20200604_cbai_diamond_blastx_daa2rma.sh: line 55: --in: command not found
20200604_cbai_diamond_blastx_daa2rma.sh: line 55: --in: command not found

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Total runtime was: 0 seconds
Version   MEGAN Community Edition (version 6.18.3, built 17 Dec 2019)
Copyright (C) 2019 Daniel H. Huson. This program comes with ABSOLUTELY NO WARRANTY.
Functional classifications to use: EGGNOG, INTERPRO2GO
Loading ncbi.map: 2,175,506
Loading ncbi.tre: 2,175,510
Opening file: /home/sam/data/databases/MEGAN/prot_acc2tax-Jul2019X1.abin
Loading eggnog.map:    30,875
Loading eggnog.tre:    30,986
Opening file: /home/sam/data/databases/MEGAN/acc2eggnog-Jul2019X.abin
Loading interpro2go.map:    13,501
Loading interpro2go.tre:    29,204
Opening file: /home/sam/data/databases/MEGAN/acc2interpro-Jul2019X.abin
In DAA file:  cbai_transcriptome_v2.0.fasta.blastx.daa
Output file:  cbai_transcriptome_v2.0.daa2rma.rma6
Classifications: Taxonomy, EGGNOG, INTERPRO2GO
Annotating RMA6 file using EXTENDED mode
Parsing file: cbai_transcriptome_v2.0.fasta.blastx.daa
10% 20% 30% 40% 50% 60% 70% 80% 90% 100% (1398.3s)
Total reads:           268,106
Alignments:          3,438,845
100% (0.0s)
Binning reads: Initializing...
Initializing binning...
Using 'Naive LCA' algorithm for binning: Taxonomy
Using Best-Hit algorithm for binning: EGGNOG
Using Best-Hit algorithm for binning: INTERPRO2GO
Binning reads...
Binning reads: Analyzing alignments
Total reads:          268,106
With hits:             268,106 
Alignments:          3,438,845
Assig. Taxonomy:       265,506
Assig. EGGNOG:          38,106
Assig. INTERPRO2GO:     76,679
MinSupport set to: 134
Binning reads: Applying min-support & disabled filter to Taxonomy...
Min-supp. changes:       4,016
Binning reads: Writing classification tables
Numb. Tax. classes:        461
Numb. EGG. classes:      4,571
Numb. INT. classes:      7,471
Binning reads: Syncing
Class. Taxonomy:           461
Class. EGGNOG:           4,571
Class. INTERPRO2GO:      7,471
100% (244.6s)
Total time:  1653s
Peak memory: 19.6 of 52.4G
Version   MEGAN Community Edition (version 6.18.3, built 17 Dec 2019)
Copyright (C) 2019 Daniel H. Huson. This program comes with ABSOLUTELY NO WARRANTY.
Functional classifications to use: EGGNOG, INTERPRO2GO
Loading ncbi.map: 2,175,506
Loading ncbi.tre: 2,175,510
Opening file: /home/sam/data/databases/MEGAN/prot_acc2tax-Jul2019X1.abin
Loading eggnog.map:    30,875
Loading eggnog.tre:    30,986
Opening file: /home/sam/data/databases/MEGAN/acc2eggnog-Jul2019X.abin
Loading interpro2go.map:    13,501
Loading interpro2go.tre:    29,204
Opening file: /home/sam/data/databases/MEGAN/acc2interpro-Jul2019X.abin
In DAA file:  cbai_transcriptome_v3.0.fasta.blastx.daa
Output file:  cbai_transcriptome_v3.0.daa2rma.rma6
Classifications: Taxonomy, EGGNOG, INTERPRO2GO
Annotating RMA6 file using EXTENDED mode
Parsing file: cbai_transcriptome_v3.0.fasta.blastx.daa
10% 20% 30% 40% 50% 60% 70% 80% 90% 100% (71.8s)
Total reads:           108,512
Alignments:            730,723
100% (0.0s)
Binning reads: Initializing...
Initializing binning...
Using 'Naive LCA' algorithm for binning: Taxonomy
Using Best-Hit algorithm for binning: EGGNOG
Using Best-Hit algorithm for binning: INTERPRO2GO
Binning reads...
Binning reads: Analyzing alignments
Total reads:          108,512
With hits:             108,512 
Alignments:            730,723
Assig. Taxonomy:       107,525
Assig. EGGNOG:          11,423
Assig. INTERPRO2GO:     24,096
MinSupport set to: 54
Binning reads: Applying min-support & disabled filter to Taxonomy...
Min-supp. changes:       1,491
Binning reads: Writing classification tables
Numb. Tax. classes:        389
Numb. EGG. classes:      1,044
Numb. INT. classes:      2,466
Binning reads: Syncing
Class. Taxonomy:           389
Class. EGGNOG:           1,044
Class. INTERPRO2GO:      2,466
100% (83.1s)
Total time:  165s
Peak memory: 18.3 of 52.4G

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Total runtime was: 1823 seconds