam stdin -fq1 tier1.disc.1.fq 
-fq2 tier1.disc.2.fq 

Original comment by abou...@gmail.com on 30 Jul 2010 at 6:26

[GoogleCodeExporter]

[deleted comment]

[GoogleCodeExporter]

I have the exact same issue when running the workflow as described above.

Original comment by tom.sa...@gmail.com on 15 Oct 2010 at 10:56

[GoogleCodeExporter]

Hi there,

I copy and paste the reads in files, as shown in the attachment.
Then, I run MosaikBuild, but I didn't meet the error.

I'll follow the workflow and try again later.

Original comment by WanPing....@gmail.com on 28 Oct 2010 at 6:04

• Changed state: Accepted

Attachments:

• read_1.fq
• read_2.fq

[GoogleCodeExporter]

Hi all,

I try the workflow, and in my experiment, even the first read, I didn't have 
the same read name of it. Thus, MosaikBuild cannot parse the files.

I recommend merging two fastqs as one.

mate 1:

@NA20502-ERR006287.8245462/1
GGTCAAAGGGAGTCCGAACTACTCTCAGGCTTCAAC
+
**$*%"""""$""$*"""""%"""""""""""""""

mate 2:

@NA20502-ERR006287.5052734/2
GTGTCTAAATAGCATGCCCAAAGCCACACAGCTCAC
+
********"********"**"****%*"*"**"*"*

Original comment by WanPing....@gmail.com on 28 Oct 2010 at 7:13

• Changed state: Done