expected transrate and busco output from subset
Opened this issue · 0 comments
johnsolk commented
Transrate:
(pondenv)ljcohen@js-156-234:/work/evaluation$ transrate --assembly=Trinity.fixed.fasta --threads=2 \
> --left=left.fq.gz \
> --right=right.fq.gz \
> --output=${PROJECT}/evaluation/nema
[ INFO] 2017-04-06 21:17:46 : Loading assembly: /work/evaluation/Trinity.fixed.fasta
[ INFO] 2017-04-06 21:17:46 : Analysing assembly: /work/evaluation/Trinity.fixed.fasta
[ INFO] 2017-04-06 21:17:46 : Results will be saved in /work/evaluation/nema/Trinity.fixed
[ INFO] 2017-04-06 21:17:46 : Calculating contig metrics...
[ INFO] 2017-04-06 21:17:46 : Contig metrics:
[ INFO] 2017-04-06 21:17:46 : -----------------------------------
[ INFO] 2017-04-06 21:17:46 : n seqs 77
[ INFO] 2017-04-06 21:17:46 : smallest 202
[ INFO] 2017-04-06 21:17:46 : largest 4135
[ INFO] 2017-04-06 21:17:46 : n bases 89188
[ INFO] 2017-04-06 21:17:46 : mean len 1158.29
[ INFO] 2017-04-06 21:17:46 : n under 200 0
[ INFO] 2017-04-06 21:17:46 : n over 1k 40
[ INFO] 2017-04-06 21:17:46 : n over 10k 0
[ INFO] 2017-04-06 21:17:46 : n with orf 41
[ INFO] 2017-04-06 21:17:46 : mean orf percent 63.59
[ INFO] 2017-04-06 21:17:46 : n90 590
[ INFO] 2017-04-06 21:17:46 : n70 1346
[ INFO] 2017-04-06 21:17:46 : n50 1843
[ INFO] 2017-04-06 21:17:46 : n30 2026
[ INFO] 2017-04-06 21:17:46 : n10 2469
[ INFO] 2017-04-06 21:17:46 : gc 0.46
[ INFO] 2017-04-06 21:17:46 : bases n 0
[ INFO] 2017-04-06 21:17:46 : proportion n 0.0
[ INFO] 2017-04-06 21:17:46 : Contig metrics done in 0 seconds
[ INFO] 2017-04-06 21:17:46 : Calculating read diagnostics...
[ INFO] 2017-04-06 21:18:56 : Read mapping metrics:
[ INFO] 2017-04-06 21:18:56 : -----------------------------------
[ INFO] 2017-04-06 21:18:56 : fragments 1057177
[ INFO] 2017-04-06 21:18:56 : fragments mapped 1023664
[ INFO] 2017-04-06 21:18:56 : p fragments mapped 0.97
[ INFO] 2017-04-06 21:18:56 : good mappings 882654
[ INFO] 2017-04-06 21:18:56 : p good mapping 0.83
[ INFO] 2017-04-06 21:18:56 : bad mappings 141010
[ INFO] 2017-04-06 21:18:56 : potential bridges 37
[ INFO] 2017-04-06 21:18:56 : bases uncovered 10340
[ INFO] 2017-04-06 21:18:56 : p bases uncovered 0.12
[ INFO] 2017-04-06 21:18:56 : contigs uncovbase 56
[ INFO] 2017-04-06 21:18:56 : p contigs uncovbase 0.73
[ INFO] 2017-04-06 21:18:56 : contigs uncovered 5
[ INFO] 2017-04-06 21:18:56 : p contigs uncovered 0.06
[ INFO] 2017-04-06 21:18:56 : contigs lowcovered 5
[ INFO] 2017-04-06 21:18:56 : p contigs lowcovered 0.06
[ INFO] 2017-04-06 21:18:56 : contigs segmented 30
[ INFO] 2017-04-06 21:18:56 : p contigs segmented 0.39
[ INFO] 2017-04-06 21:18:56 : Read metrics done in 70 seconds
[ INFO] 2017-04-06 21:18:56 : No reference provided, skipping comparative diagnostics
[ INFO] 2017-04-06 21:18:56 : TRANSRATE ASSEMBLY SCORE 0.076
[ INFO] 2017-04-06 21:18:56 : -----------------------------------
[ INFO] 2017-04-06 21:18:56 : TRANSRATE OPTIMAL SCORE 0.396
[ INFO] 2017-04-06 21:18:56 : TRANSRATE OPTIMAL CUTOFF 0.4189
[ INFO] 2017-04-06 21:18:56 : good contigs 20
[ INFO] 2017-04-06 21:18:56 : p good contigs 0.26
[ INFO] 2017-04-06 21:18:56 : Writing contig metrics for each contig to /work/evaluation/nema/Trinity.fixed/contigs.csv
[ INFO] 2017-04-06 21:18:56 : Writing analysis results to assemblies.csv
BUSCO:
(pondenv)ljcohen@js-156-234:/work/evaluation$ cat run_nema_busco_metazoa/short_summary_nema_busco_metazoa.txt
# BUSCO version is: 2.0.1
# The lineage dataset is: metazoa_odb9 (Creation date: 2016-02-13, number of species: 65, number of BUSCOs: 978)
# To reproduce this run: python /home/ljcohen/busco/BUSCO.py -i Trinity.fixed.fasta -o nema_busco_metazoa -l /home/ljcohen/busco/metazoa_odb9/ -m tran -c 2 -sp fly
#
# Summarized benchmarking in BUSCO notation for file Trinity.fixed.fasta
# BUSCO was run in mode: tran
C:0.1%[S:0.1%,D:0.0%],F:0.0%,M:99.9%,n:978
1 Complete BUSCOs (C)
1 Complete and single-copy BUSCOs (S)
0 Complete and duplicated BUSCOs (D)
0 Fragmented BUSCOs (F)
977 Missing BUSCOs (M)
978 Total BUSCO groups searched