{"action":"created","issue":{"url":"https://api.github.com/repos/BenLangmead/bowtie2/issues/36","repository_url":"https://api.github.com/repos/BenLangmead/bowtie2","labels_url":"https://api.github.com/repos/BenLangmead/bowtie2/issues/36/labels{/name}","comments_url":"https://api.github.com/repos/BenLangmead/bowtie2/issues/36/comments","events_url":"https://api.github.com/repos/BenLangmead/bowtie2/issues/36/events","html_url":"https://github.com/BenLangmead/bowtie2/issues/36","id":141756613,"number":36,"title":"Error in bowtie2-build if multiple threads used","user":{"login":"billzt","id":1146090,"avatar_url":"https://avatars.githubusercontent.com/u/1146090?v=3","gravatar_id":"","url":"https://api.github.com/users/billzt","html_url":"https://github.com/billzt","followers_url":"https://api.github.com/users/billzt/followers","following_url":"https://api.github.com/users/billzt/following{/other_user}","gists_url":"https://api.github.com/users/billzt/gists{/gist_id}","starred_url":"https://api.github.com/users/billzt/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/billzt/subscriptions","organizations_url":"https://api.github.com/users/billzt/orgs","repos_url":"https://api.github.com/users/billzt/repos","events_url":"https://api.github.com/users/billzt/events{/privacy}","received_events_url":"https://api.github.com/users/billzt/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"milestone":null,"comments":9,"created_at":"2016-03-18T02:32:37Z","updated_at":"2016-04-22T17:38:08Z","closed_at":"2016-04-22T17:38:08Z","body":"If I use `--threads` option in bowtie2-build, finally error occurs:\r\n```\r\nSettings:\r\n  Output files: \"test.*.bt2\"\r\n  Line rate: 6 (line is 64 bytes)\r\n  Lines per side: 1 (side is 64 bytes)\r\n  Offset rate: 4 (one in 16)\r\n  FTable chars: 10\r\n  Strings: unpacked\r\n  Max bucket size: default\r\n  Max bucket size, sqrt multiplier: default\r\n  Max bucket size, len divisor: 4\r\n  Difference-cover sample period: 1024\r\n  Endianness: little\r\n  Actual local endianness: little\r\n  Sanity checking: disabled\r\n  Assertions: disabled\r\n  Random seed: 0\r\n  Sizeofs: void*:8, int:4, long:8, size_t:8\r\nInput files DNA, FASTA:\r\n  test.fa\r\nBuilding a SMALL index\r\nReading reference sizes\r\n  Time reading reference sizes: 00:00:00\r\nCalculating joined length\r\nWriting header\r\nReserving space for joined string\r\nJoining reference sequences\r\n  Time to join reference sequences: 00:00:00\r\nbmax according to bmaxDivN setting: 1485\r\nUsing parameters --bmax 1114 --dcv 1024\r\n  Doing ahead-of-time memory usage test\r\n  Passed!  