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Description
I've run fermi on a very small dataset containing 22 fasta records using the following cmd:
run-fermi.pl -k 200 -p cdhitout_0.85 <reads.fa> | make -f -
however fermi hangs indefinitely. When I look at top I can see that fermi ropebwt is constantly in the sleep state:
45288 uqcskenn 20 0 24188 740 584 S 3 0.0 1:08.84 fermi ropebwt -a bcr -v3 -btf cdhitout_0.85.ec.tmp -
45447 uqcskenn 20 0 24188 740 584 S 2 0.0 1:08.00 fermi ropebwt -a bcr -v3 -btf cdhitout_0.90.ec.tmp -
I've tried using both the git HEAD and with release 1.1
<reads.fa> contains:
>M00920:10:000000000-A292A:1:1101:2305:13136:1
CTTCTGGTGAAACCCACTCCCATGGTGTGACGGGCGGTGTGTACAAGACCCGGGAACGTATTCACCGCGACATGCTGATCCGCGATTACTAGCGATTCCGACTTCACGCAGTCGAGTTGCAGACTGCGATCCGGACTACGATCGGCTTTGTGAGATTCGCTCCGCCTCGCGGCTTGGCAACCCTCTGTACCGACCATTGTATGACGTGTGAAGCCCTACCCATAAGGGCCATGAGGACTTGACGTCATCCCCACCTTCCTCCGGTTTGTCACCGGCAGTCTCGTTAAAGTGCCCAACCAAATGATGGCAATTAACGACAAGGGTTGCGCTCGTTGCGGGACTTAACCCAACAT
>M00920:10:000000000-A292A:1:1101:24216:16298:1
CCCTTATCCTTAGTTACCAGCACCTCGGGTGGGCACTCTAAGGAGACTGCCGGTGACAAACCGGAGGAGGGTGGGGATGACGTCAAGTCATCATGGCCCTTACGGCCAGGGCTACACACGTGCTACAATGGTCGGTACAAAGGGTTGCCAAGCCGCGAGGTGGAGCTAATCCCATAAAACCGATCGTAGTCCGGATCGCAGTCTGCAACTCGACTGCGTGAAGTCGGAATCGCTAGTAATCGTGAATCAGAATGTCACGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCATCACACCATGGGAGTGGGTTGCTCCAGAAGTAGCTAGTCTAACCGCAAGGGGGACGGTTACCA
>M00920:10:000000000-A292A:1:1110:4340:7240:1
CAGATTGAACGCTGGCGGCATGCTTTACACATGCAAGTCGAACGGCAGCGGGGGCTTCGGCCCGCCGGCGAGTGGCGAACGGGTGAGTAATGCATCGGAACGTACCCATGTTGTGGGGGATAACGTAGCGAAAGCTACGCTAATACCGCATAAGCCCTGAGGGGGAAAGCGGGGGATTCTTCGGAACCTCGCGCAATTGGAGCGGCCGATGTCAGATTAGCTAGTTGGTAGGGTAAAGGCCTACCAAGGCGACGATCTGTAGCGGGTCTGAGAGGATGATCCGCCACACTGGGACTGAGACACGGCCCGGACTCCTCCGGGAGGCAGCAGTGGGGAATTTTGGACAATGGGCGCAAGGGTGATC
>M00920:10:000000000-A292A:1:1110:21042:16009:1
ACCCAGGGGGCTGCCTTCGCCATCGGTGTTCCTCCACATCTCTACGCATTTCACTGCTACACGTGGAATTCCACCCCCCTCTGCCACACTCGAGCCTTGCAGTCACAAACGCATTTCCCAGGTTAAGCCCGGGGATTTCACATCTGTCTTACAAAGCCGCCTGCGCACGCTTTACGCCCAGT
6D12
AATTCCGATTAACGCTCGCACCCTACGTATTACCGCGGCTGCTGGCACGTAGTTAGCCGGTGCTTGTTCTTCAGTTCCCGTCATTGACAGTCTATGTTAGACCCCGCCGTTTCGTTCCTGCCGAAAGAGCTTTACAACCCGAAGGCCTTCTTCACTCACGCGGAATGGCTGGATCAGGGT
>M00920:10:000000000-A292A:1:1101:19922:4365:1
