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I am trying to perform mapping using pacbio sequences on a whole genome sequence. The back story is that i have produced a whole genome sequence with PacBio and Illumina miseq reads using Canu. My supervisor isn't convinced that the de novo assembly is accurate as there is a large inversion that hasn't been seen before in this bacterial species. I want to use the raw pacbio reads to map over the breakpoints in the genome to prove either way.
I don't really know how the BBmap works so I have been looking online for examples. This is what I have been doing:
This then outputs with an error message:
I guess i have got something wrong in my commands but I'm not sure what. Any help would be great!
Thanks
I am trying to perform mapping using pacbio sequences on a whole genome sequence. The back story is that i have produced a whole genome sequence with PacBio and Illumina miseq reads using Canu. My supervisor isn't convinced that the de novo assembly is accurate as there is a large inversion that hasn't been seen before in this bacterial species. I want to use the raw pacbio reads to map over the breakpoints in the genome to prove either way.
I don't really know how the BBmap works so I have been looking online for examples. This is what I have been doing:
Code:
cd BBtools bbmap/bbmap.sh ref=bbmap/VPI10463_Original.fna bbmap/mapPacBio.sh k=7 in=bbmap/VPI_Reads.fastq maxlen=6000 minlen=200 minratio=0.400 out=bbmap/VPI_mapped2.sam
Code:
bbmap/mapPacBio.sh k=7 in=bbmap/VPI_Reads.fastq maxlen=6000 minlen=200 minratio=0.400 out=bbmap/VPI_mapped2.samjava -Djava.library.path=/home/james/BBtools/bbmap/jni/ -ea -Xmx50283m -cp /home/james/BBtools/bbmap/current/ align2.BBMapPacBio build=1 overwrite=true minratio=0.40 fastareadlen=6000 ambiguous=best minscaf=100 startpad=10000 stoppad=10000 midpad=6000 k=7 in=bbmap/VPI_Reads.fastq maxlen=6000 minlen=200 minratio=0.400 out=bbmap/VPI_mapped2.sam Executing align2.BBMapPacBio [build=1, overwrite=true, minratio=0.40, fastareadlen=6000, ambiguous=best, minscaf=100, startpad=10000, stoppad=10000, midpad=6000, k=7, in=bbmap/VPI_Reads.fastq, maxlen=6000, minlen=200, minratio=0.400, out=bbmap/VPI_mapped2.sam] BBMap version 37.56 Set MINIMUM_ALIGNMENT_SCORE_RATIO to 0.400 Set MINIMUM_ALIGNMENT_SCORE_RATIO to 0.400 Retaining first best site only for ambiguous mappings. Set genome to 1 Loaded Reference: 0.118 seconds. Loading index for chunk 1-1, build 1 Generated Index: 0.067 seconds. Analyzed Index: 0.101 seconds. Started output stream: 0.021 seconds. Cleared Memory: 0.120 seconds. Processing reads in single-ended mode. Started read stream. Started 24 mapping threads. Exception in thread "Thread-3" java.lang.ArrayIndexOutOfBoundsException: 2047 at align2.BBIndexPacBio.getHits(BBIndexPacBio.java:353) at align2.BBIndexPacBio.prescanAllBlocks(BBIndexPacBio.java:654) at align2.BBIndexPacBio.find(BBIndexPacBio.java:566) at align2.BBIndexPacBio.findAdvanced(BBIndexPacBio.java:390) at align2.AbstractMapThread.quickMap(AbstractMapThread.java:743) at align2.BBMapThreadPacBio.processRead(BBMapThreadPacBio.java:400) at align2.AbstractMapThread.run(AbstractMapThread.java:502) Detecting