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  • megan5:Parse error: java.util.NoSuchElementException

    Hi,

    I had got error while uploading the blastp in the new Version 5.8.6 build 13 feb 2015. But when the same blastp is uploaded in to the older version Megan 5.2.3 it doesnt throw errors.How to fix the same?. Please find below the messages from both the run.


    Version 5.8.6 build 13 feb 2015


    MEGAN5 license certificate:


    Opening startup files
    Reading file: ncbi.map: 1222879
    Reading file: ncbi.tre: 1222879
    Induce Taxonomy tree, keeping 1222879 of 1222879 nodes
    Induced taxonomy tree has 12 nodes
    Executing: show window=ImportBlast;
    Executing: load seedRefSeqFile='ref2seed.map';
    Loading RefSeq2IdMap from file: ref2seed.map
    done (1345625 entries)
    Executing: set seedUseRefSeqMap=true;
    Executing: load keggRefSeqFile='ref2kegg.map';
    Loading RefSeq2IdMap from file: ref2kegg.map
    done (2108406 entries)
    Executing: set keggUseRefSeqMap=true;
    Executing: import blastFile='Sample.faa.blastp' fastaFile='Sample.faa' meganFile='Sample.rma' maxMatches=100 minScore=30.0 maxExpected=0.01 topPercent=10.0 minSupport=1 minComplexity=0.0 useMinimalCoverageHeuristic=false useSeed=true useCOG=false useKegg=true paired=false useIdentityFilter=false textStoragePolicy=Embed blastFormat=BlastP mapping='Taxonomy:BUILT_IN=true,SEED:REFSEQ_MAP=true,KEGG:REFSEQ_MAP=true';
    Importing data: 1 reads file(s), 1 blast file(s)
    Input format: BlastP
    TextStoragePolicy: Embed matches and reads in MEGAN file
    Mapping all reads in memory
    Processing Archaeoglobus_fulgidus_DSM_4304.faa: 2420
    Processing Archaeoglobus_fulgidus_DSM_4304.faa.blastp
    Parse error: java.util.NoSuchElementException
    Parse error: java.util.NoSuchElementException
    Parse error: java.util.NoSuchElementException
    Parse error: java.util.NoSuchElementException
    Parse error: java.util.NoSuchElementException

    Total reads: 2420
    Total no-hits: 0
    Total matches: 101521
    Matches discarded: 0
    Parse errors: 5
    Parsing required 7 seconds
    Loading seed.map: 8324
    Loading seed.tre: 9801
    Loading kegg.map: 9567
    Loading kegg.tre: 19920
    Loading rn.list: 8270
    Number of reads: 2420
    Low complexity: 0
    With valid hits: 2420
    With SEED-ids: 0
    With KEGG-ids: 11
    Number of taxa identified: 7
    Number of SEED classes identified: 1
    Number of KEGG classes identified: 12
    Data processor required: 1 secs
    Total reads: 2420
    Assigned reads: 2420
    Unassigned reads: 0
    Reads with no hits: 0
    Reads low comp.: 0
    Induce Taxonomy tree, keeping 14 of 1222879 nodes
    Induced taxonomy tree has 7 nodes
    Executing: show window=keggviewer;
    kegg2data: 56
    Induce KEGG tree, keeping 78 of 30787 nodes for 56 classes
    Induced KEGG tree has 6 nodes

    ##### old version ########
    Megan 5.2.3

    Opening startup files
    Reading file: ncbi.map: 1111249
    Reading file: ncbi.tre: 1111248
    Induce Taxonomy tree, keeping 1111248 of 1111248 nodes
    Induced taxonomy tree has 12 nodes
    Executing: show window=ImportBlast;
    Executing: load seedRefSeqFile='ref2seed.map';
    Loading RefSeq2IdMap from file: ref2seed.map
    done (1340236 entries)
    Executing: set seedUseRefSeqMap=true;
    Executing: load keggRefSeqFile='ref2kegg.map';
    Loading RefSeq2IdMap from file: ref2kegg.map
    done (2108406 entries)
    Executing: set keggUseRefSeqMap=true;
    Executing: import blastFile='Sample.faa.blastp' fastaFile='Sample.faa' meganFile='Sample.rma' maxMatches=50 minScore=30.0 maxExpected=0.01 topPercent=10.0 minSupport=30 minComplexity=0.0 useMinimalCoverageHeuristic=false useSeed=true useCOG=false useKegg=true paired=false useIdentityFilter=false textStoragePolicy=2 blastFormat=BlastP mapping='Taxonomy:BUILT_IN=true,SEED:REFSEQ_MAP=true,KEGG:REFSEQ_MAP=true';
    Importing data: 1 reads file(s), 1 blast file(s)
    Input format: BlastP
    TextStoragePolicy: Save read sequences and blast matches in an auxiliary .rmaz file
    Mapping all reads in memory
    Processing Sample.faa: 2420
    Processing Sample.faa.blastp
    Parse error: null
    Parse error: null
    Parse error: null
    Parse error: null
    Parse error: null
    Total reads: 2420
    Total no-hits: 0
    Total matches: 101521
    Matches discarded: 0
    Parse errors: 5
    Parsing required 6 seconds
    Loading seed.map: 10596
    Loading seed.tre: 13023
    Loading kegg.map: 9567
    Loading kegg.tre: 19920
    Loading rn.list: 8270
    Number of changes due to min-support filter: 1
    Number of reads: 2420
    Low complexity: 0
    With valid hits: 2420
    With SEED-ids: 978
    With KEGG-ids: 1462
    Number of taxa identified: 6
    Number of SEED classes identified: 723
    Number of KEGG classes identified: 1024
    Data processor required: 4 secs
    Total reads: 2420
    Assigned reads: 2420
    Unassigned reads: 0
    Reads with no hits: 0
    Reads low comp.: 0
    Induce Taxonomy tree, keeping 10 of 1111248 nodes
    Induced taxonomy tree has 4 nodes
    Executing: show window=keggviewer;
    kegg2data: 1213
    Induce KEGG tree, keeping 1678 of 30787 nodes for 1213 classes
    Induced KEGG tree has 8 nodes

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