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Old 03-03-2013, 12:57 AM   #1
Mahtab
Member
 
Location: University of Melbourne

Join Date: Aug 2011
Posts: 10
Default Error running Shrimp aligner

Hi all

I'm trying to map some reads that were found unmapped using bwa with Shrimp agaist chr18.

The command I'm running is as follows:

gmapper-cs -N 8 -E -Q Unmapped-reads.fq chrm-18/chr18-
homo.fasta

However I'm getting the following output/error.

Output:

--------------------------------------------------------------------------------
gmapper: COLOUR SPACE (AB SOLiD).
SHRiMP 2.1.1b
[ICC Intel(R) C++ g++ 4.1 mode]
--------------------------------------------------------------------------------
Settings:
Spaced Seeds (weight/span) 111110001111111 (12/15)
111100111001001111 (12/18)
111001001000111001111 (12/21)
1111001000010001001001111 (12/25)
Number of Outputs per Read: 10
Window Generation Mode: 2
Window Length: 140.00%
Window Overlap Length: 20.00%

SW Match Score: 10
SW Mismatch Score: -15
SW Gap Open Score (Ref): -40
SW Gap Open Score (Qry): -40
SW Gap Extend Score (Ref): -7
SW Gap Extend Score (Qry): -7
SW Crossover Score: -14

Window Generation Threshold: 55.00%
SW Vector Hit Threshold: 50.00%
SW Full Hit Threshold: 55.00%

Paired mode: none

Gapless mode: no
Number of threads: 8
Thread chunk size: 1000
Hash Filter Calls: yes
Anchor Width: 8
- Processing genome file [/chrm-18/chr18-homo.fasta]
- Processing contig gi|224589809|ref|NC_000018.9|
Loaded Genome
Automatically trimming genome index lists longer than: 1000
- Processing read file [Unmapped-reads.fq]
gmapper-cs: common/fasta.c:380: bool fasta_get_next_read_with_range(_fasta_t *, read_entry *): Assertion `quality_length <= sequence_length' failed.

Any suggestions is highly appreciated.

Thanks
Mahtab
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Old 03-03-2013, 03:11 AM   #2
Bukowski
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Location: UK

Join Date: Jan 2010
Posts: 390
Default

It would appear that you have some sequences that have longer qualities than there are bases in the sequence - i.e. the length of the quality is not less than or equal to the sequence length, which is what that error is suggesting.
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Old 03-03-2013, 04:52 PM   #3
Mahtab
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Location: University of Melbourne

Join Date: Aug 2011
Posts: 10
Default

Thanks for you response.

The problem is I'm getting the same error across different sets of input fastq data both synthetic and real data which I had previously mapped using bwa.
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