ATCTAATCCTGTTTGCTCCCCACGCTTTCGTGCATGAGCGACAGACCAGGTCCAGGGGGCTGCCTTCGCCTTCGATGTTCCTCCTGATATCTACGTATTTCACTGCTACACCCGGATTTCCACCCCCCTCTACCGCACTCTAGGCACACAGTCACAAACGCATTTCCCAGGTTAAGCCCGGGGGTTTCAAATCTGAATTATTTAACCGCCTGCGCACGCTTTACGCCCAGTAATTCCGATTAACGCTCGCACCCTCGGTATGACCGCGACTGCCAGCGGGTAGGAAGGCGGTACTTTTTATTCCGGTGCCGACATCCTCCCCGGATATTCACCGCGGCTATTTCTTTCCGTCCGACAGAGGTGTAAAACCCGAAGGCGAGCTTG
>M00920:10:000000000-A292A:1:1101:18095:13295:1
GGAGGCAGCAGTGGGGAATTTTGGACAATGGGCGGAAGCCTGATCCAGCCATGCCGCGTGAGTGAAGAAGGCCTTCGGGTTGTAAAGCTCTTTCGGTGGGGAAGAAATTGCACGGGTTAATACCCTGTGTAGATGACGGTACCCGACTAAGAAGCACCGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGTGCGAGCGTTAATCGGAATTACTGGGCGTAAAGCGTGCGCAGGCGGTTTGGTAAGTCAGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATTTGAGACTGCCAAGCTGGAGTGTGGCAGAGGGGGGTGGAATTCCACGTGTAGCAGTGAAATGCGTAGAGATCAGGAG
>M00920:10:000000000-A292A:1:2102:3086:14182:1
GTAGTGACCCAGGGGGCTGCCTTCGCCATCGGTGTTCCTCCACATCTCTACGCATTTCACTGCTACACGTGGAATTCCACCCCCCTCTGCCACACTCCAGCCTGGCAGTCTCAAATGCAGTTCCCAGGTTGAGCCCGGGGCTTTCACATCTGACTTACCAAACCGCCTGCGCACGCTTTACGCCCAGTAATTCCGATTAACGCTCGCACCCTACGTATTAACGCGGCTGCTGGCACGTAGTTCGCCGGTGCTTCTTAGTCGGGTACCGTCATCTACACAGGATATTAGCCCGTGCAATTTCTTCCCCACCGAAAGAGCTTTACAACCCGAAGGCCTTCTTCACTCACGCGGCATGGCTGGATCAGGCTTCCGCCC
>M00920:10:000000000-A292A:1:2108:13711:22806:1
GATTAAACGCTGGCGGCATGCCTTACACATGCAAGTCGAACGGCAGCACGGGGGCAACCCTGGTGGCGAGTGGTGGACGGGTGAGTAAAGCATCGGAACGTATCCTGAAGTGGAGTATAACGTAGCGAAAGTTACGCTAATACCGCATAGTCTGTGAGCAGGAAAGCAGGGGATCGCAAGACCTTGCGCTCTGGGAGCGGCCGATGTCGGATTAGCTAGTTGGGGGGGTAAAGGCCTACCAAGGCGCGGCTCCGTAGCGGGGATTGGAGTATGAAACGCCACACTGTGACTGAGAAACGGCCCGGACTCCTACGTGAGGAAGCAGCGGTGAATTTTTTCCAATGGGTTCAAGCC
>M00920:10:000000000-A292A:1:2110:11377:9313:1
GCATCGGAACGTGCCCTGGAATGGGGGATAACGTAGCGAAAGTTACGCTAATACCGCATATTCTGTGAGCAGGAAAGCAGGGGATCGCAAGACCTTGCGTTCTGGGATCGGCCGATGTCGTATGAGCTAGTTGGTGGGGAAAAGGCCTACCACGGCGACGATCCGTAGCGGGTCTGAGAGGATGATCCGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCCGTGGGGAATTTTGGACAATGGGCGCAAGCCTGATCCAGCCATGCCGCGTGAGTGAAGAAGGCCTTCGGGTTGTAAAGCTCTTTCGGTGGGGAAGAAATTGCATGGGTTAATTCCC
>M00920:10:000000000-A292A:1:1105:17264:25408:1
GAATTACTGGGCGTAAAGCGTGCGCAGGCGGCGCCATAAGACAGACGTGAAATCCCCGGGCTTAACCTGGGAACTGCGTTTGTGACTGTGGTGCTCGAGTGTGGCAGAGGGGGGTGGAATTCCACGTGTAGCAGTGAAATGCGTAGAGATGTGGAGGAACACCGATGGCGAAGGCAGCCCCCTGGGTCAACACTGACGCTCATGCACGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCCTAAACGATGCGAACTAGGTGTTGGGGAAGGAGACGTTCTTAGTACCGCAGCTAACGCGTGAAGTTCGCCGCCTGGGGAGTACGGTCGCAAGATTAAAACTCAAAGGAATGGACA
>M00920:10:000000000-A292A:1:2105:19316:26848:1
