Question: Megan microbiome analysis
0
gravatar for MAPK
15 months ago by
MAPK1.4k
United States
MAPK1.4k wrote:

I am trying to perform Megan (http://ab.inf.uni-tuebingen.de/software/megan/) analysis. I have a paired-end sequenced sample. I have extracted all the reads in fastq from both R1 and R2 files and concatenated them as a single fasta file. I then aligned the concatenated fasta file with ncbi nr database using diamond blastx (using -f 0 option). I am now trying use the aligned output file in Megan by importing as blastfile. I also provided R1 and R2 fasta file for the input data, but for some reason it keeps giving me this error below. Would someone be kind enough to clarify what's wrong here? Thanks for your help in advance.

Opening startup files
Loading ncbi.map: 1,601,128
Loading ncbi.tre: 1,601,131
Induced tree has 1,601,131 of 1,601,131 nodes
Executing: show window=ImportBlast;
Loading eggnog.map:    30,875
Loading eggnog.tre:    30,985
Loading interpro2go.map:    11,294
Loading interpro2go.tre:    26,787
Loading seed.map:    13,662
Loading seed.tre:    21,084
Executing: import blastFile='/media/owner/b45f8e7a-003c-4573-8841-bcb5f76f281f/diamond/matches_SF_1_CGATGT_R1_R2_concatenated.m0' meganFile='/media/owner/b45f8e7a-003c-4573-8841-bcb5f76f281f/diamond/matches_SF_1_CGATGT_R1_R2_concatenated.rma6' useCompression=false format=References_as_FastA mode=Classifier maxMatches=100 minScore=50.0 maxExpected=0.01 minPercentIdentity=0.0 topPercent=10.0 minSupportPercent=0.05 minSupport=1 lcaAlgorithm=naive minPercentReadToCover=0.0 minComplexity=0.0 useIdentityFilter=false readAssignmentMode=readCount fNames=EGGNOG INTERPRO2GO SEED paired=true pairSuffixLength=2;
Assuming paired-reads distinguishing suffix has length: 2
Classifications: Taxonomy,SEED,EGGNOG,INTERPRO2GO
Parsing file: /media/owner/b45f8e7a-003c-4573-8841-bcb5f76f281f/diamond/matches_SF_1_CGATGT_R1_R2_concatenated.m0
null
Command usage: import blastFile=<name> [,<name>...] [fastaFile=<name> [,<name>...]] meganFile=<name> [useCompression={true|false}]
    format={DAA|BlastText|BlastXML|BlastTab|LastMAF|RapSearch2Aln|IlluminaReporter|RDPAssignmentDetails|RDPStandalone|Mothur|SAM|References_as_FastA}
    mode={BlastN|BlastP|BlastX|Classifier} [maxMatches=<num>] [minScore=<num>] [maxExpected=<num>] [minPercentIdentity=<num>]
    [topPercent=<num>] [minSupportPercent=<num>] [minSupport=<num>] [weightedLCA={false|true}] [lcaCoveragePercent=<num>] [minPercentReadToCover=<num>] [minComplexity=<num>] [useIdentityFilter={false|true}]
    [readAssignmentMode={readCount|readLength|alignedBases|readMagnitude}] [fNames={EGGNOG|INTERPRO2GO|KEGG|SEED|Taxonomy...} [longReads={false|true}] [paired={false|true} [pairSuffixLength={number}]]
    [description=<text>]; - Import BLAST (or RDP or Silva or SAM) and reads files to create a new MEGAN file
null
Error: Execute failed: java.io.IOException
megan • 539 views
ADD COMMENTlink modified 15 months ago • written 15 months ago by MAPK1.4k
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