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
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