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
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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