[2023-03-17 04:15:16,776] [INFO] DFAST_QC pipeline started.
[2023-03-17 04:15:16,776] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 04:15:16,776] [INFO] DQC Reference Directory: /var/lib/cwl/stg23b41afd-e7ab-4dc2-948b-e16870c988f6/dqc_reference
[2023-03-17 04:15:17,908] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 04:15:17,908] [INFO] Task started: Prodigal
[2023-03-17 04:15:17,908] [INFO] Running command: cat /var/lib/cwl/stgba0a8f73-48a7-4fdd-b907-1e0766ca8992/OceanDNA-b35288.fa | prodigal -d OceanDNA-b35288/cds.fna -a OceanDNA-b35288/protein.faa -g 11 -q > /dev/null
[2023-03-17 04:15:30,662] [INFO] Task succeeded: Prodigal
[2023-03-17 04:15:30,663] [INFO] Task started: HMMsearch
[2023-03-17 04:15:30,663] [INFO] Running command: hmmsearch --tblout OceanDNA-b35288/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg23b41afd-e7ab-4dc2-948b-e16870c988f6/dqc_reference/reference_markers.hmm OceanDNA-b35288/protein.faa > /dev/null
[2023-03-17 04:15:30,900] [INFO] Task succeeded: HMMsearch
[2023-03-17 04:15:30,900] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgba0a8f73-48a7-4fdd-b907-1e0766ca8992/OceanDNA-b35288.fa]
[2023-03-17 04:15:30,915] [INFO] Query marker FASTA was written to OceanDNA-b35288/markers.fasta
[2023-03-17 04:15:30,916] [INFO] Task started: Blastn
[2023-03-17 04:15:30,916] [INFO] Running command: blastn -query OceanDNA-b35288/markers.fasta -db /var/lib/cwl/stg23b41afd-e7ab-4dc2-948b-e16870c988f6/dqc_reference/reference_markers.fasta -out OceanDNA-b35288/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 04:15:31,595] [INFO] Task succeeded: Blastn
[2023-03-17 04:15:31,595] [INFO] Selected 10 target genomes.
[2023-03-17 04:15:31,596] [INFO] Target genome list was writen to OceanDNA-b35288/target_genomes.txt
[2023-03-17 04:15:31,599] [INFO] Task started: fastANI
[2023-03-17 04:15:31,600] [INFO] Running command: fastANI --query /var/lib/cwl/stgba0a8f73-48a7-4fdd-b907-1e0766ca8992/OceanDNA-b35288.fa --refList OceanDNA-b35288/target_genomes.txt --output OceanDNA-b35288/fastani_result.tsv --threads 1
[2023-03-17 04:15:38,485] [INFO] Task succeeded: fastANI
[2023-03-17 04:15:38,485] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg23b41afd-e7ab-4dc2-948b-e16870c988f6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 04:15:38,485] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg23b41afd-e7ab-4dc2-948b-e16870c988f6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 04:15:38,492] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2023-03-17 04:15:38,492] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-17 04:15:38,492] [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
Vibrio hibernica	strain=B1.19	GCA_015223435.1	2587465	2587465	type	True	98.4522	708	780	95	conclusive
Vibrio casei	strain=DSM 22364	GCA_002218025.2	673372	673372	type	True	80.9423	356	780	95	below_threshold
Vibrio algicola	strain=SM1977	GCA_009601765.2	2662262	2662262	type	True	80.8459	456	780	95	below_threshold
Vibrio litoralis	strain=DSM 17657	GCA_000426765.1	335972	335972	type	True	79.4438	333	780	95	below_threshold
Vibrio rumoiensis	strain=FERM P-14531	GCA_002218045.2	76258	76258	type	True	79.4433	350	780	95	below_threshold
Vibrio algivorus	strain=SA2	GCA_002218005.2	1667024	1667024	type	True	79.4297	337	780	95	below_threshold
Vibrio aphrogenes	strain=CA-1004	GCA_002157735.2	1891186	1891186	type	True	79.1567	311	780	95	below_threshold
Vibrio gangliei	strain=SZDIS-1	GCA_002934045.1	2077090	2077090	type	True	79.0694	323	780	95	below_threshold
Vibrio ezurae	strain=HDS1-1	GCA_003568985.1	252583	252583	type	True	77.9884	130	780	95	below_threshold
