Recently I have been using bbwrap.sh from BBMap. It has been perfectly working but there are some problem with the data I am working on now.
So the reference sequence is actually a set of assembled sequences resulted from MegaHit.
The result from head -4 contigs.fa is as follow:
>k49_7 flag=1 multi=2.0000 len=222
GGGACGCACGGCTGGCTCGCTGGAAGAACGAGTGCGGCAGAACAACTACATCATGATCTACCCCGTGCAGGCGGGCGAAACGGGAAGTCGATACATATAGACAGGAGCTTTCGAGTACGCATCGCGAACCGCCTGCGGCACCAAAAACGGCGGATCGACCGGAAAATCCGGAAAATTGCACTATCTTTGTCCGGATTAACAAGAAAGAACATGAGCCTCGTA
>k49_9 flag=1 multi=3.0000 len=783
ATATTGAAGCTCAATCCAATTTTTTATTGCCCCTAAATAATTACCAAGTGTCAATTCGCCTGAAGGTTGAACTCCGCTAAAAATCACTTTTTTATCACTCATTTTATCACCTTCCTTTTTGAACCTGCCACCATCCTCGAATCGCTTTAGTCAAATATGTATCTACTACTCTTATTCATCATTTTTTCGTATTTCTTTTTATTATACCATATAACCAAACATATTCAATATAAAAGCATCTTTTTGGCAATAAAATCTTCCACCGTATTTTTCTAATTGAATAGGTATTATTTTACCAGGATAAGGTGCTCCAAATGCAACATGTCCTTTCCCTCTACCCTGATACATAAATGTTATAATTTAGGATCTAATTCAATCTCAACAATCTGCATATCATCTCCATAAATTTTGTAGTCAATAATATCACCCATATATTTACCACCTTTCATAATTAGTTAATATTTATTATTTAATTATATCATCATTGAAAAAAATATATCCATATTCTCTTATTTAATCTTCATAAAATAATCCCCGAAAATTCGGGGATTATTTTCATTCTTGCTGCGGATAAAAATCTTTATACAAATCTGTATTTGTATTATTAAACTCTCTACATATATCATTATATTCTTCACATTTACATCCTGAAACGTTTTGACAGTATCCAAACGAAGGAAGCAACAATTGTACTTTTAATGCGGCTGATATGATATTATAGATTCCTACTGTTAACGTTTTATTCACTTCATCGATATAAAGTACATTACTATATGTGTCTAA
Where the sequence used to align is originally a fastq file and I transform it to a fasta file.
The result from head -4 input.fas is as follow:
>Seq_1
ATAAACCTTTTTGCTTCTTCTACAATTTTCAATATCGGATATTCAATGTTGGTATCTTTAATCATATTCATCTGCGTACCAACACCCGCCGATGTTCCGTC
>Seq_2
TGTGGGTAACAGAACCTCTGGAGGGTAAAACTTGAATAAGTTGCACGATTGCACTATAAGTGGCAAAGTGCACAGAGACATCATCCTAGATATTATGAAGA
The command I typed is
bbwrap.sh ref=./contigs.fa in=./input.fas out=./aln.sam.gz kfilter=22 subfilter=15 maxindel=80
Where the expected result is that a aln.sam.gz file will be created so I can extract those unassembled reads using Samtools.
However, the following error popped out:
Executing align2.BBMap [build=1, overwrite=true, fastareadlen=500, kfilter=22, subfilter=15, maxindel=80, ref=./contigs.fa, in=./input.fas, out=./aln.sam.gz]
BBMap version 37.61
Retaining first best site only for ambiguous mappings.
Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: 1
at fileIO.SummaryFile.<init>(SummaryFile.java:135)
at fileIO.SummaryFile.compare(SummaryFile.java:110)
at align2.RefToIndex.makeIndex(RefToIndex.java:63)
at align2.BBMap.setup(BBMap.java:278)
at align2.AbstractMapper.<init>(AbstractMapper.java:57)
at align2.BBMap.<init>(BBMap.java:43)
at align2.BBMap.main(BBMap.java:31)
at align2.BBWrap.execute(BBWrap.java:148)
at align2.BBWrap.main(BBWrap.java:24)
It has been working so well but all of a sudden, this error popped up.
Do anyone ever met the same problem and perhaps could help me out.
Thank you very much!
