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
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