[2023-03-15 11:20:29,245] [INFO] DFAST_QC pipeline started.
[2023-03-15 11:20:29,246] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 11:20:29,247] [INFO] DQC Reference Directory: /var/lib/cwl/stg0177437f-3b1c-4658-b281-4a3bcbce34bc/dqc_reference
[2023-03-15 11:20:30,385] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 11:20:30,386] [INFO] Task started: Prodigal
[2023-03-15 11:20:30,386] [INFO] Running command: cat /var/lib/cwl/stgdb09f0a4-1cae-4204-bbac-df4b45a3ffd3/OceanDNA-b36690.fa | prodigal -d OceanDNA-b36690/cds.fna -a OceanDNA-b36690/protein.faa -g 11 -q > /dev/null
[2023-03-15 11:20:56,355] [INFO] Task succeeded: Prodigal
[2023-03-15 11:20:56,355] [INFO] Task started: HMMsearch
[2023-03-15 11:20:56,355] [INFO] Running command: hmmsearch --tblout OceanDNA-b36690/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0177437f-3b1c-4658-b281-4a3bcbce34bc/dqc_reference/reference_markers.hmm OceanDNA-b36690/protein.faa > /dev/null
[2023-03-15 11:20:56,596] [INFO] Task succeeded: HMMsearch
[2023-03-15 11:20:56,597] [INFO] Found 6/6 markers.
[2023-03-15 11:20:56,639] [INFO] Query marker FASTA was written to OceanDNA-b36690/markers.fasta
[2023-03-15 11:20:56,641] [INFO] Task started: Blastn
[2023-03-15 11:20:56,641] [INFO] Running command: blastn -query OceanDNA-b36690/markers.fasta -db /var/lib/cwl/stg0177437f-3b1c-4658-b281-4a3bcbce34bc/dqc_reference/reference_markers.fasta -out OceanDNA-b36690/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:20:57,283] [INFO] Task succeeded: Blastn
[2023-03-15 11:20:57,292] [INFO] Selected 22 target genomes.
[2023-03-15 11:20:57,292] [INFO] Target genome list was writen to OceanDNA-b36690/target_genomes.txt
[2023-03-15 11:20:57,309] [INFO] Task started: fastANI
[2023-03-15 11:20:57,309] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb09f0a4-1cae-4204-bbac-df4b45a3ffd3/OceanDNA-b36690.fa --refList OceanDNA-b36690/target_genomes.txt --output OceanDNA-b36690/fastani_result.tsv --threads 1
[2023-03-15 11:21:11,308] [INFO] Task succeeded: fastANI
[2023-03-15 11:21:11,308] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0177437f-3b1c-4658-b281-4a3bcbce34bc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 11:21:11,308] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0177437f-3b1c-4658-b281-4a3bcbce34bc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 11:21:11,315] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2023-03-15 11:21:11,315] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-15 11:21:11,315] [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
Saccharophagus degradans	strain=2-40	GCA_000013665.1	86304	86304	type	True	96.0974	1315	1463	95	conclusive
Teredinibacter purpureus	strain=Bs12	GCA_014217335.1	2731756	2731756	type	True	77.4009	82	1463	95	below_threshold
Teredinibacter purpureus	strain=Bs12	GCA_000966245.1	2731756	2731756	type	True	77.2886	81	1463	95	below_threshold
Teredinibacter haidensis	strain=Bs08	GCA_014211975.1	2731755	2731755	type	True	76.9984	75	1463	95	below_threshold
Teredinibacter waterburyi	strain=Bs02	GCA_001922985.1	1500538	1500538	type	True	76.8853	84	1463	95	below_threshold
Agaribacterium haliotis	strain=feces2	GCA_002312815.1	2013869	2013869	type	True	76.6208	69	1463	95	below_threshold
Teredinibacter turnerae	strain=T7902	GCA_000379165.1	2426	2426	type	True	76.499	76	1463	95	below_threshold
Gilvimarinus chinensis	strain=DSM 19667	GCA_000377745.1	396005	396005	type	True	76.2817	58	1463	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 11:21:11,320] [INFO] DFAST Taxonomy check result was written to OceanDNA-b36690/tc_result.tsv
[2023-03-15 11:21:11,326] [INFO] ===== Taxonomy check completed =====
[2023-03-15 11:21:11,326] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 11:21:11,326] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0177437f-3b1c-4658-b281-4a3bcbce34bc/dqc_reference/checkm_data
