[2023-03-18 07:29:30,336] [INFO] DFAST_QC pipeline started.
[2023-03-18 07:29:30,336] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 07:29:30,336] [INFO] DQC Reference Directory: /var/lib/cwl/stgaac4bb27-a2dc-49e5-8baa-c70a3e07171a/dqc_reference
[2023-03-18 07:29:31,934] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 07:29:31,934] [INFO] Task started: Prodigal
[2023-03-18 07:29:31,935] [INFO] Running command: cat /var/lib/cwl/stg69b44187-fb5e-4a67-9120-8f287ba45394/OceanDNA-b35292.fa | prodigal -d OceanDNA-b35292/cds.fna -a OceanDNA-b35292/protein.faa -g 11 -q > /dev/null
[2023-03-18 07:29:57,239] [INFO] Task succeeded: Prodigal
[2023-03-18 07:29:57,239] [INFO] Task started: HMMsearch
[2023-03-18 07:29:57,239] [INFO] Running command: hmmsearch --tblout OceanDNA-b35292/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaac4bb27-a2dc-49e5-8baa-c70a3e07171a/dqc_reference/reference_markers.hmm OceanDNA-b35292/protein.faa > /dev/null
[2023-03-18 07:29:57,480] [INFO] Task succeeded: HMMsearch
[2023-03-18 07:29:57,481] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg69b44187-fb5e-4a67-9120-8f287ba45394/OceanDNA-b35292.fa]
[2023-03-18 07:29:57,507] [INFO] Query marker FASTA was written to OceanDNA-b35292/markers.fasta
[2023-03-18 07:29:57,507] [INFO] Task started: Blastn
[2023-03-18 07:29:57,507] [INFO] Running command: blastn -query OceanDNA-b35292/markers.fasta -db /var/lib/cwl/stgaac4bb27-a2dc-49e5-8baa-c70a3e07171a/dqc_reference/reference_markers.fasta -out OceanDNA-b35292/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:29:58,112] [INFO] Task succeeded: Blastn
[2023-03-18 07:29:58,113] [INFO] Selected 14 target genomes.
[2023-03-18 07:29:58,113] [INFO] Target genome list was writen to OceanDNA-b35292/target_genomes.txt
[2023-03-18 07:29:58,121] [INFO] Task started: fastANI
[2023-03-18 07:29:58,122] [INFO] Running command: fastANI --query /var/lib/cwl/stg69b44187-fb5e-4a67-9120-8f287ba45394/OceanDNA-b35292.fa --refList OceanDNA-b35292/target_genomes.txt --output OceanDNA-b35292/fastani_result.tsv --threads 1
[2023-03-18 07:30:10,565] [INFO] Task succeeded: fastANI
[2023-03-18 07:30:10,566] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaac4bb27-a2dc-49e5-8baa-c70a3e07171a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 07:30:10,566] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaac4bb27-a2dc-49e5-8baa-c70a3e07171a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 07:30:10,575] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 07:30:10,575] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 07:30:10,575] [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 tritonius	strain=JCM 16456	GCA_001547935.1	1435069	1435069	type	True	92.8175	1322	1459	95	below_threshold
Vibrio porteresiae	strain=MSSRF30	GCA_024347055.1	435912	435912	type	True	86.9119	1207	1459	95	below_threshold
Vibrio nitrifigilis	strain=NFV-1	GCA_015686695.1	2789781	2789781	type	True	80.1313	597	1459	95	below_threshold
Vibrio furnissii	strain=PartQ-Vfurnissii-RM8376	GCA_022869905.1	29494	29494	type	True	78.4067	295	1459	95	below_threshold
Vibrio furnissii	strain=CIP 102972	GCA_000176175.1	29494	29494	type	True	78.3831	296	1459	95	below_threshold
Vibrio furnissii	strain=FDAARGOS_777	GCA_006364355.1	29494	29494	type	True	78.3533	299	1459	95	below_threshold
Vibrio plantisponsor	strain=LMG 24470	GCA_013041605.1	664643	664643	type	True	78.2534	281	1459	95	below_threshold
Vibrio ziniensis	strain=ZWAL4003	GCA_011064285.1	2711221	2711221	type	True	78.2365	278	1459	95	below_threshold
Vibrio diazotrophicus	strain=NBRC 103148	GCA_000740015.1	685	685	type	True	78.1597	279	1459	95	below_threshold
Vibrio antiquarius	strain=EX25	GCA_000024825.1	150340	150340	suspected-type	True	77.7897	222	1459	95	below_threshold
Vibrio coralliilyticus	strain=ATCC BAA-450	GCA_000176135.1	190893	190893	type	True	77.7464	218	1459	95	below_threshold
Vibrio crassostreae	strain=LMG 22240	GCA_024347415.1	246167	246167	type	True	77.6299	198	1459	95	below_threshold
Vibrio atlanticus	strain=CECT 7223	GCA_900089855.1	693153	693153	type	True	77.5946	197	1459	95	below_threshold
Vibrio atlanticus	strain=CECT 7223	GCA_024347315.1	693153	693153	type	True	77.5656	191	1459	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 07:30:10,575] [INFO] DFAST Taxonomy check result was written to OceanDNA-b35292/tc_result.tsv