ATCCGTAGCTGGTCTGAGAGGACGACCAGCCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGGGGAATTTTGGACAATGGGGGCAACCCTGATCCAGCCATTCCGCGTGAGTGAAGAAGGCCTTCGGGTTGTAAAGCTCTTTCAGCAGGAACGAAACGGCTCTCTCTAACATAGGGAGTTAATGACGGTACCTGAAGAAGAAGCACCGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGTGCGAGCGTTAATCGGAATTACTGGGCGTAAAGCGTGCACAGGCGGCGCCATAAGACAGATGTGAAATCCCCGGGCTTAACCTGGGAAC
>M00920:10:000000000-A292A:1:1111:13173:15398:1
TGGTTTAATTCGATGCAACGCGAAGAACCTTACCTGGTCTTGACATCCACAGAACTTGCCAGAGATGGCTTGGTGCCTTCGGGAACTGTGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTTGTGAAATGTTGGGTTAAGTCCCGCACCGAGCGCAACCCTTATCCTTTGTTGCCAGCGGTTCGGCCGGGAACTCAAAGGAGACTGCCAGTGATAAACTGGAGGAAGGTGGGGCTGAAGTCAAGTCATCATGGCCCTTATGGGTAGGGCGTCACACGTCATACAATGGTCGGAACAGAGGGTTGCCAAGCCGCGAGGTGGAGCCAATCCCAGAAAACCGATCGTAGTCCGGATCGC
>M00920:10:000000000-A292A:1:1102:8010:26367:1
GCCTTACACATGCAAGTCGAACGGCAGCGGAACTTCGGGTGCCGGCGAGTGGCGAACGGGTGAGTAATGCATCGGAACGTGCCATTGAGTGGGGGATAACGTAGCGAAAGTTGCGCTAATACCGCATATTCTGTGAGCAGGAAAGCAGGGGACCGCAAGGCCTTGCGCTCTTTGAGCGGCCGATGTCAGATTAGCTAGTTGGTGAGGTAAAGGCTTACCAAGGCGACGATCTGTAGCGGGTCTGAGAGGATGATCCGCCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGGGGAATTTTGGACAATGGGGGCAACCCTGATCCAGCCATGCCGCGTGAGTGAAGAAGGCCTTCGGGT
>M00920:10:000000000-A292A:1:1106:8344:21464:1
GTTCCTACCATTGTAGCACGTGTGTAGCCCTGGGCATAAAGGCCATGATGACTTGACATCATCCCCTCCTTCCTCGCGTCTTACGACGGCAGTTTCTTTAGAGTTCCCAGCTTAACCTGTTGGCAACTAAAGATAGGGGTTGCGCTCGTTGCGGGACTTAACCCAACACCTCACGGCACGAGCTGACGACAGCCATGCAGCACCTGTGTGACGGCTCCCTTTCGGGCACCCTCAACTCTCATCGAGGTTCCGTCCATGTCAAGGGTAGGTAAGGTTTTTCGCGTTGCATCGAATTAATCCACATCATCCACCGCTTGTGCGGGTCCCCGTCAATTCCTTTGAGTTTTAATC
>M00920:10:000000000-A292A:1:1109:11262:3539:1
TTTACCCACCCAACACCTAGTTGACATAGTTTAGGGCGTGGACTACCAGGGTATCTAATCCTGTTTGCTACCCACGCTTTCGTGCATGAGCGTCAGTATCGGCCCAGGGGGCTGCCTTCGCCATAGGTGTTCCTCCCCATCTCTACGCTTTTCACTGCTACACGTGGAATTCCACCCCCCTCTGCCGTACTCTAGTGAGGCAGTCACAAACGCAGTTCCCAGGTTACGCCCGGGGATTTCACGCCTGTCTTACCAATCCGCCTGCGCACGCTTTACGCCCAGTAATTCCGATTAACGCTCGCACCCTACGTATTACCGCGGCTGCTGGCACGTAGTTAGCCGGTGCTTCTTATGCCGGTACCG
>M00920:10:000000000-A292A:1:1113:21063:11515:1
ACACAGGGTATTAACCCATGCGATTTCTTCCCGGCCGAAAGAGCTTTACAACCCGAAGGCCTTCTTCACTCACGCGGCATGGCTGGATCAGGGTTGCCCCCATTGTCCAAAATTCCCCACTGCTGCCTCCCGGAGGAGTCTGGCCCGTGTCTCAGTTCCAGTGTGGCGGATCATCCTCTCAGACCCGCTCCAGATCGTCGCCTTGGTAAGCCGTTACCTCACCAACTAGCTAATCTGACATAGGCCGCTCAAAGAGCGCAAGGCCTTGCGGTCCCCTGCTTTCCTGCTCACAGAATATGCGGTATTAGCGCAACTTTCGCTACGTTATCCCCCACTCAATGGCACGTTCCGATGCATTACTCACC
>M00920:10:000000000-A292A:1:2109:18065:11577:1