[2023-03-15 11:21:11,327] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 11:21:11,341] [INFO] Task started: CheckM
[2023-03-15 11:21:11,341] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b36690/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b36690/checkm_input OceanDNA-b36690/checkm_result
[2023-03-15 11:22:14,520] [INFO] Task succeeded: CheckM
[2023-03-15 11:22:14,521] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 11:22:14,540] [INFO] ===== Completeness check finished =====
[2023-03-15 11:22:14,541] [INFO] ===== Start GTDB Search =====
[2023-03-15 11:22:14,541] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b36690/markers.fasta)
[2023-03-15 11:22:14,542] [INFO] Task started: Blastn
[2023-03-15 11:22:14,542] [INFO] Running command: blastn -query OceanDNA-b36690/markers.fasta -db /var/lib/cwl/stg0177437f-3b1c-4658-b281-4a3bcbce34bc/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b36690/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:22:15,588] [INFO] Task succeeded: Blastn
[2023-03-15 11:22:15,597] [INFO] Selected 25 target genomes.
[2023-03-15 11:22:15,597] [INFO] Target genome list was writen to OceanDNA-b36690/target_genomes_gtdb.txt
[2023-03-15 11:22:15,620] [INFO] Task started: fastANI
[2023-03-15 11:22:15,620] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb09f0a4-1cae-4204-bbac-df4b45a3ffd3/OceanDNA-b36690.fa --refList OceanDNA-b36690/target_genomes_gtdb.txt --output OceanDNA-b36690/fastani_result_gtdb.tsv --threads 1
[2023-03-15 11:22:32,835] [INFO] Task succeeded: fastANI
[2023-03-15 11:22:32,842] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 11:22:32,842] [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
GCF_000013665.1	s__Saccharophagus degradans	96.083	1316	1463	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Saccharophagus	95.0	96.22	96.22	0.89	0.89	2	conclusive
GCF_014217335.1	s__Teredinibacter purpureus	77.4394	83	1463	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Teredinibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014211975.1	s__Teredinibacter haidensis	77.074	76	1463	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Teredinibacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001922985.1	s__Teredinibacter waterburyi	76.8853	84	1463	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Teredinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014218805.1	s__Teredinibacter franksiae	76.859	91	1463	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Teredinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002312815.1	s__Agaribacterium haliotis	76.6208	69	1463	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Agaribacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900177435.1	s__Teredinibacter sp900177435	76.5767	90	1463	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Teredinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000379165.1	s__Teredinibacter turnerae	76.5226	75	1463	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Teredinibacter	95.0	98.03	97.55	0.91	0.90	6	-
GCA_007827375.1	s__Teredinibacter sp007827375	76.2342	74	1463	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Teredinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008806975.1	s__Cellvibrio sp008806975	76.1623	53	1463	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Cellvibrio	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 11:22:32,844] [INFO] GTDB search result was written to OceanDNA-b36690/result_gtdb.tsv
[2023-03-15 11:22:32,849] [INFO] ===== GTDB Search completed =====
[2023-03-15 11:22:32,854] [INFO] DFAST_QC result json was written to OceanDNA-b36690/dqc_result.json
[2023-03-15 11:22:32,854] [INFO] DFAST_QC completed!
[2023-03-15 11:22:32,854] [INFO] Total running time: 0h2m4s