diamond
eg:
makedb:
diamond makedb --in /data_raid1/gene_data/MetaDatabase/NCBI_blast_db_FASTA/nr.gz -d nr --taxonnames /data_raid1/gene_data/MetaDatabase/taxonomy/taxdump/names.dmp --taxonnodes /data_raid1/gene_data/MetaDatabase/taxonomy/taxdump/nodes.dmp --taxonmap /data_raid1/gene_data/MetaDatabase/taxonomy/accession2taxid/prot.accession2taxid.gz --threads 20
blastx:
diamond blastx -c 1 --db nr -t /tmp -p 34 -q ~/metagenomics/functional_annotation/kneaddata_result3/C1_2.fastq.gz --daa ./C2.2.daa
megan
eg:
daa2rma -i C1.1.daa C1.2.daa --paired -ms 50 -me 0.01 -top 50 -mdf /data_raid1/gene_data/MetaDatabase/megan/megan-map-Jul2020.db -o C1.rma
error
DAA2RMA - Computes a MEGAN .rma6 file from a DIAMOND .daa file
Options:
Input
–in: mg1.daa
–metaDataFile: /data_raid1/gene_data/MetaDatabase/megan/megan-map-Jul2020.db
Output
–out: mg1.rma
–useCompression: true
Reads
–paired: false
–pairedSuffixLength: 0
–pairedReadsInOneFile: false
Parameters
–longReads: false
–maxMatchesPerRead: 100
–classify: true
–minScore: 50.0
–maxExpected: 0.01
–minPercentIdentity: 0.0
–topPercent: 50.0
–minSupportPercent: 0.05
–minSupport: 0
–minPercentReadCover: 0.0
–minPercentReferenceCover: 0.0
–lcaAlgorithm: naive
–lcaCoveragePercent: 100.0
–readAssignmentMode: readCount
Classification support:
–parseTaxonNames: true
Other:
–firstWordIsAccession: true
–accessionTags: gb| ref|
–verbose: true
Version MEGAN Community Edition (version 6.12.3, built 14 Aug 2018)
Copyright © 2018 Daniel H. Huson. This program comes with ABSOLUTELY NO WARRANTY.
Loading ncbi.map: 1,787,384
Loading ncbi.tre: 1,787,388
In DAA file: mg1.daa
Output file: mg1.rma
Classifications: Taxonomy
Parsing file: mg1.daa
10% 20% 30% 40% 50% 60% 70% 80% 90% 100% (1.2s)
Total reads: 1,771
Alignments: 17,122
100% (0.0s)
Binning reads: Initializing…
Initializing binning…
Using ‘Naive LCA’ algorithm for binning: Taxonomy
Binning reads…
Binning reads: Analyzing alignments
Total reads: 1,771
With hits: 1,771
Alignments: 17,122
Assig. Taxonomy: 0
MinSupport set to: 1
Binning reads: Applying min-support & disabled filter to Taxonomy…
Min-supp. changes: 0
Binning reads: Writing classification tables
Numb. Tax. classes: 1
Binning reads: Syncing
Class. Taxonomy: 1
100% (2.0s)
Saving metadata:
Caught:
java.io.IOException: #SampleID tag not found, no sample-attributes data…
at megan.core.SampleAttributeTable.read(SampleAttributeTable.java:890)
at megan.tools.DAA2RMA6.run(DAA2RMA6.java:315)
at megan.tools.DAA2RMA6.main(DAA2RMA6.java:64)
Total time: 8s
How to deal with it?,help!!!
Is there a problem with my diamond input?