Constructing with these parameters: --bmax 1114 --dcv 1024\r\nConstructing suffix-array element generator\r\nBuilding DifferenceCoverSample\r\n  Building sPrime\r\n  Building sPrimeOrder\r\n  V-Sorting samples\r\n  V-Sorting samples time: 00:00:00\r\n  Allocating rank array\r\n  Ranking v-sort output\r\n  Ranking v-sort output time: 00:00:00\r\n  Invoking Larsson-Sadakane on ranks\r\n  Invoking Larsson-Sadakane on ranks time: 00:00:00\r\n  Sanity-checking and returning\r\nBuilding samples\r\nReserving space for 12 sample suffixes\r\nGenerating random suffixes\r\nQSorting 12 sample offsets, eliminating duplicates\r\nQSorting sample offsets, eliminating duplicates time: 00:00:00\r\nMultikey QSorting 12 samples\r\n  (Using difference cover)\r\n  Multikey QSorting samples time: 00:00:00\r\nCalculating bucket sizes\r\nSplitting and merging\r\n  Splitting and merging time: 00:00:00\r\nSplit 1, merged 5; iterating...\r\nSplitting and merging\r\n  Splitting and merging time: 00:00:00\r\nAvg bucket size: 741.625 (target: 1113)\r\nConverting suffix-array elements to index image\r\nAllocating ftab, absorbFtab\r\nEntering Ebwt loop\r\nGetting block 1 of 8\r\nGetting block 2 of 8\r\nGetting block 4 of 8\r\nCould not open file for reading a reference graph: \"test.0.saGetting block 5 of 8\r\n\"\r\n  Reserving size (1114) for bucket 5\r\n  Reserving size (1114) for bucket 4\r\n  Reserving size (1114) for bucket 2\r\nGetting block 6 of 8\r\nGetting block 7 of 8\r\nGetting block 3 of 8\r\n  Calculating Z arrays for bucket 2\r\n  Calculating Z arrays for bucket 5\r\n  Reserving size (1114) for bucket 6\r\nGetting block 8 of 8\r\n  Entering block accumulator loop for bucket 5:\r\n  Calculating Z arrays for bucket 6\r\n  Calculating Z arrays for bucket 4\r\n  bucket 5: 10%\r\n  Entering block accumulator loop for bucket 2:\r\n  Reserving size (1114) for bucket 8\r\n  bucket 5: 20%\r\n  Reserving size (1114) for bucket 1\r\n  Reserving size (1114) for bucket 7\r\n  Entering block accumulator loop for bucket 4:\r\n  bucket 5: 30%\r\n  Reserving size (1114) for bucket 3\r\n  Calculating Z arrays for bucket 1\r\n  Calculating Z arrays for bucket 7\r\n  bucket 2: 10%\r\n  bucket 4: 10%\r\n  Entering block accumulator loop for bucket 1:\r\n  bucket 2: 20%\r\n  Entering block accumulator loop for bucket 7:\r\n  Calculating Z arrays for bucket 3\r\n  bucket 5: 40%\r\n  Entering block accumulator loop for bucket 6:\r\n  bucket 2: 30%\r\n  Calculating Z arrays for bucket 8\r\n  bucket 4: 20%\r\n  bucket 5: 50%\r\n  bucket 1: 10%\r\n  bucket 7: 10%\r\n  Entering block accumulator loop for bucket 8:\r\n  bucket 1: 20%\r\n  bucket 7: 20%\r\n  bucket 8: 10%\r\n  bucket 2: 40%\r\n  bucket 4: 30%\r\n  Entering block accumulator loop for bucket 3:\r\n  bucket 8: 20%\r\n  bucket 2: 50%\r\n  bucket 6: 10%\r\n  bucket 4: 40%\r\n  bucket 5: 60%\r\n  bucket 3: 10%\r\n  bucket 2: 60%\r\n  bucket 7: 30%\r\n  bucket 1: 30%\r\n  bucket 5: 70%\r\n  bucket 3: 20%\r\n  bucket 1: 40%\r\n  bucket 6: 20%\r\n  bucket 4: 50%\r\n  bucket 8: 30%\r\n  bucket 2: 70%\r\n  bucket 7: 40%\r\n  bucket 1: 50%\r\n  bucket 6: 30%\r\n  bucket 4: 60%\r\n  bucket 8: 40%\r\n  bucket 3: 30%\r\n  