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guanchangge / mosaik-aligner

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MosaikBuild #71

Open GoogleCodeExporter opened 8 years ago

GoogleCodeExporter commented 8 years ago 
What steps will reproduce the problem?

1.MosaikBuild -q 0019.fq  -out  19.bin -st illumina
2.MosaikBuild -assignQual 10 -q 0019.fq  -out  19.bin -st illumina
3.

What is the expected output? 
------------------------------------------------------------------------------
MosaikBuild 1.0.1388                                                2010-02-01
Michael Stromberg                 Marth Lab, Boston College Biology Department
------------------------------------------------------------------------------
- setting read group ID to: ZD3SZSNGG1W
- setting library name to: K4562
- 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 FASTQ file:
reads: 10,864,248 (172,057.8 reads/s)

Filtering statistics:
============================================
# reads deleted:             48751 (  0.4 %)
# leading N's trimmed:        8952
# lagging N's trimmed:      269797
--------------------------------------------
# reads written:          10815497
# bases written:         821699023

MosaikBuild CPU time: 53.820 s, wall time: 63.165 s

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: ZDCNI7JPQBG
- setting library name to: MS
- 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 FASTQ file:
reads: 11,940,367 /ERROR: The number of qualities (15) do not match the number 
of bases (36) in HWUSI-EAS1665_31:6:35:10984:18443:0/1.

What version of the product are you using? 
MosaikBuild 1.1.0014  2010-10-01                                             

On what operating system? 
Linux (64-bit)

Thansk for your time and help,
-britt

Original issue reported on code.google.com by britt...@gmail.com on 22 Oct 2010 at 5:26

GoogleCodeExporter commented 8 years ago 
Hi Britt,

Are you trying to reassign all base qualities to 10?

Since the input is FASTQ (-q), both bases and qualities are present in the 
given file. So, MOSAIK parses quality values from the FASTQ file; that means 
"-assignQual" wouldn't be enabled.

I tested several FASTQs here using the same parameter combination, -q and 
-assignQual, but I didn't meet the same error. If I could have your file, 
that'll help a lot.

Original comment by WanPing....@gmail.com on 27 Oct 2010 at 3:37