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dib-lab / eel-pond

mRNAseq assembly, evaluation, and expression analysis
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expected transrate and busco output from subset #48

Open johnsolk opened 7 years ago

johnsolk commented 7 years ago

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