bucket 1: 60%\r\n  bucket 7: 50%\r\n  bucket 4: 70%\r\n  bucket 2: 80%\r\n  bucket 3: 40%\r\n  bucket 8: 50%\r\n  bucket 6: 40%\r\n  bucket 7: 60%\r\n  bucket 3: 50%\r\n  bucket 4: 80%\r\n  bucket 5: 80%\r\n  bucket 2: 90%\r\n  bucket 3: 60%\r\n  bucket 8: 60%\r\n  bucket 6: 50%\r\n  bucket 2: 100%\r\n  bucket 8: 70%\r\n  Sorting block of length 866 for bucket 2\r\n  bucket 1: 70%\r\n  bucket 5: 90%\r\n  bucket 8: 80%\r\n  (Using difference cover)\r\n  bucket 3: 70%\r\n  bucket 7: 70%\r\n  bucket 1: 80%\r\n  bucket 8: 90%\r\n  bucket 6: 60%\r\n  bucket 5: 100%\r\n  bucket 3: 80%\r\n  bucket 4: 90%\r\n  bucket 6: 70%\r\n  bucket 8: 100%\r\n  bucket 3: 90%\r\n  Sorting block of length 449 for bucket 8\r\n  (Using difference cover)\r\n  bucket 7: 80%\r\n  bucket 1: 90%\r\n  bucket 4: 100%\r\n  bucket 6: 80%\r\n  Sorting block of length 973 for bucket 4\r\n  bucket 3: 100%\r\n  (Using difference cover)\r\n  bucket 6: 90%\r\n  bucket 7: 90%\r\n  Sorting block of length 853 for bucket 5\r\n  (Using difference cover)\r\n  Sorting block of length 909 for bucket 3\r\n  (Using difference cover)\r\n  bucket 1: 100%\r\n  bucket 6: 100%\r\n  bucket 7: 100%\r\n  Sorting block of length 439 for bucket 1\r\n  (Using difference cover)\r\n  Sorting block of length 761 for bucket 6\r\n  (Using difference cover)\r\n  Sorting block of length 683 for bucket 7\r\n  (Using difference cover)\r\n  Sorting block time: 00:00:00\r\nReturning block of 867 for bucket 2\r\n  Sorting block time: 00:00:00\r\n  Sorting block time: 00:00:00\r\n  Sorting block time: 00:00:00\r\n  Sorting block time: 00:00:00\r\nReturning block of 440 for bucket 1\r\n  Sorting block time: 00:00:00\r\nReturning block of 974 for bucket 4\r\nReturning block of 450 for bucket 8\r\nReturning block of 910 for bucket 3\r\nReturning block of 854 for bucket 5\r\n  Sorting block time: 00:00:00\r\n  Sorting block time: 00:00:00\r\nReturning block of 762 for bucket 6\r\nReturning block of 684 for bucket 7\r\nTotal time for call to driver() for forward index: 00:00:00\r\nError: Encountered internal Bowtie 2 exception (#1)\r\nCommand: bowtie2-build --wrapper basic-0 --threads 10 test.fa test \r\nDeleting \"test.3.bt2\" file written during aborted indexing attempt.\r\nDeleting \"test.4.bt2\" file written during aborted indexing attempt.\r\nDeleting \"test.1.bt2\" file written during aborted indexing attempt.\r\nDeleting \"test.2.bt2\" file written during aborted indexing attempt.\r\n\r\n```\r\n\r\nHowever, if I delete `--threads` option, it is OK.\r\n```\r\nSettings:\r\n  Output files: \"test.