[2023-03-18 07:30:10,575] [INFO] ===== Taxonomy check completed =====
[2023-03-18 07:30:10,575] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 07:30:10,575] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaac4bb27-a2dc-49e5-8baa-c70a3e07171a/dqc_reference/checkm_data
[2023-03-18 07:30:10,576] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 07:30:10,582] [INFO] Task started: CheckM
[2023-03-18 07:30:10,582] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b35292/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b35292/checkm_input OceanDNA-b35292/checkm_result
[2023-03-18 07:31:13,703] [INFO] Task succeeded: CheckM
[2023-03-18 07:31:13,703] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 45.83%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 07:31:13,706] [INFO] ===== Completeness check finished =====
[2023-03-18 07:31:13,707] [INFO] ===== Start GTDB Search =====
[2023-03-18 07:31:13,707] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b35292/markers.fasta)
[2023-03-18 07:31:13,707] [INFO] Task started: Blastn
[2023-03-18 07:31:13,707] [INFO] Running command: blastn -query OceanDNA-b35292/markers.fasta -db /var/lib/cwl/stgaac4bb27-a2dc-49e5-8baa-c70a3e07171a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b35292/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:31:14,589] [INFO] Task succeeded: Blastn
[2023-03-18 07:31:14,590] [INFO] Selected 16 target genomes.
[2023-03-18 07:31:14,590] [INFO] Target genome list was writen to OceanDNA-b35292/target_genomes_gtdb.txt
[2023-03-18 07:31:14,669] [INFO] Task started: fastANI
[2023-03-18 07:31:14,669] [INFO] Running command: fastANI --query /var/lib/cwl/stg69b44187-fb5e-4a67-9120-8f287ba45394/OceanDNA-b35292.fa --refList OceanDNA-b35292/target_genomes_gtdb.txt --output OceanDNA-b35292/fastani_result_gtdb.tsv --threads 1
[2023-03-18 07:31:28,691] [INFO] Task succeeded: fastANI
[2023-03-18 07:31:28,700] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 07:31:28,700] [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_001547935.1	s__Vibrio tritonius	92.8355	1320	1459	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015686695.1	s__Vibrio nitrifigilis	80.1143	598	1459	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.79	98.79	0.95	0.95	2	-
GCF_000176175.1	s__Vibrio furnissii	78.3831	296	1459	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.58	97.97	0.95	0.91	12	-
GCF_900460245.1	s__Vibrio fluvialis	78.2701	322	1459	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.04	97.07	0.93	0.86	63	-
GCF_013041605.1	s__Vibrio plantisponsor	78.2662	280	1459	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.35	98.35	0.93	0.93	2	-
GCF_011064285.1	s__Vibrio ziniensis	78.2365	278	1459	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002741985.1	s__Vibrio rotiferianus	77.8222	224	1459	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.35	95.73	0.89	0.85	14	-
GCF_000817815.1	s__Vibrio owensii	77.8141	228	1459	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.72	96.06	0.85	0.79	29	-
GCF_000176135.1	s__Vibrio coralliilyticus	77.7424	219	1459	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.33	96.21	0.92	0.87	36	-
GCF_009938165.1	s__Vibrio taketomensis	77.7239	218	1459	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.31	98.31	0.99	0.99	2	-
GCF_002163755.1	s__Vibrio campbellii	77.6845	226	1459	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.60	95.95	0.87	0.77	78	-
GCF_000808535.1	s__Vibrio sinaloensis	77.6622	218	1459	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.52	97.23	0.92	0.89	7	-
GCA_001048675.1	s__Vibrio diabolicus	77.643	226	1459	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.98	97.44	0.93	0.90	43	-
GCF_900089855.1	s__Vibrio atlanticus	77.5946	197	1459	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	96.5791	N/A	N/A	N/A	N/A	1	-
GCF_000967545.1	s__Vibrio galatheae	77.5138	196	1459	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013113835.1	s__Vibrio sp013113835	77.471	222	1459	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 07:31:28,701] [INFO] GTDB search result was written to OceanDNA-b35292/result_gtdb.tsv
[2023-03-18 07:31:28,701] [INFO] ===== GTDB Search completed =====
[2023-03-18 07:31:28,702] [INFO] DFAST_QC result json was written to OceanDNA-b35292/dqc_result.json
[2023-03-18 07:31:28,703] [INFO] DFAST_QC completed!
[2023-03-18 07:31:28,703] [INFO] Total running time: 0h1m58s