[2023-03-17 01:23:45,158] [INFO] DFAST_QC pipeline started.
[2023-03-17 01:23:45,158] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 01:23:45,158] [INFO] DQC Reference Directory: /var/lib/cwl/stg5eb74df2-91c6-4063-8257-344fa0072c67/dqc_reference
[2023-03-17 01:23:46,317] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 01:23:46,317] [INFO] Task started: Prodigal
[2023-03-17 01:23:46,317] [INFO] Running command: cat /var/lib/cwl/stg94fbc738-238b-4e9b-ab34-3308d45f7948/OceanDNA-b35314.fa | prodigal -d OceanDNA-b35314/cds.fna -a OceanDNA-b35314/protein.faa -g 11 -q > /dev/null
[2023-03-17 01:24:11,691] [INFO] Task succeeded: Prodigal
[2023-03-17 01:24:11,691] [INFO] Task started: HMMsearch
[2023-03-17 01:24:11,691] [INFO] Running command: hmmsearch --tblout OceanDNA-b35314/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5eb74df2-91c6-4063-8257-344fa0072c67/dqc_reference/reference_markers.hmm OceanDNA-b35314/protein.faa > /dev/null
[2023-03-17 01:24:11,922] [INFO] Task succeeded: HMMsearch
[2023-03-17 01:24:11,923] [INFO] Found 6/6 markers.
[2023-03-17 01:24:11,950] [INFO] Query marker FASTA was written to OceanDNA-b35314/markers.fasta
[2023-03-17 01:24:11,950] [INFO] Task started: Blastn
[2023-03-17 01:24:11,950] [INFO] Running command: blastn -query OceanDNA-b35314/markers.fasta -db /var/lib/cwl/stg5eb74df2-91c6-4063-8257-344fa0072c67/dqc_reference/reference_markers.fasta -out OceanDNA-b35314/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 01:24:12,643] [INFO] Task succeeded: Blastn
[2023-03-17 01:24:12,644] [INFO] Selected 24 target genomes.
[2023-03-17 01:24:12,644] [INFO] Target genome list was writen to OceanDNA-b35314/target_genomes.txt
[2023-03-17 01:24:12,658] [INFO] Task started: fastANI
[2023-03-17 01:24:12,658] [INFO] Running command: fastANI --query /var/lib/cwl/stg94fbc738-238b-4e9b-ab34-3308d45f7948/OceanDNA-b35314.fa --refList OceanDNA-b35314/target_genomes.txt --output OceanDNA-b35314/fastani_result.tsv --threads 1
[2023-03-17 01:24:32,115] [INFO] Task succeeded: fastANI
[2023-03-17 01:24:32,116] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5eb74df2-91c6-4063-8257-344fa0072c67/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 01:24:32,116] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5eb74df2-91c6-4063-8257-344fa0072c67/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 01:24:32,128] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 01:24:32,128] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 01:24:32,129] [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 coralliilyticus	strain=ATCC BAA-450	GCA_000176135.1	190893	190893	type	True	88.463	1205	1492	95	below_threshold
Vibrio tubiashii	strain=ATCC 19109	GCA_000772105.1	29498	29498	suspected-type	True	81.4007	553	1492	95	below_threshold
Vibrio tubiashii	strain=ATCC 19109	GCA_000222665.2	29498	29498	suspected-type	True	81.3037	527	1492	95	below_threshold
Vibrio europaeus	strain=PP-638	GCA_001695575.1	300876	300876	type	True	81.1806	545	1492	95	below_threshold
Vibrio aquaticus	strain=BEI207	GCA_003970385.1	2496559	2496559	type	True	80.7013	473	1492	95	below_threshold
Vibrio orientalis	strain=CIP 102891	GCA_000176235.1	28175	28175	type	True	80.6661	483	1492	95	below_threshold
Vibrio orientalis	strain=CIP 102891	GCA_000222645.2	28175	28175	type	True	80.5467	474	1492	95	below_threshold
Vibrio rotiferianus	strain=CAIM 577	GCA_002741985.1	190895	190895	type	True	80.3323	350	1492	95	below_threshold
Vibrio nereis	strain=DSM 19584	GCA_001274805.1	693	693	type	True	80.1938	450	1492	95	below_threshold
Vibrio nereis	strain=NBRC 15637	GCA_001591105.1	693	693	type	True	80.1645	443	1492	95	below_threshold
Vibrio campbellii	strain=CAIM 519	GCA_000334195.1	680	680	type	True	79.9777	351	1492	95	below_threshold
Vibrio alginolyticus	strain=NCTC12160	GCA_900460285.1	663	663	type	True	79.8669	338	1492	95	below_threshold
Vibrio natriegens	strain=14048	GCA_024508015.1	691	691	type	True	79.8488	326	1492	95	below_threshold
Vibrio hyugaensis	strain=090810a	GCA_002906655.1	1534743	1534743	type	True	79.8302	376	1492	95	below_threshold
Vibrio alginolyticus	strain=FDAARGOS_97	GCA_001471275.2	663	663	type	True	79.8264	339	1492	95	below_threshold
Vibrio hyugaensis	strain=090810a	GCA_000818435.1	1534743	1534743	type	True	79.7424	368	1492	95	below_threshold
Vibrio antiquarius	strain=EX25	GCA_000024825.1	150340	150340	suspected-type	True	79.7414	349	1492	95	below_threshold
Vibrio fortis	strain=LMG 21557	GCA_024347475.1	212667	212667	type	True	79.6445	333	1492	95	below_threshold
Vibrio pelagius	strain=ATCC 25916	GCA_024347575.1	28169	28169	type	True	79.5954	311	1492	95	below_threshold
Vibrio panuliri	strain=JCM 19500	GCA_009938205.1	1381081	1381081	type	True	79.5632	330	1492	95	below_threshold
Vibrio panuliri	strain=LBS 2	GCA_008830195.1	1381081	1381081	type	True	79.5368	339	1492	95	below_threshold
Vibrio antiquarius	strain=EX25	GCA_000152485.1	150340	150340	suspected-type	True	79.2965	308	1492	95	below_threshold