*.bt2\"\r\n  Line rate: 6 (line is 64 bytes)\r\n  Lines per side: 1 (side is 64 bytes)\r\n  Offset rate: 4 (one in 16)\r\n  FTable chars: 10\r\n  Strings: unpacked\r\n  Max bucket size: default\r\n  Max bucket size, sqrt multiplier: default\r\n  Max bucket size, len divisor: 4\r\n  Difference-cover sample period: 1024\r\n  Endianness: little\r\n  Actual local endianness: little\r\n  Sanity checking: disabled\r\n  Assertions: disabled\r\n  Random seed: 0\r\n  Sizeofs: void*:8, int:4, long:8, size_t:8\r\nInput files DNA, FASTA:\r\n  test.fa\r\nBuilding a SMALL index\r\nReading reference sizes\r\n  Time reading reference sizes: 00:00:00\r\nCalculating joined length\r\nWriting header\r\nReserving space for joined string\r\nJoining reference sequences\r\n  Time to join reference sequences: 00:00:00\r\nbmax according to bmaxDivN setting: 1485\r\nUsing parameters --bmax 1114 --dcv 1024\r\n  Doing ahead-of-time memory usage test\r\n  Passed!  Constructing with these parameters: --bmax 1114 --dcv 1024\r\nConstructing suffix-array element generator\r\nBuilding DifferenceCoverSample\r\n  Building sPrime\r\n  Building sPrimeOrder\r\n  V-Sorting samples\r\n  V-Sorting samples time: 00:00:00\r\n  Allocating rank array\r\n  Ranking v-sort output\r\n  Ranking v-sort output time: 00:00:00\r\n  Invoking Larsson-Sadakane on ranks\r\n  Invoking Larsson-Sadakane on ranks time: 00:00:00\r\n  Sanity-checking and returning\r\nBuilding samples\r\nReserving space for 12 sample suffixes\r\nGenerating random suffixes\r\nQSorting 12 sample offsets, eliminating duplicates\r\nQSorting sample offsets, eliminating duplicates time: 00:00:00\r\nMultikey QSorting 12 samples\r\n  (Using difference cover)\r\n  Multikey QSorting samples time: 00:00:00\r\nCalculating bucket sizes\r\nSplitting and merging\r\n  Splitting and merging time: 00:00:00\r\nSplit 1, merged 5; iterating...\r\nSplitting and merging\r\n  Splitting and merging time: 00:00:00\r\nSplit 1, merged 1; iterating...\r\nSplitting and merging\r\n  Splitting and merging time: 00:00:00\r\nAvg bucket size: 741.625 (target: 1113)\r\nConverting suffix-array elements to index image\r\nAllocating ftab, absorbFtab\r\nEntering Ebwt loop\r\nGetting block 1 of 8\r\n  Reserving size (1114) for bucket 1\r\n  Calculating Z arrays for bucket 1\r\n  Entering block accumulator loop for bucket 1:\r\n  bucket 1: 10%\r\n  bucket 1: 20%\r\n  bucket 1: 30%\r\n  bucket 1: 40%\r\n  bucket 1: 50%\r\n  bucket 1: 60%\r\n  bucket 1: 70%\r\n  bucket 1: 80%\r\n  bucket 1: 90%\r\n  bucket 1: 100%\r\n  Sorting block of length 439 for bucket 1\r\n  (Using difference cover)\r\n  Sorting block time: 00:00:00\r\nReturning block of 440 for bucket 1\r\nGetting block 2 of 8\r\n  Reserving size (1114) for bucket 2\r\n  Calculating Z arrays for bucket 2\r\n  Entering block accumulator loop for bucket 2:\r\n  bucket 2: 10%\r\n  bucket 2: 20%\r\n  bucket 2: 30%\r\n  bucket 2: 40%\r\n  bucket 2: 50%\r\n  bucket 2: 60%\r\n  bucket 2: 70%\r\n  bucket 2: 80%\r\n  bucket 2: 90%\r\n  bucket 2: 100%\r\n  Sorting block of length 866 for bucket 2\r\n  (Using difference cover)\r\n  Sorting block time: 00:00:00\r\nReturning block of 867 for bucket 2\r\nGetting block 3 of 8\r\n  Reserving size (1114) for bucket 3\r\n  Calculating Z arrays for bucket 3\r\n  Entering block accumulator loop for bucket 3:\r\n  bucket 3: 10%\r\n  bucket 3: 20%\r\n  bucket 3: 30%\r\n  bucket 3: 40%\r\n  bucket 3: 50%\r\n  bucket 3: 60%\r\n  bucket 3: 70%\r\n  bucket 3: 80%\r\n  bucket 3: 90%\r\n  bucket 3: 100%\r\n  Sorting block of length 1035 for bucket 3\r\n  (Using difference cover)\r\n  Sorting block time: 00:00:00\r\nReturning block of 1036 for bucket 3\r\nGetting block 4 of 8\r\n  Reserving size (1114) for bucket 4\r\n  Calculating Z arrays for bucket 4\r\n  Entering block accumulator loop for bucket 4:\r\n  bucket 4: 10%\r\n  bucket 4: 20%\r\n  bucket 4: 30%\r\n  bucket 4: 40%\r\n  bucket 4: 50%\r\n  bucket 4: 60%\r\n  bucket 4: 70%\r\n  bucket 4: 80%\r\n  bucket 4: 90%\r\n  bucket 4: 100%\r\n  Sorting block of length 731 for bucket 4\r\n  (Using difference cover)\r\n  Sorting block time: 00:00:00\r\nReturning block of 732 for bucket 4\r\nGetting block 5 of 8\r\n  Reserving size (1114) for bucket 5\r\n  Calculating Z arrays for bucket 5\r\n  Entering block accumulator loop for bucket 5:\r\n  bucket 5: 10%\r\n  bucket 5: 20%\r\n  bucket 5: 30%\r\n  bucket 5: 40%\r\n  bucket 5: 50%\r\n  bucket 5: 60%\r\n  bucket 5: 70%\r\n  bucket 5: 80%\r\n  bucket 5: 90%\r\n  bucket 5: 100%\r\n  Sorting block of length 969 for bucket 5\r\n  (Using difference cover)\r\n  Sorting block time: 00:00:00\r\nReturning block of 970 for bucket 5\r\nGetting block 6 of 8\r\n  Reserving size (1114) for bucket 6\r\n  Calculating Z arrays for bucket 6\r\n  Entering block accumulator loop for bucket 6:\r\n  bucket 6: 10%\r\n  bucket 6: 20%\r\n  bucket 6: 30%\r\n  bucket 6: 40%\r\n  bucket 6: 50%\r\n  bucket 6: 60%\r\n  bucket 6: 70%\r\n  bucket 6: 80%\r\n  bucket 6: 90%\r\n  bucket 6: 100%\r\n  Sorting block of length 761 for bucket 6\r\n  (Using difference cover)\r\n  Sorting block time: 00:00:00\r\nReturning block of 762 for bucket 6\r\nGetting block 7 of 8\r\n  Reserving size (1114) for bucket 7\r\n  Calculating Z arrays for bucket 7\r\n  Entering block accumulator loop for bucket 7:\r\n  bucket 7: 10%\r\n  bucket 7: 20%\r\n  bucket 7: 30%\r\n  bucket 7: 40%\r\n  bucket 7: 50%\r\n  bucket 7: 60%\r\n  bucket 7: 70%\r\n  bucket 7: 80%\r\n  bucket 7: 90%\r\n  bucket 7: 100%\r\n  Sorting block of length 683 for bucket 7\r\n  (Using difference cover)\r\n  Sorting block time: 00:00:00\r\nReturning block of 684 for bucket 7\r\nGetting block 8 of 8\r\n  Reserving size (1114) for bucket 8\r\n  Calculating Z arrays for bucket 8\r\n  Entering block accumulator loop for bucket 8:\r\n  bucket 8: 10%\r\n  bucket 8: 20%\r\n  bucket 8: 30%\r\n  bucket 8: 40%\r\n  bucket 8: 50%\r\n  bucket 8: 60%\r\n  bucket 8: 70%\r\n  bucket 8: 80%\r\n  bucket 8: 90%\r\n  bucket 8: 100%\r\n  Sorting block of length 449 for bucket 8\r\n  (Using difference cover)\r\n  Sorting block time: 00:00:00\r\nReturning