finished threads: 0Exception in thread "Thread-18" java.lang.ArrayIndexOutOfBoundsException: 2047 at align2.BBIndexPacBio.getHits(BBIndexPacBio.java:353) at align2.BBIndexPacBio.prescanAllBlocks(BBIndexPacBio.java:654) at align2.BBIndexPacBio.find(BBIndexPacBio.java:566) at align2.BBIndexPacBio.findAdvanced(BBIndexPacBio.java:390) at align2.AbstractMapThread.quickMap(AbstractMapThread.java:743) at align2.BBMapThreadPacBio.processRead(BBMapThreadPacBio.java:400) at align2.AbstractMapThread.run(AbstractMapThread.java:502) Exception in thread "Thread-26" java.lang.ArrayIndexOutOfBoundsException: 2047 at align2.BBIndexPacBio.getHits(BBIndexPacBio.java:353) at align2.BBIndexPacBio.prescanAllBlocks(BBIndexPacBio.java:654) at align2.BBIndexPacBio.find(BBIndexPacBio.java:566) at align2.BBIndexPacBio.findAdvanced(BBIndexPacBio.java:390) at align2.AbstractMapThread.quickMap(AbstractMapThread.java:743) at align2.BBMapThreadPacBio.processRead(BBMapThreadPacBio.java:400) at align2.AbstractMapThread.run(AbstractMapThread.java:502) Exception in thread "Thread-21" java.lang.ArrayIndexOutOfBoundsException: 2047 at align2.BBIndexPacBio.getHits(BBIndexPacBio.java:353) at align2.BBIndexPacBio.prescanAllBlocks(BBIndexPacBio.java:654) at align2.BBIndexPacBio.find(BBIndexPacBio.java:566) at align2.BBIndexPacBio.findAdvanced(BBIndexPacBio.java:390) at align2.AbstractMapThread.quickMap(AbstractMapThread.java:743) at align2.BBMapThreadPacBio.processRead(BBMapThreadPacBio.java:400) at align2.AbstractMapThread.run(AbstractMapThread.java:502) Exception in thread "Thread-13" java.lang.ArrayIndexOutOfBoundsException: 2047 at align2.BBIndexPacBio.getHits(BBIndexPacBio.java:353) at align2.BBIndexPacBio.prescanAllBlocks(BBIndexPacBio.java:654) at align2.BBIndexPacBio.find(BBIndexPacBio.java:566) at align2.BBIndexPacBio.findAdvanced(BBIndexPacBio.java:390) at align2.AbstractMapThread.quickMap(AbstractMapThread.java:743) at align2.BBMapThreadPacBio.processRead(BBMapThreadPacBio.java:400) at align2.AbstractMapThread.run(AbstractMapThread.java:502) Exception in thread "Thread-6" java.lang.ArrayIndexOutOfBoundsException: 2047 at align2.BBIndexPacBio.getHits(BBIndexPacBio.java:353) at align2.BBIndexPacBio.prescanAllBlocks(BBIndexPacBio.java:654) at align2.BBIndexPacBio.find(BBIndexPacBio.java:566) at align2.BBIndexPacBio.findAdvanced(BBIndexPacBio.java:390) at align2.AbstractMapThread.quickMap(AbstractMapThread.java:743) at align2.BBMapThreadPacBio.processRead(BBMapThreadPacBio.java:400) at align2.AbstractMapThread.run(AbstractMapThread.java:502) Exception in thread "Thread-14" java.lang.ArrayIndexOutOfBoundsException: 2047 at align2.BBIndexPacBio.getHits(BBIndexPacBio.java:353) at align2.BBIndexPacBio.prescanAllBlocks(BBIndexPacBio.java:654) at align2.BBIndexPacBio.find(BBIndexPacBio.java:566) at align2.BBIndexPacBio.findAdvanced(BBIndexPacBio.java:390) at align2.AbstractMapThread.quickMap(AbstractMapThread.java:743) at align2.BBMapThreadPacBio.processRead(BBMapThreadPacBio.java:400) at align2.AbstractMapThread.run(AbstractMapThread.java:502) Exception in thread "Thread-9" java.lang.ArrayIndexOutOfBoundsException: 2047 at align2.BBIndexPacBio.getHits(BBIndexPacBio.java:353) at