threads crashing

[ghost]

Hi,

repeatedly getting this error when using:

mapPacBio.sh ref=in.fa nodisk=t ambig=all local=t maxindel=50 nzo=t outm=mapped.fa in=reads.fa nodisk=t

I'm mapping an assembled ~4Mbp chromosome onto another draft one of similar size.

Thanks,

Theo

java -Djava.library.path=/home/theoa/bin/bbmap/jni/ -ea -Xmx276730m -cp /home/theoa/bin/bbmap/current/ align2.BBMapPacBio build=1 overwrite=true minratio=0.40 fastareadlen=6000 ambiguous=best minscaf=100 startpad=10000 stoppad=10000 midpad=6000 ref=../chr20/chr20scafs.fa nodisk=t ambig=all local=t maxindel=50 nzo=t outm=.//drom_chr20scafs.outm.fa in=genomes/drom.fa nodisk=t
Executing align2.BBMapPacBio [build=1, overwrite=true, minratio=0.40, fastareadlen=6000, ambiguous=best, minscaf=100, startpad=10000, stoppad=10000, midpad=6000, ref=../chr20/chr20scafs.fa, nodisk=t, ambig=all, local=t, maxindel=50, nzo=t, outm=.//drom_chr20scafs.outm.fa, in=genomes/drom.fa, nodisk=t]

BBMap version 36.11
Set MINIMUM_ALIGNMENT_SCORE_RATIO to 0.400
Retaining all best sites for ambiguous mappings.
Executing dna.FastaToChromArrays2 [../chr20/chr20scafs.fa, 1, writeinthread=false, genscaffoldinfo=true, retain, waitforwriting=false, gz=true, maxlen=536670912, writechroms=false, minscaf=100, midpad=6000, startpad=10000, stoppad=10000, nodisk=true]