block of 450 for bucket 8\r\nExited Ebwt loop\r\nfchr[A]: 0\r\nfchr[C]: 2117\r\nfchr[G]: 3176\r\nfchr[T]: 4236\r\nfchr[$]: 5940\r\nExiting Ebwt::buildToDisk()\r\nReturning from initFromVector\r\nWrote 4196453 bytes to primary EBWT file: test.1.bt2\r\nWrote 1492 bytes to secondary EBWT file: test.2.bt2\r\nRe-opening _in1 and _in2 as input streams\r\nReturning from Ebwt constructor\r\nHeaders:\r\n    len: 5940\r\n    bwtLen: 5941\r\n    sz: 1485\r\n    bwtSz: 1486\r\n    lineRate: 6\r\n    offRate: 4\r\n    offMask: 0xfffffff0\r\n    ftabChars: 10\r\n    eftabLen: 20\r\n    eftabSz: 80\r\n    ftabLen: 1048577\r\n    ftabSz: 4194308\r\n    offsLen: 372\r\n    offsSz: 1488\r\n    lineSz: 64\r\n    sideSz: 64\r\n    sideBwtSz: 48\r\n    sideBwtLen: 192\r\n    numSides: 31\r\n    numLines: 31\r\n    ebwtTotLen: 1984\r\n    ebwtTotSz: 1984\r\n    color: 0\r\n    reverse: 0\r\nTotal time for call to driver() for forward index: 00:00:00\r\nReading reference sizes\r\n  Time reading reference sizes: 00:00:00\r\nCalculating joined length\r\nWriting header\r\nReserving space for joined string\r\nJoining reference sequences\r\n  Time to join reference sequences: 00:00:00\r\n  Time to reverse reference sequence: 00:00:00\r\nbmax according to bmaxDivN setting: 1485\r\nUsing parameters --bmax 1114 --dcv 1024\r\n  Doing ahead-of-time memory usage test\r\n  Passed!  Constructing with these parameters: --bmax 1114 --dcv 1024\r\nConstructing suffix-array element generator\r\nBuilding DifferenceCoverSample\r\n  Building sPrime\r\n  Building sPrimeOrder\r\n  V-Sorting samples\r\n  V-Sorting samples time: 00:00:00\r\n  Allocating rank array\r\n  Ranking v-sort output\r\n  Ranking v-sort output time: 00:00:00\r\n  Invoking Larsson-Sadakane on ranks\r\n  Invoking Larsson-Sadakane on ranks time: 00:00:00\r\n  Sanity-checking and returning\r\nBuilding samples\r\nReserving space for 12 sample suffixes\r\nGenerating random suffixes\r\nQSorting 12 sample offsets, eliminating duplicates\r\nQSorting sample offsets, eliminating duplicates time: 00:00:00\r\nMultikey QSorting 12 samples\r\n  (Using difference cover)\r\n  Multikey QSorting samples time: 00:00:00\r\nCalculating bucket sizes\r\nSplitting and merging\r\n  Splitting and merging time: 00:00:00\r\nAvg bucket size: 741.625 (target: 1113)\r\nConverting suffix-array elements to index image\r\nAllocating ftab, absorbFtab\r\nEntering Ebwt loop\r\nGetting block 1 of 8\r\n  Reserving size (1114) for bucket 1\r\n  Calculating Z arrays for bucket 1\r\n  Entering block accumulator loop for bucket 1:\r\n  bucket 1: 10%\r\n  bucket 1: 20%\r\n  bucket 1: 30%\r\n  bucket 1: 40%\r\n  bucket 1: 50%\r\n  bucket 1: 60%\r\n  bucket 1: 70%\r\n  bucket 1: 80%\r\n  bucket 1: 90%\r\n  bucket 1: 100%\r\n  Sorting block of length 1020 for bucket 1\r\n  (Using difference cover)\r\n  Sorting block time: 00:00:00\r\nReturning block of 1021 for bucket 