ViReport-COVID-19/vireport.log at master · niemasd/ViReport-COVID-19 · GitHub

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/--------------------\
|  ViReport v0.0.1   |
| Niema Moshiri 2020 |
\--------------------/

========================   Workflow Process   ========================
[2020-09-20 18:36:10] ViReport was run as follows: ./ViReport/ViReport.py -o COVID19 -s GISAID-BetaCoV-Analysis/data/current/sequences.no_short_seqs.fas.gz -r MT072688 -t GISAID-BetaCoV-Analysis/data/current/dates.tsv -c GISAID-BetaCoV-Analysis/data/current/countries.tsv -og GISAID-BetaCoV-Analysis/data/current/outgroups.txt --format Markdown --continue --max_threads --msa Minimap2 --phylo None --root None --date None --ancestral None --dists_tree None --trans_clust None --dists_seq tn93NoDists
[2020-09-20 18:36:10] Output directory: /home/niemamoshiri/COVID19
[2020-09-20 18:36:10] Starting viral analysis workflow...

[2020-09-20 18:36:10] Initializing module implementations...
[2020-09-20 18:36:10] Finished initializing 13 module implementations

[2020-09-20 18:36:10] Running 'Preprocessing_SafeNames'...
[2020-09-20 18:36:42] Preprocessed sequences output to: /home/niemamoshiri/COVID19/output_files/sequences_safe.fas
[2020-09-20 18:36:42] Preprocessed reference ID: MT072688
[2020-09-20 18:36:42] Preprocessed sample times output to: /home/niemamoshiri/COVID19/output_files/times_safe.txt
[2020-09-20 18:36:42] Preprocessed outgroups list output to: /home/niemamoshiri/COVID19/output_files/outgroups_safe.txt
[2020-09-20 18:36:42] Preprocessed sample categories output to: /home/niemamoshiri/COVID19/output_files/categories_safe.txt

[2020-09-20 18:36:42] Running 'MultipleSequenceAlignment_Minimap2'...
[2020-09-20 18:50:57] Multiple sequence alignment output to: /home/niemamoshiri/COVID19/output_files/sequences_safe.no_outgroup.aln

[2020-09-20 18:50:57] Running 'PairwiseDistancesSequence_tn93NoDists'...

[2020-09-20 22:48:38] Running 'PhylogeneticInference_None'...

[2020-09-20 22:48:38] Running 'PairwiseDistancesTree_None'...

[2020-09-20 22:48:38] Running 'Rooting_None'...

[2020-09-20 22:48:38] Running 'Dating_None'...

[2020-09-20 22:48:38] Running 'AncestralSequenceReconstruction_None'...

[2020-09-20 22:48:38] Running 'TransmissionClustering_None'...

[2020-09-20 22:48:38] Writing report using 'WriteReport_Default'...
[2020-09-20 23:18:15] Report written to: /home/niemamoshiri/COVID19/Report.md


==========================   Information   ===========================
Output Size (bytes): 15788208818
Execution Time (seconds): 16924


===========================   Citations   ============================
Li H. (2018). "Minimap2: pairwise alignment for nucleotide sequences". Bioinformatics. 34(18), 3094-3100.
Moshiri N. (2020). "ViReport" (https://github.com/niemasd/ViReport).
Pond S.L.K., Weaver S., Leigh Brown A.J., Wertheim J.O. (2018). "HIV-TRACE (TRAnsmission Cluster Engine): a Tool for Large Scale Molecular Epidemiology of HIV-1 and Other Rapidly Evolving Pathogens". Molecular Biology and Evolution. 35(7), 1812-1819.