Vibrio ziniensis	strain=ZWAL4003	GCA_011064285.1	2711221	2711221	type	True	77.6611	128	780	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 04:15:38,492] [INFO] DFAST Taxonomy check result was written to OceanDNA-b35288/tc_result.tsv
[2023-03-17 04:15:38,493] [INFO] ===== Taxonomy check completed =====
[2023-03-17 04:15:38,493] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 04:15:38,493] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg23b41afd-e7ab-4dc2-948b-e16870c988f6/dqc_reference/checkm_data
[2023-03-17 04:15:38,494] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 04:15:38,497] [INFO] Task started: CheckM
[2023-03-17 04:15:38,497] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b35288/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b35288/checkm_input OceanDNA-b35288/checkm_result
[2023-03-17 04:16:13,649] [INFO] Task succeeded: CheckM
[2023-03-17 04:16:13,650] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 04:16:13,652] [INFO] ===== Completeness check finished =====
[2023-03-17 04:16:13,652] [INFO] ===== Start GTDB Search =====
[2023-03-17 04:16:13,652] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b35288/markers.fasta)
[2023-03-17 04:16:13,652] [INFO] Task started: Blastn
[2023-03-17 04:16:13,652] [INFO] Running command: blastn -query OceanDNA-b35288/markers.fasta -db /var/lib/cwl/stg23b41afd-e7ab-4dc2-948b-e16870c988f6/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b35288/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 04:16:14,501] [INFO] Task succeeded: Blastn
[2023-03-17 04:16:14,502] [INFO] Selected 9 target genomes.
[2023-03-17 04:16:14,502] [INFO] Target genome list was writen to OceanDNA-b35288/target_genomes_gtdb.txt
[2023-03-17 04:16:14,534] [INFO] Task started: fastANI
[2023-03-17 04:16:14,534] [INFO] Running command: fastANI --query /var/lib/cwl/stgba0a8f73-48a7-4fdd-b907-1e0766ca8992/OceanDNA-b35288.fa --refList OceanDNA-b35288/target_genomes_gtdb.txt --output OceanDNA-b35288/fastani_result_gtdb.tsv --threads 1
[2023-03-17 04:16:20,816] [INFO] Task succeeded: fastANI
[2023-03-17 04:16:20,822] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 04:16:20,822] [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_015223435.1	s__Vibrio hibernica	98.4522	708	780	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014694375.1	s__Vibrio sp014694375	92.0454	682	780	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002218025.2	s__Vibrio casei	80.9423	356	780	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.63	99.33	0.95	0.89	5	-
GCF_009601765.2	s__Vibrio sp009601765	80.8459	456	780	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.01	99.01	0.85	0.85	2	-
GCF_000286955.2	s__Vibrio rumoiensis_A	79.7758	352	780	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000426765.1	s__Vibrio litoralis	79.4464	332	780	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.36	97.06	0.89	0.86	3	-
GCF_002218005.2	s__Vibrio algivorus	79.4446	336	780	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.65	98.65	0.88	0.88	2	-
GCF_002157735.2	s__Vibrio aphrogenes	79.1567	311	780	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002934045.1	s__Vibrio gangliei	79.0966	321	780	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 04:16:20,822] [INFO] GTDB search result was written to OceanDNA-b35288/result_gtdb.tsv
[2023-03-17 04:16:20,822] [INFO] ===== GTDB Search completed =====
[2023-03-17 04:16:20,824] [INFO] DFAST_QC result json was written to OceanDNA-b35288/dqc_result.json
[2023-03-17 04:16:20,824] [INFO] DFAST_QC completed!
[2023-03-17 04:16:20,824] [INFO] Total running time: 0h1m4s