1\r\nGetting block 2 of 8\r\n  Reserving size (1114) for bucket 2\r\n  Calculating Z arrays for bucket 2\r\n  Entering block accumulator loop for bucket 2:\r\n  bucket 2: 10%\r\n  bucket 2: 20%\r\n  bucket 2: 30%\r\n  bucket 2: 40%\r\n  bucket 2: 50%\r\n  bucket 2: 60%\r\n  bucket 2: 70%\r\n  bucket 2: 80%\r\n  bucket 2: 90%\r\n  bucket 2: 100%\r\n  Sorting block of length 469 for bucket 2\r\n  (Using difference cover)\r\n  Sorting block time: 00:00:00\r\nReturning block of 470 for bucket 2\r\nGetting block 3 of 8\r\n  Reserving size (1114) for bucket 3\r\n  Calculating Z arrays for bucket 3\r\n  Entering block accumulator loop for bucket 3:\r\n  bucket 3: 10%\r\n  bucket 3: 20%\r\n  bucket 3: 30%\r\n  bucket 3: 40%\r\n  bucket 3: 50%\r\n  bucket 3: 60%\r\n  bucket 3: 70%\r\n  bucket 3: 80%\r\n  bucket 3: 90%\r\n  bucket 3: 100%\r\n  Sorting block of length 975 for bucket 3\r\n  (Using difference cover)\r\n  Sorting block time: 00:00:00\r\nReturning block of 976 for bucket 3\r\nGetting block 4 of 8\r\n  Reserving size (1114) for bucket 4\r\n  Calculating Z arrays for bucket 4\r\n  Entering block accumulator loop for bucket 4:\r\n  bucket 4: 10%\r\n  bucket 4: 20%\r\n  bucket 4: 30%\r\n  bucket 4: 40%\r\n  bucket 4: 50%\r\n  bucket 4: 60%\r\n  bucket 4: 70%\r\n  bucket 4: 80%\r\n  bucket 4: 90%\r\n  bucket 4: 100%\r\n  Sorting block of length 469 for bucket 4\r\n  (Using difference cover)\r\n  Sorting block time: 00:00:00\r\nReturning block of 470 for bucket 4\r\nGetting block 5 of 8\r\n  Reserving size (1114) for bucket 5\r\n  Calculating Z arrays for bucket 5\r\n  Entering block accumulator loop for bucket 5:\r\n  bucket 5: 10%\r\n  bucket 5: 20%\r\n  bucket 5: 30%\r\n  bucket 5: 40%\r\n  bucket 5: 50%\r\n  bucket 5: 60%\r\n  bucket 5: 70%\r\n  bucket 5: 80%\r\n  bucket 5: 90%\r\n  bucket 5: 100%\r\n  Sorting block of length 677 for bucket 5\r\n  (Using difference cover)\r\n  Sorting block time: 00:00:00\r\nReturning block of 678 for bucket 5\r\nGetting block 6 of 8\r\n  Reserving size (1114) for bucket 6\r\n  Calculating Z arrays for bucket 6\r\n  Entering block accumulator loop for bucket 6:\r\n  bucket 6: 10%\r\n  bucket 6: 20%\r\n  bucket 6: 30%\r\n  bucket 6: 40%\r\n  bucket 6: 50%\r\n  bucket 6: 60%\r\n  bucket 6: 70%\r\n  bucket 6: 80%\r\n  bucket 6: 90%\r\n  bucket 6: 100%\r\n  Sorting block of length 964 for bucket 6\r\n  (Using difference cover)\r\n  Sorting block time: 00:00:00\r\nReturning block of 965 for bucket 6\r\nGetting block 7 of 8\r\n  Reserving size (1114) for bucket 7\r\n  Calculating Z arrays for bucket 7\r\n  Entering block accumulator loop for bucket 7:\r\n  bucket 7: 10%\r\n  bucket 7: 20%\r\n  bucket 7: 30%\r\n  bucket 7: 40%\r\n  bucket 7: 50%\r\n  bucket 7: 60%\r\n  bucket 7: 70%\r\n  bucket 7: 80%\r\n  bucket 7: 90%\r\n  bucket 7: 100%\r\n  Sorting block of length 912 for bucket 7\r\n  (Using difference cover)\r\n  