[2023-03-17 09:33:09,737] [INFO] DFAST_QC pipeline started.
[2023-03-17 09:33:09,737] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 09:33:09,737] [INFO] DQC Reference Directory: /var/lib/cwl/stgf74a09ea-158d-4bd0-beb7-70b6fe11507f/dqc_reference
[2023-03-17 09:33:11,451] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 09:33:11,452] [INFO] Task started: Prodigal
[2023-03-17 09:33:11,452] [INFO] Running command: cat /var/lib/cwl/stg5a62967d-6c7b-4d50-92e9-56be471d9ac9/OceanDNA-b26335.fa | prodigal -d OceanDNA-b26335/cds.fna -a OceanDNA-b26335/protein.faa -g 11 -q > /dev/null
[2023-03-17 09:33:19,602] [INFO] Task succeeded: Prodigal
[2023-03-17 09:33:19,602] [INFO] Task started: HMMsearch
[2023-03-17 09:33:19,602] [INFO] Running command: hmmsearch --tblout OceanDNA-b26335/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf74a09ea-158d-4bd0-beb7-70b6fe11507f/dqc_reference/reference_markers.hmm OceanDNA-b26335/protein.faa > /dev/null
[2023-03-17 09:33:19,762] [INFO] Task succeeded: HMMsearch
[2023-03-17 09:33:19,762] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg5a62967d-6c7b-4d50-92e9-56be471d9ac9/OceanDNA-b26335.fa]
[2023-03-17 09:33:19,773] [INFO] Query marker FASTA was written to OceanDNA-b26335/markers.fasta
[2023-03-17 09:33:19,774] [INFO] Task started: Blastn
[2023-03-17 09:33:19,774] [INFO] Running command: blastn -query OceanDNA-b26335/markers.fasta -db /var/lib/cwl/stgf74a09ea-158d-4bd0-beb7-70b6fe11507f/dqc_reference/reference_markers.fasta -out OceanDNA-b26335/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 09:33:20,303] [INFO] Task succeeded: Blastn
[2023-03-17 09:33:20,304] [INFO] Selected 20 target genomes.
[2023-03-17 09:33:20,304] [INFO] Target genome list was writen to OceanDNA-b26335/target_genomes.txt
[2023-03-17 09:33:20,591] [INFO] Task started: fastANI
[2023-03-17 09:33:20,591] [INFO] Running command: fastANI --query /var/lib/cwl/stg5a62967d-6c7b-4d50-92e9-56be471d9ac9/OceanDNA-b26335.fa --refList OceanDNA-b26335/target_genomes.txt --output OceanDNA-b26335/fastani_result.tsv --threads 1
[2023-03-17 09:33:30,828] [INFO] Task succeeded: fastANI
[2023-03-17 09:33:30,828] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf74a09ea-158d-4bd0-beb7-70b6fe11507f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 09:33:30,829] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf74a09ea-158d-4bd0-beb7-70b6fe11507f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 09:33:30,829] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 09:33:30,829] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 09:33:30,829] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
--------------------------------------------------------------------------------
[2023-03-17 09:33:30,829] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26335/tc_result.tsv
[2023-03-17 09:33:30,829] [INFO] ===== Taxonomy check completed =====
[2023-03-17 09:33:30,829] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 09:33:30,829] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf74a09ea-158d-4bd0-beb7-70b6fe11507f/dqc_reference/checkm_data
[2023-03-17 09:33:30,832] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 09:33:30,836] [INFO] Task started: CheckM
[2023-03-17 09:33:30,836] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26335/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26335/checkm_input OceanDNA-b26335/checkm_result
[2023-03-17 09:33:55,630] [INFO] Task succeeded: CheckM
[2023-03-17 09:33:55,630] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 09:33:55,632] [INFO] ===== Completeness check finished =====
[2023-03-17 09:33:55,632] [INFO] ===== Start GTDB Search =====
[2023-03-17 09:33:55,633] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26335/markers.fasta)
[2023-03-17 09:33:55,634] [INFO] Task started: Blastn
[2023-03-17 09:33:55,634] [INFO] Running command: blastn -query OceanDNA-b26335/markers.fasta -db /var/lib/cwl/stgf74a09ea-158d-4bd0-beb7-70b6fe11507f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26335/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 09:33:56,422] [INFO] Task succeeded: Blastn
[2023-03-17 09:33:56,423] [INFO] Selected 18 target genomes.
[2023-03-17 09:33:56,423] [INFO] Target genome list was writen to OceanDNA-b26335/target_genomes_gtdb.txt
[2023-03-17 09:33:57,293] [INFO] Task started: fastANI
[2023-03-17 09:33:57,293] [INFO] Running command: fastANI --query /var/lib/cwl/stg5a62967d-6c7b-4d50-92e9-56be471d9ac9/OceanDNA-b26335.fa --refList OceanDNA-b26335/target_genomes_gtdb.txt --output OceanDNA-b26335/fastani_result_gtdb.tsv --threads 1
[2023-03-17 09:34:03,510] [INFO] Task succeeded: fastANI
[2023-03-17 09:34:03,514] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 09:34:03,515] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCA_018666135.1	s__UBA5951 sp018666135	99.5795	450	502	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA5951	95.0	99.32	99.32	0.87	0.87	2	conclusive
GCA_016779005.1	s__UBA5951 sp016779005	78.0599	191	502	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA5951	95.0	96.62	95.51	0.89	0.87	4	-
GCA_009936885.1	s__UBA5951 sp009936885	77.4409	130	502	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA5951	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012269555.1	s__UBA5951 sp012269555	76.8634	103	502	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA5951	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902632595.1	s__UBA5951 sp902632595	76.7455	69	502	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA5951	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902520885.1	s__UBA5951 sp902520885	76.7126	102	502	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA5951	95.0	99.20	99.20	0.88	0.88	2	-
--------------------------------------------------------------------------------
[2023-03-17 09:34:03,515] [INFO] GTDB search result was written to OceanDNA-b26335/result_gtdb.tsv
[2023-03-17 09:34:03,515] [INFO] ===== GTDB Search completed =====
[2023-03-17 09:34:03,516] [INFO] DFAST_QC result json was written to OceanDNA-b26335/dqc_result.json
[2023-03-17 09:34:03,516] [INFO] DFAST_QC completed!
[2023-03-17 09:34:03,516] [INFO] Total running time: 0h0m54s