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SHRIMP Not genearating SAM file #1

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pinninti19 opened this issue Apr 16, 2018 · 0 comments
Open

SHRIMP Not genearating SAM file #1

pinninti19 opened this issue Apr 16, 2018 · 0 comments

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@pinninti19
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Hi, I given the below command, after running for 72 hours It didn't generated any SAM file ?
Is their any problem with the cmd which i given ?
Thanks for your comments
Server - 1 TB RAM (128 threads)
CMD
./gmapper-ls -L /data/Likith/LikithReddy/hg38.fa -V _N 50 /data/Likith/LikithReddy/SRR098401testsickle_1.fasta /data/Likith/LikithReddy/SRR098401testsickle_2.fasta -E SRR098401.sam

Output:
Statistics:
Overall:
Load Genome Time: 10149.34 seconds
Read Mapping Time: 162941.05 seconds
Reads per hour: 4,088,342
Reads per core-hour: 81,766

Spaced Seed Scan:
    Run-time:               5425022.89 seconds

Vector Smith-Waterman:
    Run-time:               2604188.89 seconds
    Invocations:            298,501,996,315
    Bypassed Calls:         62,434,527,385
    Cells Computed:         2113992961.79 million
    Cells per Second:       811.77 million

Scalar Smith-Waterman:
    Run-time:               45347.31 seconds
    Invocations:            1,387,429,141
    Cells Computed:         1842293.65 million
    Cells per Second:       40.63 million

Miscellaneous Totals:
    Fasta Lib Time:         704.80 seconds
    Read Load Time:         72467.56 seconds
    Wait Time:              25.79 seconds

General:
    Reads Matched:          184,524,029    (99.7189%)
    ... with QV >= 10:      164,072,573    (88.6667%)
    Reads Dropped:          0    (0.0000%)
    Total Matches:          590,834,848
    Avg Hits/Matched Read:  3.20
    Duplicate Hits Pruned:  15,810,341

Memory usage:
    Genomemap:              0
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