Sorting block time: 00:00:00\r\nReturning block of 913 for bucket 7\r\nGetting block 8 of 8\r\n  Reserving size (1114) for bucket 8\r\n  Calculating Z arrays for bucket 8\r\n  Entering block accumulator loop for bucket 8:\r\n  bucket 8: 10%\r\n  bucket 8: 20%\r\n  bucket 8: 30%\r\n  bucket 8: 40%\r\n  bucket 8: 50%\r\n  bucket 8: 60%\r\n  bucket 8: 70%\r\n  bucket 8: 80%\r\n  bucket 8: 90%\r\n  bucket 8: 100%\r\n  Sorting block of length 447 for bucket 8\r\n  (Using difference cover)\r\n  Sorting block time: 00:00:00\r\nReturning block of 448 for bucket 8\r\nExited Ebwt loop\r\nfchr[A]: 0\r\nfchr[C]: 2117\r\nfchr[G]: 3176\r\nfchr[T]: 4236\r\nfchr[$]: 5940\r\nExiting Ebwt::buildToDisk()\r\nReturning from initFromVector\r\nWrote 4196453 bytes to primary EBWT file: test.rev.1.bt2\r\nWrote 1492 bytes to secondary EBWT file: test.rev.2.bt2\r\nRe-opening _in1 and _in2 as input streams\r\nReturning from Ebwt constructor\r\nHeaders:\r\n    len: 5940\r\n    bwtLen: 5941\r\n    sz: 1485\r\n    bwtSz: 1486\r\n    lineRate: 6\r\n    offRate: 4\r\n    offMask: 0xfffffff0\r\n    ftabChars: 10\r\n    eftabLen: 20\r\n    eftabSz: 80\r\n    ftabLen: 1048577\r\n    ftabSz: 4194308\r\n    offsLen: 372\r\n    offsSz: 1488\r\n    lineSz: 64\r\n    sideSz: 64\r\n    sideBwtSz: 48\r\n    sideBwtLen: 192\r\n    numSides: 31\r\n    numLines: 31\r\n    ebwtTotLen: 1984\r\n    ebwtTotSz: 1984\r\n    color: 0\r\n    reverse: 1\r\nTotal time for backward call to driver() for mirror index: 00:00:00\r\n\r\n```\r\n\r\nThis makes me very sad..."},"comment":{"url":"https://api.github.com/repos/BenLangmead/bowtie2/issues/comments/213523164","html_url":"https://github.com/BenLangmead/bowtie2/issues/36#issuecomment-213523164","issue_url":"https://api.github.com/repos/BenLangmead/bowtie2/issues/36","id":213523164,"user":{"login":"val-antonescu","id":3092260,"avatar_url":"https://avatars.githubusercontent.com/u/3092260?v=3","gravatar_id":"","url":"https://api.github.com/users/val-antonescu","html_url":"https://github.com/val-antonescu","followers_url":"https://api.github.com/users/val-antonescu/followers","following_url":"https://api.github.com/users/val-antonescu/following{/other_user}","gists_url":"https://api.github.com/users/val-antonescu/gists{/gist_id}","starred_url":"https://api.github.com/users/val-antonescu/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/val-antonescu/subscriptions","organizations_url":"https://api.github.com/users/val-antonescu/orgs","repos_url":"https://api.github.com/users/val-antonescu/repos","events_url":"https://api.github.com/users/val-antonescu/events{/privacy}","received_events_url":"https://api.github.com/users/val-antonescu/received_events","type":"User","site_admin":false},"created_at":"2016-04-22T17:38:08Z","updated_at":"2016-04-22T17:38:08Z","body":"Release 2.2.9 is fixing this issue. I will close this for now.\r\n\r\nthanks,\r\nVal"}}