align2.BBIndexPacBio.prescanAllBlocks(BBIndexPacBio.java:654) at align2.BBIndexPacBio.find(BBIndexPacBio.java:566) at align2.BBIndexPacBio.findAdvanced(BBIndexPacBio.java:390) at align2.AbstractMapThread.quickMap(AbstractMapThread.java:743) at align2.BBMapThreadPacBio.processRead(BBMapThreadPacBio.java:400) at align2.AbstractMapThread.run(AbstractMapThread.java:502) Exception in thread "Thread-11" java.lang.ArrayIndexOutOfBoundsException: 2047 at align2.BBIndexPacBio.getHits(BBIndexPacBio.java:353) at align2.BBIndexPacBio.prescanAllBlocks(BBIndexPacBio.java:654) at align2.BBIndexPacBio.find(BBIndexPacBio.java:566) at align2.BBIndexPacBio.findAdvanced(BBIndexPacBio.java:390) at align2.AbstractMapThread.quickMap(AbstractMapThread.java:743) at align2.BBMapThreadPacBio.processRead(BBMapThreadPacBio.java:400) at align2.AbstractMapThread.run(AbstractMapThread.java:502) Exception in thread "Thread-4" java.lang.ArrayIndexOutOfBoundsException , 1Exception in thread "Thread-8" java.lang.ArrayIndexOutOfBoundsException Exception in thread "Thread-15" java.lang.ArrayIndexOutOfBoundsException Exception in thread "Thread-16" java.lang.ArrayIndexOutOfBoundsException Exception in thread "Thread-12" java.lang.ArrayIndexOutOfBoundsException Exception in thread "Thread-20" java.lang.ArrayIndexOutOfBoundsException Exception in thread "Thread-24" java.lang.ArrayIndexOutOfBoundsException Exception in thread "Thread-5" java.lang.ArrayIndexOutOfBoundsException , 2, 3Exception in thread "Thread-7" java.lang.ArrayIndexOutOfBoundsException , 4, 5, 6Exception in thread "Thread-23" java.lang.ArrayIndexOutOfBoundsException Exception in thread "Thread-10" java.lang.ArrayIndexOutOfBoundsException , 7, 8, 9, 10, 11, 12, 13Exception in thread "Thread-17" java.lang.ArrayIndexOutOfBoundsException , 14, 15Exception in thread "Thread-22" java.lang.ArrayIndexOutOfBoundsException Exception in thread "Thread-19" java.lang.ArrayIndexOutOfBoundsException , 16, 17, 18, 19, 20, 21Exception in thread "Thread-25" java.lang.ArrayIndexOutOfBoundsException , 22, 23 ************************************************************************** Warning! 24 mapping threads 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: 7 Max Indel: 100 Minimum Score Ratio: 0.4 Mapping Mode: normal Reads Used: 197 (623932 bases) Mapping: 508.781 seconds. Reads/sec: 0.39 kBases/sec: 1.23 Read 1 data: pct reads num reads pct bases num bases mapped: 59.3909% 117 46.5219% 290265 unambiguous: 53.2995% 105 39.0331% 243540 ambiguous: 6.0914% 12 7.4888% 46725 low-Q discards: 0.0000% 0 0.0000% 0 perfect best site: 0.0000% 0 0.0000% 0 semiperfect site: 0.0000% 0 0.0000% 0 Match Rate: NA NA 75.5887% 249581 Error Rate: 80.6897% 117 24.4113% 80602 Sub Rate: 80.6897% 117 5.2444% 17316 Del Rate: 80.6897% 117 12.0897% 39918 Ins Rate: 80.6897% 117 7.0773% 23368 N Rate: 0.0000% 0 0.0000% 0 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. 53+64+0+56+0 = 173 != 197 at align2.AbstractMapper.printOutput(AbstractMapper.java:1878) at align2.BBMapPacBio.testSpeed(BBMapPacBio.java:462) at align2.BBMapPacBio.main(BBMapPacBio.java:37)
Thanks
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