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Old 10-05-2017, 01:31 AM   #43
wlokhorst
Junior Member
 
Location: The Netherlands

Join Date: Oct 2017
Posts: 5
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No error messages are produced, but you might be right about it crashing. (It also crashes when I put ./ in front of the input file.) Maybe you can see what goes wrong from the output text, so here it is:
Code:
BBMap version 37.53
Set MINIMUM_ALIGNMENT_SCORE_RATIO to 0.560
Retaining first best site only for ambiguous mappings.
NOTE:   Ignoring reference file because it already appears to have been processed.
NOTE:   If you wish to regenerate the index, please manually delete ref/genome/1/summary.txt
Set genome to 1

Loaded Reference:       1.506 seconds.
Loading index for chunk 1-1, build 1
Generated Index:        1.482 seconds.
Analyzed Index:         3.715 seconds.
Cleared Memory:         6.933 seconds.
Processing reads in single-ended mode.
Started read stream.
Started 48 mapping threads.
Detecting finished threads: 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47

   ------------------   Results   ------------------

Genome:                 1
Key Length:             13
Max Indel:              20
Minimum Score Ratio:    0.56
Mapping Mode:           normal
Reads Used:             40428   (3919820 bases)

Mapping:                13.209 seconds.
Reads/sec:              3060.74
kBases/sec:             296.76


Read 1 data:            pct reads       num reads       pct bases          num bases

mapped:                   4.5464%            1838         4.3524%             170607
unambiguous:              1.2120%             490         1.2217%              47890
ambiguous:                3.3343%            1348         3.1307%             122717
low-Q discards:           0.0000%               0         0.0000%                  0

perfect best site:        0.7173%             290         0.6776%              26561
semiperfect site:         0.7297%             295         0.6905%              27066

Match Rate:                   NA               NA        91.4514%             156445
Error Rate:              42.4134%            1543         8.4773%              14502
Sub Rate:                42.1935%            1535         7.7799%              13309
Del Rate:                 2.2265%              81         0.2701%                462
Ins Rate:                 4.1506%             151         0.4273%                731
N Rate:                   0.2474%               9         0.0713%                122

Total time:             27.078 seconds.
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