Set genScaffoldInfo=true
Set genome to 1

Loaded Reference: 0.001 seconds.
Loading index for chunk 1-1, build 1
Indexing threads started for block 0-1
Indexing threads finished for block 0-1
Generated Index: 2.883 seconds.
Analyzed Index: 0.798 seconds.
Started output stream: 0.024 seconds.
Cleared Memory: 0.384 seconds.
Processing reads in single-ended mode.
Started read stream.
Started 46 mapping threads.
Exception in thread "Thread-48" java.lang.AssertionError: -22, -22
259420, 1,0,17646635,17654197,0,00,293,97148,404340,0,365546,,mmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmSmSmSSSSmmSSSSmSSSmSSSSSSSmSSmmSSSSmSSSmmSmSSSmSSSSmmSSSSSmSSSSSSSSSSSmSSSmSSSSSSmmSSSSmSmSmSSSmmSSmSSSmmSSSSSSSSmSSmmSSSSSSSmmSmSmSmSSSmmSSSSmSSmmSSSmSSSSmSSmmSmSSSmSSSSSSSmmSSmSSSSmSSSSmmSSSSSSSSSmSmSSSSSSSSSSmmmmmmSSSmSSSSSSSmSSSSSSSSmmSSmSSSSSmmSSSmSSSSmSmSSmSSSSSSSmSSSSSSSSSSSSmSSmSSSSmSSmmmSmmmSSSSmSSSSSSmmSSSSSSSSSSSSSSmSSSmmSSSSSSSmmSSSmSSmSSSSmSSmSSSSSmSmSmSSSmmSSSmSSSSSmSmSSmSmSSmSmSSSSmSSmSSSSmSmSSSSSmmSSSSSmSmSSmSSSSmSSmSmSmSmmmSmSSSSSmSSSmSSSmSmSSSSSSSSmmSSmSSSSSmSSSSSSSSmSSSSSmSSSSSSSmSSSmSmSSmSSSSSmSSSmSSSSmSSSSSSmSSSSSSSSSSSSSSSmSSSmSSSSSSmmSSSSSSSSSSSSSmSSSSSSSmmSSSSSmSmSmSSmmSmSSSSSmSSSSSmmSSmSSSSSmSSSSSmSSSSSSSSSSSmSSSSSSSSSmSmSSSSSSSSSSSSSmSSSmSSmSSSSSSSSSSSSSmSSSmSmmSSSSmmSSmmSSSSSmSSmmSSSSSSSSmSSSSSSSmSSSSSSSmmSSmmmmSmSSSmSSSSmmSSmSmSSSSmSSSSSSmmmSmmmmSSmmSmSmSSmSSSSSSSmSSSSSSSSSSmSSSSSSmSSmSSmSmSSSSSSmmmSSSSSSSSmSmmSSSSSSSSSSSSmSSSSSSSmmSSSSSSSSmmSSSSSSSSSmSSmSSSSSmSSmSSSSSSSSSmmSSmSSSSmmSSSmSSmSSSSmSSmSSSmmSSSmmSmSSSSSSSSmmSSSmSSSSmSSSmSSSmSSmmmSSSmmSSSmmSSSmmSSSSSSSSSSmmSSSSSmSmSSSSSSSmSmSmSmSmSSSmSSmSmmSmSmSSmSmSSmSSmSSmSSSSmSSSSmSSSSSSSSSmSSSSSSSSSSmSmmSmSmmSSSSSmSSSSSmSmSSSSSSmSmSSSSmmSSmSSSSmSSSSmmSSSSSmmSSSSmSSSSmSSSSSSmSSSSSSmSSmSSmmSmSSmSSSSSSSSSSSSSmSmSSmmSSSSmSSSmSmmSSSmmSSSSmSmSSmmmSSSSmmmSmmSSSSSSSSSSSSmSmSSmSSSSSSSSSmmSSSSSmSSSmmmSmmSmmmSmSmSSmSSSmmSSSSSSSmSSSSSSSmSSmmmSSSSmSmSSSSmmSSSSSmSSSSSmSSSSmSSSmSSSSmmSSSSmSSmSmSSSSSSmSSmSSSSSmSSmSSSmmmmSmSSSSmSSSSSSSSSmSSmSSSSSSSSSSSSSmSSSSSmSSSSmSmSSSSSSSSSSSSSSSSSSSSSmSSSSSSSSSSSSSSSSSSmSmSSSmSSSSmSSSmSmSmSSSSmSSSSSSSSmSmSSSSmSmSSSmmmSSSmSSmSSmSSSSmmSSSSSmSSSmmSSmSSSSSSmSSSSSSSSSSSSSSSSSSSSmSSSSSmmmSSmSSSmmmSSmSSSmmSSmSmSSmSSmmSSmSmSSSSSSSSmSSSSSSSSNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNmSSSSSSSSSmSSSSSSSmmSSmSmSSSmSSSSmmmmSSSSSSSSSSSSmSSSSSSmmSSmSSSSSSSSSSSSmSSSmmSSSSmmmSSmSSSSmSSSmSmSSmmmSmSSSmmmSSSSSSmmSSSSSSSmSSSSSSSSSSSSSSSSSSSSSSmSmSSSmmSmSSSSmSmmSSSSSSSSSSmSSSSmSSSmSSSSSSSmSSSmSSSSSSSSSSSmSSSSmmSSSSSSSmSSSSSSSSSSSSmmSSmSSSSmSSSmSSmSmmmSSmSSmSmmSSSmSSSSmmSSSSSSmmSSmSmSSSSmmSmSmSSmmSSSSSSSmSmmSSSmSmSSSSSmmSSSSmmSSmSSSSmSSSSmSSmmSSSmmSmSSSSmmSSSSSSSmSSmmSSmmSSSSSSSSSSSSSSSSSSSSSSSSSSSSmSmmSmSmmmSSSmSmSmSmSSSSSmSSSSmSSSSSmSmmSSSSSmmSmmSmSSSmSSmSmSmSSSmSmSSmmmSSSSSSmmmSSSSSSSSmmSmSSSSSSSmSmmSSSSSSmmSSSSSSmSmSSSSSSSSSSmSmSSSmSSSmSSmmSmSSSmSmSSSSSSSmmmSSSmSSSmSSSmSSmSSSSSSSSSSSSSSSmmSSmSSmSSmSmSSSSSSSSSSSSmSmSSmmSSSSSmmmmSSSSSSSSSmSmSSSmSSmSSSSSmSSSSSSmSmmmmSSSSmSmSSSSSSmmSSSSSSmSSSSSSmSSSSSmSmSSSSmmSSSSSSmSmSmSmSSSSmSSSSSSmSmSSSSSmmmSSmSmSSSmmSSSSSSSSSSSSmSSSSSmSmSmmSmmSSSSSSSSSSSmSSSSSSSSSSSSSSmSmSSSSmSSSSmSSSSSSmSmSmSmSSSmmSSSmmSSSmSSSmSmSSmmmmSmSmSmSSSmSmSmSSSSmSSSSSmmSSSmmSSSmSmSSmSmSmSmmSSSSmmSSSSSSSSmSSSSSSSmmSmmmSSmmSSSmSmSSSSSmSSmSSSmSmSSmSSSSSSmSmSSmSSSSSmmSmSSSSSmSmSSSmmSSSSSmSSmSSmmSSmmSmmSSSSSmSSmSmmmSSSSSSSmSSmSmSSSSSSSSSmSmSSmSSSSSSmSSSSSSSmSSSmSmmSSSSSSSSSSSSmmSmSmmmmSmmSSmSmmSSSmmSmSSSSSSmmmSSmSmSSSSSSSSSmSSmSSSSSmSmSSmmmSSSmmmSSSmSmmSmSSSSmSSSSSSSmmSSSSmSmmSSSSmSSSmSmSSSSSSmSSSSmSSSSmSSmSSSSSSSmSSSSmSmSSmmSSSSmSSSmSSSmSSSmSSmSSmmSSSSmSSSSmSSSSSSmSSSmSSSSSSmmmSSSSSmSSSSSSSSSSmmSSSSSSSSSSSSSSSSSSSSSmSSSmSSSmmSSmSSSSSmSSSmmSSSSSSmmSSSSSSmSSSSSSmSSmmSmmSSSSSSSSmmSSSSmmmmSSSSSSmSSSSSmmSSSmmmSmSSSSSmSmSSSSSmSSmSSmSmmSmmSSSSSmSSSSSSSSSSSSmSSmSSSSSSSSSSSSSSSSSSSmSSSSSSSSSSmmSSSSSmSSSSSSmmmSSSSSSSSmSmSSSSmSmmSSSSSSSSmSSSSSSSmmSSmSSmSSSSSSSmmSSmSmmSSSSSSSmSSmSmmSSSSSmSSmSSSSSSmmmmSSSSSSSSSSSmmSSSSSSmSSSmSSSSSSSSSSmSSmmSSSSSmSSSSSSSmSSSmSSSSmSSSSSSSSSSSmSmmSSSSSSmSSSSmSSSSSmSSSSSSSSSSmSmSSSSSmmSSSSmSSmmmmSmSSmmmSSSSmSSSSmmmSSmmmSSmmSSmSSSSmSSSSSSSSSSmSmSmmSSSSSSmSSSmSmSmmSSSSSSmSSmSSSSSSmSSSSmSSmSSmSSSSSSSSSmmSSmSSSSSSSSSSmSSSmSSSSSSSSSSSSmSmSmSSSSSSSSSmSSSSSmSSSSSmSSSSSSSmSSSmSSmSSSSmSSSmmSSSmSSmSSmSmSSmSSSSSSmSSSSmSSSSSSSSSSmmmSSSmSSSSSSSSSSSmSSSmSmSSSmSmSSmSmmmmSSSSmSSmmSSSmSSSmmSmSSSSSSSSSSmmSSmSSmmSmSSmmmSSSSSmSSSSSSmmSSmSSSSmSSSSSSSSSSSSSSmSSSSSSmSSSmSSSSSSmSSSmSSSSSSSmSmSSmSSSSSSSmmmSSSmSSmSSSSSSSSSSSSmmSSSSSSmSmSSSmSSSSSSSSmSSSSSSmmSSSSSSSSSSSSSSSSmmSSSmSmmSSSSmSSSSSmSSSmSSSmSSSSmSSmSmSSmSSSSSSSmSSSSSSSSmmSSSSSSSSmSSSSSSSSSSSSSSSSmSSSSSSSSSSSSSSSSSSSSSmSSmSSSSmSmSSmSSSSSSSmSSmSSSSSSmmSSSmSSmSSSSSmmSSSSSSSSSSSSSmSSmmmSmSSmSSmmSSSSSSSSmSSSSmSmSmSSSmSSSSSSSSSSSmSSSSSSSmSSSSSSSmmSmSmSSmmSSSSSmSSSSSmSSSSmSSSSSSSSSSmSmSSSSSSSSmSmSSSSmmmSmSSSmmSSSmSSSSSmSmSmmSSSmSSmSmmSSSmmmmmmSSmSSmSSSSmSSSSmmSSSSSSSSSmmSmSSSSmmSmSSmmSSSSSmSSSSSSmSSmSSmSmmSmSSSSmmSSmSSSSSSSSmSSSSmmSmmmSSSSSSSmmmSmSmmmSSSSmSmmmmSmmSSSmSmmmSmSSSmmSSSSmSSSSSSSSSmSSSSSmSmmSSSSSSSSSSSSmmSmSSSSSSSSSSmSSSmSSSSSmmSSSSSSSSSSSmSSSSSSSSSSSmSSmmSmSSmSSSSmSSSSSSSSSSmmmSSSSSmSmSSSSmSSSSSSSSSSmSSSSSSS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AGCTACAAGGTACAAAATCAACACACAAAAATCAGTTGTCTTTCTACACATTAATAATGAAACATCAGAAAGAGACATTTTTTTAAAATCCCATTTACCATTGCACCCAAAAAAAATACCTAGGAATATATTTAATCAAGGGTGTGAAAGACCTGCACACTGAAAATCCTAAGACACTGAGGAAAGAGACTGAACAGACACAAATAAATGGAAGCTTACCCTCTGCTCACAGACAGAACGAATTAATGTTGTTAAAATGTCCATTCTACCCAAAGCAGTGCTCAAATTCAAAGCAAGCCTCGTCAAATCACTGTGCCCTCCACCAGAAAATAACAGAACATCGTGAATTGACTATACTTCAATAAAAAAAAAAAAAAAAACTTCAGTGGCATTTTTCACAGAAACAGAACAAACATTCCTAACATTCCTGTGGAAACACAAAGGACCCTGAACAGCCAAAGAGATTCTACAAAAGGGAAACAGGCTGGAGGCATCTCCCTCCCTGACTTCACACAGCATTACAAAAGCACAGTCACCAAAAAGGTGTGGAATTGGCACAACCACAGGGACATGGACCAGAGAGAGTCCAGTCTACAAACAAACCTACGGGTGTGTGGTCAGTCAATTCACAAGAAAGGAGCCAGGAACCTGCACCGGGGAAAGGACAGTCCCCTCGATGAATGGTGCTGGGAAAACTGGACACCACACGCCAAAGAAGGACGCGGCACACCGTCTGCACCACACACAGAACCTGACTAAAAACCCACAGCTTCCCACATCCGGCTATTCCTCTCCCGGGGCCTCTGAGGAGGGCCTCCCCTCAGCAGTCAGCCCCTCACGGGAAGCTTCTCCTCACTTCCCCTCACTTTCCCTTCCTCCTCACCTTCCCTCAGGGCAGCACCTCCTGTTGCGTCCTGAGGAGACTGGGCTCCTGTCAGCGTGGACCTAACCCCCTGTTGTCCCAAAGCCCCGGCAGGTCCAGAGGAGACGCGGCTCCAGTCAGGTGCGCAGGACGCCAAGTCCTCGGGCGGAACGCACGCACGGTTCCCGCTGCAGGTGGGGGAGGCGGGGCCCCGGGCCACCCCGCCCAAAAAAACGCGGACCCAGTCGCCCTCACTGCCAGTGGAGGCCCCGCCCTGACAGCGGTTCTGCTCAGTCCTTTAAACTGGAAATTCAAACTGAAATGGAGCCAAGTATCTGTAACTTCTCCAAATGCTTAGAAACAATCGACTGGAAGCCCTACGGAATGAAGTGAACGGAGACACAAACTTTAAACCTTACACCCTTGTCTACTGAGCTTTCATGGTAACCTGCCATAAATGACTTCCTCCCTCCCCGAGGCCTCGCTTTTGTTTTTAGCTGAAGGTGATATTCAAGGTGATGCTTCTGGCCATTTCAGGGAGGGAGTCAGTGTTCCTGGGTCTCTCCCCTGTATACAGGAGGTATGCAAGTTATTAAACCTGTTTGTTCTTCTCCCAGTAATCTGTCTTATTAGGGGCTGGGAGGTCTCTTCCCAGAACCTAGAAGGACAGAGGGAAAGCTGGTTTTCCTCCCACACACACGCAATGGAATTCTTCTCAGCAATAGACATTACACCATCAGCCCAGGGAAAGGCACGGGTAAGTCTTACTTGTGATGCAGGAAACCAGATGCGGGGCATGAGGGCCGTGTCCCAGGTCTCACTTGAGCCCCTGGGACGTGCCCCGCCAAGTGTGGGTCCTTGGCTTCACGCAGGAAAGAATTCAAGGGCGAGCCACAGTTGAGTGAAGGTAGATTTATTCAGAGAGATACATTGAAAGGCAAGAGAAAGGCCACGAGGGGTCGGGGTTGGGTGCTCAGATTAAAATAGGTACACATTCCATAGACAGAATGCGGGCCATCTCTGAAGAGGGAGAGAGAGAGGGGTGGCCGCGAGGTGCCATGTTGCTGGCTTTTATGGGCTTGGTGGCTTCATACGCTAGTAAGTGGAAGGACCAGTCTAAGGGGAAGGGGCTGGGATTCCCAGGAAGTTGGCCATTTCCCACCCTTTGACCTTTTGTGGCTAGCCTTGGGACTGCCACGGTGCCTGTGGGTGTGTTAGTCACCATGTTAATATATTACAATGGGTGTATAATGAAGCTCAAGATCTACTAGAAGTTAAATCTCCCATCATCCTGAGCCTCAAGGCCTACAGGAGGTTGAATCTTTCACCATTTTGATGTTAATTGCTGTGGCATTCCTTGAGTGGCTGTGCCCTGCCCCCTTCCTGTCTCACTTGCAAATTACTAAGTGAAAGAATCCAGTCCGAGGAGGCTGCACACAGTATGACCCTATTTACGACAATTATGGAAAAGGCAAAACTACGCACATGAGCAGATCATTGGGTGGGAGTGGGGGGGTGAAGTGTTCCATGTGAAACTTCAGCTGGTGTCACTATAAGTATGTCTAAGCCCACACCTTTGCACAGCCCAAAGGTCAGTCATAATCTATTCAAATTTAGTTGTTTAGGGTGTAGCAGCATCACAGGATGGAACATACAGGGTGACAGAATCTAACTGTATTAGAAATAGGTGGAAAAACTCTCAGCCGGTGGTGGGGCAAGAGGTGCTGGCCTAAGTGAACTTTGGAAATGCACAGAATCATTCTGCAAAGGCAGAATGGACCACTGTTAACCTGTGGGCTTTGTATTATAGAGTTCTTTCTGGGGTGTAGTGGCTAACAATTCTGAAGCCACTGTGAATGGAACCTGGAAAAGAGAAATGAGTTGATAAAGGGCAGGTGGTGGGAGCCAGGCTCCTCGCTGTGGGAATGGCAAGTCAGAGATGAGCAAGGGGAGGGCCTTGGCCCTCATACTCCTGGATCTGAGTTTCCTAGGTGGATGGCGTGGGGAGTGGACTGGCCAGGGGAAGGCACAGCTCTTTACCCTGGGAAGGCCCTGCAGATGTAGGAACCTCACACCCCTTTCTTCCCCCCATACCTGCTGGAAACACCCAGACCTTTGAAATCAGCCAATGCAGCTTTTCAGACATTCTCACCCCGAGGCAGATAAAGGAGCGTGAGGGTCTTGCACCACCCCCAAGCTGTCCCTGGAGGGTGGAGCCAGGATGGGGTAACTGGATCTCTGACCAGCAGGCCAAAGCAAGGAAGAAGACCAGTCCTGAGGGCAGGGGTCTCCTGAAGTCTGTGAGCCCGGTGCCCTGATGGGATTCATTCCCTGTGGGGACATGGGCGGGGCCTGCAGTGGTTCTGTTTTCCACCTGTGCCCCTTGAATGAGGTCAGGGCAGAACTGGACTCAGGGATCCCCTGGCAGTGTTTCAGTCTCACACAGTGGCTTTATAAAGGAACAGGAGAGTGAAGCTGAGCACCTGACAGCCACTCCTCTCTGGCTCTGAGCTGCTTCCATCAGGACCACAGTCCCCTGCATGGAGTCTGCTGTAACCCACCTGCCCCAACCTGGGCTCTCCTCTTCCTGGATCCCACTCCCAGGCCAGATGCATCTGTCTAACCACTGCATCCTCCTCTCACCTTGAGGCTGACAGGCTCCACACAGGACTGTTGTCCTGCCACTCCCCACACCCCAGGAGGCAGCCCCACCTTCCCTGGTTGCTGAGCTGAGACGCCTGGGGCTTCCCAATCCCCCACTTTCCTACTGCCCTGGTGACAGTCAGCTCTTCCTCCCAAAATCCCAGGTGGGGTTTTGCAGAAATTGACAACCAATCTAAAATTCATGTGGAAAAGGCAAGGAGCTCAGAATAGACCAAGGAATCCTGAAAAAGAAGAACAAATTTGGAGGTATGGAAAACCAGGCAGAATCCCATAGTTGGTATAAAGCCACACTAGCCTTAGTCTAGCCCTGACTCATACCCATACCTTACCCTAACCCTAAATTTAACCCATACCCCTTAACCATAACAGGTTTAAAAAAAAAAAAAAAAAAAAAGATCGTGTACTACAAGCGTCTCTACACCAGAAACCCAGGTTTTTCAACATATTAAAACCAAGCAATGTAATATACCATAGTAACTATGTGACATAAAAACACAAGGTTATGTCAATTGATACAGAAAAAACTTTACACAAAATCCAGTGCTGTTTCATATTCATAAACACGCAAGACAGTAAAAGGAAATTTGTTCAACATGATAAAATGCATTATGCAAAACCCGTAGCAAACTTCATGCTCAATGATGAAGAACTAAAAGGTTTACTCCTGAAATCAAGAACAAGGCCATGATGCTGGCTTTCCCCACTGTTACTCAGTATTGCACTGGAATAACTGCACTGAGCAATGAGGAAAGAAGGAAGATGCAACCACATGTGAAAGGAAAAAGTAAAACGGCTTCTATTCAAAGACACAATTCACATCATCTTATATATAGACCCTCCTAAAGAATCAACTAAAGACTATTTGAGCTTCTAAACTAATTCAGCAAAAGAGTAGAACAAAACATCAATCAACAAAAATCAACTTTATTTGTAGACACTAGCAATGAATAATCTGTAAAAGATTTTAACAAAACAATTCCCTTTTAAATAATTTCAACATTAATGCAATACTTTGGGAGGAGGTTTAATAAGGATGCAAGACTGGTACACTGAAAGTTATAAAGCACTGGTGAAAGAAATACTAAGTAAATATGCAGACATCCCATGGTGATGGAAGCACTTAATCTTGTTAAGATGGCAAAGATCGCAACAGTACATGATGCAACCTACAGATTCAATGTGATTCCTGTGAAAAGTCCCAAGGCCTAAGGGAAGAAGTACACAAGCCTATCCTACCTTACATATGGAATCACAGGGGACTCCAAAGTCCCAAAACAATCTTGAAAAAGAAAATCAAATTTGGAGGCTCACATTTTCCAATTTCAAATCTTAGCACAAAGCAACAGGAAATGAAACAGTGTGATACTGGCACAAATATATACTTATAGATCTGTGGGACTGAATGGTGAGCCCAGAAATAAACCCATCTGTCTAGGATCACCTGATTTTTGACAACCGTGGGCAATATTAAACTGGGAAAAAATAATGTTTTCAACAAATGGTGCTGGGCAATTGGGTACCCAAGTGTAGAGGAATAAAACTGGGTCCTTACTTCACACCACACACAAAACTAACTCAAGATACATTAAAAAGCTTAAATTTAAAAATAAAAAGAAAAATTACAGTCAACCCTCCTTACCTGCAAGTTCCACATCCACAGAATCAACCAACTTCAAATAGGGAAAAAAACATATTTCGAGAAAGTTCCATTCCGGAAAACTTGAATTTGCTGCATGTCAGCAACTATTTCACATTACTATTTTTCAGAAATATTTACATATCATTTACATTGTATTAGGTGCTATAACTGATCTAGAAATGATTTAAAGTAAACAGGAATTTGTGCTTAGATTATTTGCAAATACTACACCATTTTATATAAAGGACTTGAGCACTGGAACCAATACTTCACAGATAAGGAAGGACAGCTGTATAAACTGTCAAAAAAAAAAATGGGGATAAATCATCTTACCTTGGATTTAGCAATTTTCTTAGATCTGACACCAAAACACAAGCAATGAAAGAAAAAAGATAATTTGCATTTCCTCAAAAGTAAAATTTGTGTGCGTCAAAGATGCTATCCAGAAAGTGAAAAGACAGCCCACAAAATCAAAGAAAATATCTGCACATTATATACCTGAAAAGAATCTTTATCAAGAATATACCAAGAACTTTTACAACTCATAAACAAAAAGACAAACAAGCCAATTTTTAAAACAGTTAAAGAACTTGAAGAGACCCTTCTCCAGACAAGACATACAAAGTCAACAAGCACATGACAATATCATTAGTCATGATGTAAATGCCAATTAGTACAATGCCATCCCCCTTCAAACACACTTAGAATGCTTACAATCAAAAACTGAATAAAAATAACAAATATTCGCAAACCTTAGAGAAACTGGAACCCTTAAACGTTACTTGTGGAATTGGAAAATGGCACAGACTATATGGACAACAGTTTGTCATTTCCT
at align2.TranslateColorspaceRead.realign_new(TranslateColorspaceRead.java:407)
at align2.TranslateColorspaceRead.realign_new(TranslateColorspaceRead.java:638)
at align2.AbstractMapThread.genMatchStringForSite(AbstractMapThread.java:999)
at align2.AbstractMapThread.genMatchString(AbstractMapThread.java:895)
at align2.BBMapThreadPacBio.processRead(BBMapThreadPacBio.java:562)
at align2.AbstractMapThread.run(AbstractMapThread.java:495)
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

