Following is the code that I am using currently:
time daa-meganizer --verbose -i $infile -alg weighted -lcp 25
-a2t $DB/prot_acc2tax-Jul2019X1.abin
Computation resource specified:
–time=04:00:00
–mem=512G (RAM)
– node 1
–core 40
Note the size of .daa file is 2.5 Gb
Megan installation
Megan was install by creating a Conda env.
Megan – 6.12.3 – bioconda/label/cf201901
Attached is yml file for the Conda env.
environment.yml (9.4 KB)
Following is my logfile:
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Meganizer - Prepares (‘meganizes’) a DIAMOND .daa file for use with MEGAN
Options:
Files
–in: /project/gbru/gbru_fy18_apple_microbiome/rp_apple_microbiome/diamond_out_test/A1_run2_lane1.daa
Reads
–paired: false
–pairedSuffixLength: 0
Parameters
–longReads: false
–classify: true
–minScore: 50.0
–maxExpected: 0.01
–minPercentIdentity: 0.0
–topPercent: 10.0
–minSupportPercent: 0.05
–minSupport: 0
–minPercentReadCover: 0.0
–minPercentReferenceCover: 0.0
–lcaAlgorithm: weighted
–lcaCoveragePercent: 25.0
–readAssignmentMode: readCount
Classification support:
–parseTaxonNames: true
–acc2taxa: /project/gbru/gbru_fy18_apple_microbiome/megan/megan_data//prot_acc2tax-Jul2019X1.abin
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.
Java version: 1.8.0_152-release
Loading ncbi.map: 1,787,384
Loading ncbi.tre: 1,787,388
Opening file: /project/gbru/gbru_fy18_apple_microbiome/megan/megan_data/prot_acc2tax-Jul2019X1.abin
Meganizing: /project/gbru/gbru_fy18_apple_microbiome/rp_apple_microbiome/diamond_out_test/A1_run2_lane1.daa
slurmstepd: error:
*** JOB 823840 ON sn-mem-4 CANCELLED AT 2019-08-09T17:27:06 DUE TO TIME LIMIT ***
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