CCTTTGTATTGTCCATTGTAGCACGTGTGTAGCCCAAATCATAAGGGGCATGATGATTTGACGTCATCCCCACCTTCCTCCGGTTTGTCACCGGCAGTCAACTTAGAGTGCCCAACTTAATGATGGCAACTAAGCTTAAGGGTTGCGCTCGTTGCGGGACTTAACCCAACATCTCACGACACGAGCTGACGACAGCCATGCAGCACCAGTGTGACGGCTCCCTTTCGGGCACCCTCAACTCTCATCGAGGTTCCGTCCATGTCAAGGGTAGGTAAGGTTTTTCGCGTTGCATCGAATTAATCCACATCATCCACCGCTTGTGCGGGTCCCCGTCAATTCCTTTGAGTTTTAATC
>M00920:10:000000000-A292A:1:2113:10809:18271:1
GTACGGTCGCAAGATTAAAACTCAAAGGAATTGACGGGGACCCGCACAAGCGGTGGATGATGTGGATTAATTCGATGCAACGCGAAAAACCTCACCTACCCTTGACATGGACGGAACCTCGATGAGAGTTGAGGGTGCCCGAAAGGGAGCCGTCACACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTAAGCTTAGTTGCCATCATTAAGTTGGGCACTCTAAGTTGACTGCCGGTGACAAACCGGAGGAAGGTGGGGATGACGTCAAATCATCATGCCCCTTATGATTTGGGCTACACACGTGCTACAA
>M00920:10:000000000-A292A:1:2101:18998:6292:1
GTGGAGCATGTGGTTTAATTCGATGCAACGCGAAGAACCTTACCTGGTCTTGACATCCACAGAACTTAGCAGAGATGCTTTGGTGCCTTCGGGAACTGTGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTTGTGAAAGGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATCCTTTGTTGCCAGCGGTCCGGCCGGGAACTCAAAGGAGACTGCCAGTGATAAACTGGAGGAAGGTGGGGATGACGTCAAGTCCTCATGGCCCTTATGGGTAGGGCTTCACACGTCATACAATGGTCGGAACAGAGGGTTGCCAAGCCGCGAGGTGGAGCCAATCCCAGAAAACCGATCGTAGTCCGGATCGCAGTCTGCAACTCGAC
>M00920:10:000000000-A292A:1:2108:17778:22051:1
ATCCACAGAACTTAGCAGAGATGCTTTGGTGCCTTCGGGAACTGTGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTTGTGAAATGTTGGGTTAAGTCCCGTAACGAGCGCAACCCTTGTCCTTAGTTACCAGCACCTCGGGTGGGCACTCTAAGGAGACTGCCGGTGACAAACCGGGGGAAGGTGGGGATGACGTCAAGTCATCATGGCCCTTACGGCCAGGGCTACACACGTGCTACAATGGTCGGTACAAAGGGTTGCCAAGCCGCGAGGTGGAGCTAATCCCATAAAACCGATCGTAGTCCGGATCGCAGTCTGCAACTCGACTGCGTGAAGTCGGAATCGCTAGTAATCGTGAATC
>M00920:10:000000000-A292A:1:1104:5131:15907:1
GTACTGACGCTCATGCACGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCCTAAACGATGTCGACTAGTCGTTCGGAGCAGCAATGCACTGAGTGACGCAGCTAACGCGTGAAGTCGACCGCCTGGGGAGTACGGCCGCAAGGTTAAAACTCAAAGGAATTGACGGGGACCCGCACAAGCGGTGGATGATGTGGATTAATTCGATGCAACGCGAAAAACCTTACCTACCCTTGACATGTCTGGAGCCTTGGTGAGAGCCGAGGGTGCCTTCGGGAGCCAGAACACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGT
>M00920:10:000000000-A292A:1:1113:7839:16644:1
CGTTTAGGGCGTGGACTACCAGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGTGCATGAGCGTCAGTACAGGCCCAGGGGGCTGCCTTCGCCATCGGTGTTCCTCCTGATCTCTACGCATTTCACTGCTACACCAGGAATTCCACACACTTCTGCCGTACTCTAGCCTTGCAGTCACAAACGCAGTTCCCAGGTTAAGCCCGGGGATTTCACATCTGTCTTACAAAAACGCCTCCGCACGCTTTACGCCCAGTAATTCCGATTAACGCTCGCACCCTACGTTTTACCGCGGCTGCTGGCACGTTTTTAGCCGGTGCTTCTTAGTCCGGTACCGTCATCCATGGCCTATGTTAGAGAC
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