---

Warning! 1 mapping thread did not terminate normally.
Check the error log; the output may be corrupt or incomplete.
Please submit the full stderr output as a bug report, not just this message.

---

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

Genome: 1
Key Length: 12
Max Indel: 50
Minimum Score Ratio: 0.4
Mapping Mode: normal
Reads Used: 362346 (2003953468 bases)

Mapping: 1904.373 seconds.
Reads/sec: 190.27
kBases/sec: 1052.29

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

mapped: 2.3202% 8407 1.9465% 39006630
unambiguous: 2.2070% 7997 1.9356% 38787559
ambiguous: 0.1132% 410 0.0109% 219071
low-Q discards: 0.4460% 1616 0.3609% 7231533

perfect best site: 0.0003% 1 0.0000% 17
semiperfect site: 0.0003% 1 0.0000% 17

Match Rate: NA NA 90.8816% 36276111
Error Rate: 62.2730% 8400 6.6342% 2648107
Sub Rate: 62.2655% 8399 2.9901% 1193520
Del Rate: 58.6700% 7914 2.2777% 909169
Ins Rate: 58.8035% 7932 1.3664% 545418
N Rate: 28.0080% 3778 2.4842% 991581
Exception in thread "main" java.lang.AssertionError:
The number of reads out does not add up to the number of reads in.
This may indicate that a mapping thread crashed.
If you submit a bug report, include the entire console output, not just this error message.
5768+2639+0+352322+1616 = 362345 != 362346
at align2.AbstractMapper.printOutput(AbstractMapper.java:1867)
at align2.BBMapPacBio.testSpeed(BBMapPacBio.java:458)
at align2.BBMapPacBio.main(BBMapPacBio.java:35)