Vibrio sonorensis	strain=CAIM 1076	GCA_001854765.1	1004316	1004316	type	True	78.995	309	1492	95	below_threshold
Vibrio diazotrophicus	strain=NBRC 103148	GCA_000740015.1	685	685	type	True	78.8722	275	1492	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 01:24:32,129] [INFO] DFAST Taxonomy check result was written to OceanDNA-b35314/tc_result.tsv
[2023-03-17 01:24:32,129] [INFO] ===== Taxonomy check completed =====
[2023-03-17 01:24:32,129] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 01:24:32,129] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5eb74df2-91c6-4063-8257-344fa0072c67/dqc_reference/checkm_data
[2023-03-17 01:24:32,130] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 01:24:32,136] [INFO] Task started: CheckM
[2023-03-17 01:24:32,136] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b35314/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b35314/checkm_input OceanDNA-b35314/checkm_result
[2023-03-17 01:25:37,589] [INFO] Task succeeded: CheckM
[2023-03-17 01:25:37,589] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 01:25:37,592] [INFO] ===== Completeness check finished =====
[2023-03-17 01:25:37,592] [INFO] ===== Start GTDB Search =====
[2023-03-17 01:25:37,592] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b35314/markers.fasta)
[2023-03-17 01:25:37,592] [INFO] Task started: Blastn
[2023-03-17 01:25:37,592] [INFO] Running command: blastn -query OceanDNA-b35314/markers.fasta -db /var/lib/cwl/stg5eb74df2-91c6-4063-8257-344fa0072c67/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b35314/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 01:25:38,691] [INFO] Task succeeded: Blastn
[2023-03-17 01:25:38,692] [INFO] Selected 17 target genomes.
[2023-03-17 01:25:38,692] [INFO] Target genome list was writen to OceanDNA-b35314/target_genomes_gtdb.txt
[2023-03-17 01:25:38,793] [INFO] Task started: fastANI
[2023-03-17 01:25:38,793] [INFO] Running command: fastANI --query /var/lib/cwl/stg94fbc738-238b-4e9b-ab34-3308d45f7948/OceanDNA-b35314.fa --refList OceanDNA-b35314/target_genomes_gtdb.txt --output OceanDNA-b35314/fastani_result_gtdb.tsv --threads 1
[2023-03-17 01:25:54,588] [INFO] Task succeeded: fastANI
[2023-03-17 01:25:54,598] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 01:25:54,598] [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_000967495.1	s__Vibrio neptunius	97.9795	1371	1492	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.83	96.84	0.91	0.89	7	conclusive
GCF_000176135.1	s__Vibrio coralliilyticus	88.463	1205	1492	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.33	96.21	0.92	0.87	36	-
GCF_013113835.1	s__Vibrio sp013113835	88.1181	1173	1492	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000772105.1	s__Vibrio tubiashii	81.4003	553	1492	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.61	95.85	0.96	0.87	4	-
GCF_001695575.1	s__Vibrio europaeus	81.1931	544	1492	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.44	98.30	0.92	0.91	4	-
GCF_000189275.1	s__Vibrio sinaloensis_B	80.984	436	1492	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000808535.1	s__Vibrio sinaloensis	80.8603	484	1492	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.52	97.23	0.92	0.89	7	-
GCF_004551525.1	s__Vibrio ouci	80.7583	490	1492	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001399455.2	s__Vibrio bivalvicida	80.7532	527	1492	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.39	98.39	0.93	0.93	2	-
GCF_003970385.1	s__Vibrio aquaticus	80.722	471	1492	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000189255.1	s__Vibrio brasiliensis	80.6923	488	1492	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006124995.1	s__Vibrio sp006124995	80.3947	466	1492	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001591105.1	s__Vibrio nereis	80.1825	442	1492	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	100.00	100.00	0.99	0.99	2	-
GCF_000354175.2	s__Vibrio alginolyticus	79.8095	340	1492	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.52	98.30	0.93	0.90	169	-
GCA_001048675.1	s__Vibrio diabolicus	79.6733	350	1492	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.98	97.44	0.93	0.90	43	-
GCF_009938205.1	s__Vibrio panuliri	79.5678	331	1492	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.52	98.57	0.98	0.94	4	-
GCF_000740015.1	s__Vibrio diazotrophicus	78.8493	277	1492	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.42	96.82	0.87	0.85	7	-
--------------------------------------------------------------------------------
[2023-03-17 01:25:54,598] [INFO] GTDB search result was written to OceanDNA-b35314/result_gtdb.tsv
[2023-03-17 01:25:54,598] [INFO] ===== GTDB Search completed =====
[2023-03-17 01:25:54,600] [INFO] DFAST_QC result json was written to OceanDNA-b35314/dqc_result.json
[2023-03-17 01:25:54,600] [INFO] DFAST_QC completed!
[2023-03-17 01:25:54,600] [INFO] Total running time: 0h2m9s