[2023-06-17 05:04:35,616] [INFO] DFAST_QC pipeline started.
[2023-06-17 05:04:35,619] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 05:04:35,619] [INFO] DQC Reference Directory: /var/lib/cwl/stg9186347b-01fc-4eb4-b126-c91f44ced18c/dqc_reference
[2023-06-17 05:04:36,813] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 05:04:36,814] [INFO] Task started: Prodigal
[2023-06-17 05:04:36,815] [INFO] Running command: gunzip -c /var/lib/cwl/stg690fed1d-259a-4fa3-ace2-6da33c77ae0e/GCA_013214045.1_ASM1321404v1_genomic.fna.gz | prodigal -d GCA_013214045.1_ASM1321404v1_genomic.fna/cds.fna -a GCA_013214045.1_ASM1321404v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 05:04:49,180] [INFO] Task succeeded: Prodigal
[2023-06-17 05:04:49,180] [INFO] Task started: HMMsearch
[2023-06-17 05:04:49,180] [INFO] Running command: hmmsearch --tblout GCA_013214045.1_ASM1321404v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9186347b-01fc-4eb4-b126-c91f44ced18c/dqc_reference/reference_markers.hmm GCA_013214045.1_ASM1321404v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 05:04:49,444] [INFO] Task succeeded: HMMsearch
[2023-06-17 05:04:49,445] [INFO] Found 6/6 markers.
[2023-06-17 05:04:49,484] [INFO] Query marker FASTA was written to GCA_013214045.1_ASM1321404v1_genomic.fna/markers.fasta
[2023-06-17 05:04:49,484] [INFO] Task started: Blastn
[2023-06-17 05:04:49,485] [INFO] Running command: blastn -query GCA_013214045.1_ASM1321404v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9186347b-01fc-4eb4-b126-c91f44ced18c/dqc_reference/reference_markers.fasta -out GCA_013214045.1_ASM1321404v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 05:04:50,241] [INFO] Task succeeded: Blastn
[2023-06-17 05:04:50,244] [INFO] Selected 24 target genomes.
[2023-06-17 05:04:50,244] [INFO] Target genome list was writen to GCA_013214045.1_ASM1321404v1_genomic.fna/target_genomes.txt
[2023-06-17 05:04:50,251] [INFO] Task started: fastANI
[2023-06-17 05:04:50,251] [INFO] Running command: fastANI --query /var/lib/cwl/stg690fed1d-259a-4fa3-ace2-6da33c77ae0e/GCA_013214045.1_ASM1321404v1_genomic.fna.gz --refList GCA_013214045.1_ASM1321404v1_genomic.fna/target_genomes.txt --output GCA_013214045.1_ASM1321404v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 05:05:13,084] [INFO] Task succeeded: fastANI
[2023-06-17 05:05:13,085] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9186347b-01fc-4eb4-b126-c91f44ced18c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 05:05:13,085] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9186347b-01fc-4eb4-b126-c91f44ced18c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 05:05:13,103] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 05:05:13,103] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-17 05:05:13,104] [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	88.5637	1302	1662	95	below_threshold
Vibrio tubiashii	strain=ATCC 19109	GCA_000222665.2	29498	29498	suspected-type	True	81.6782	575	1662	95	below_threshold
Vibrio tubiashii	strain=ATCC 19109	GCA_000772105.1	29498	29498	suspected-type	True	81.6628	602	1662	95	below_threshold
Vibrio europaeus	strain=PP-638	GCA_001695575.1	300876	300876	type	True	81.4342	599	1662	95	below_threshold
Vibrio aquaticus	strain=BEI207	GCA_003970385.1	2496559	2496559	type	True	80.7155	539	1662	95	below_threshold
Vibrio orientalis	strain=CIP 102891	GCA_000176235.1	28175	28175	type	True	80.6937	549	1662	95	below_threshold
Vibrio orientalis	strain=CIP 102891	GCA_000222645.2	28175	28175	type	True	80.5493	536	1662	95	below_threshold
Vibrio rotiferianus	strain=CAIM 577	GCA_002741985.1	190895	190895	type	True	80.4181	402	1662	95	below_threshold
Vibrio campbellii	strain=CAIM 519	GCA_000334195.1	680	680	type	True	80.4088	388	1662	95	below_threshold
Vibrio nereis	strain=DSM 19584	GCA_001274805.1	693	693	type	True	80.3127	491	1662	95	below_threshold
Vibrio nereis	strain=NBRC 15637	GCA_001591105.1	693	693	type	True	80.2707	484	1662	95	below_threshold
Vibrio hyugaensis	strain=090810a	GCA_002906655.1	1534743	1534743	type	True	80.2108	417	1662	95	below_threshold
Vibrio hyugaensis	strain=090810a	GCA_000818435.1	1534743	1534743	type	True	80.192	405	1662	95	below_threshold
Vibrio natriegens	strain=14048	GCA_024508015.1	691	691	type	True	80.1304	363	1662	95	below_threshold
Vibrio pelagius	strain=ATCC 25916	GCA_024347575.1	28169	28169	type	True	80.0611	349	1662	95	below_threshold
Vibrio alginolyticus	strain=FDAARGOS_97	GCA_001471275.2	663	663	type	True	79.927	391	1662	95	below_threshold
Vibrio fortis	strain=LMG 21557	GCA_024347475.1	212667	212667	type	True	79.899	371	1662	95	below_threshold
Vibrio alginolyticus	strain=NCTC12160	GCA_900460285.1	663	663	type	True	79.8829	386	1662	95	below_threshold
Vibrio antiquarius	strain=EX25	GCA_000024825.1	150340	150340	suspected-type	True	79.8734	405	1662	95	below_threshold
Vibrio panuliri	strain=JCM 19500	GCA_009938205.1	1381081	1381081	type	True	79.7821	373	1662	95	below_threshold
Vibrio panuliri	strain=LBS 2	GCA_008830195.1	1381081	1381081	type	True	79.6562	377	1662	95	below_threshold
Vibrio sonorensis	strain=CAIM 1076	GCA_001854765.1	1004316	1004316	type	True	79.3027	342	1662	95	below_threshold
Vibrio antiquarius	strain=EX25	GCA_000152485.1	150340	150340	suspected-type	True	79.2395	342	1662	95	below_threshold
Vibrio diazotrophicus	strain=NBRC 103148	GCA_000740015.1	685	685	type	True	78.8354	321	1662	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 05:05:13,106] [INFO] DFAST Taxonomy check result was written to GCA_013214045.1_ASM1321404v1_genomic.fna/tc_result.tsv
[2023-06-17 05:05:13,107] [INFO] ===== Taxonomy check completed =====
[2023-06-17 05:05:13,107] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 05:05:13,107] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9186347b-01fc-4eb4-b126-c91f44ced18c/dqc_reference/checkm_data
[2023-06-17 05:05:13,108] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 05:05:13,158] [INFO] Task started: CheckM
[2023-06-17 05:05:13,159] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_013214045.1_ASM1321404v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_013214045.1_ASM1321404v1_genomic.fna/checkm_input GCA_013214045.1_ASM1321404v1_genomic.fna/checkm_result
[2023-06-17 05:05:52,721] [INFO] Task succeeded: CheckM
[2023-06-17 05:05:52,722] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 05:05:52,739] [INFO] ===== Completeness check finished =====
[2023-06-17 05:05:52,739] [INFO] ===== Start GTDB Search =====
[2023-06-17 05:05:52,740] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_013214045.1_ASM1321404v1_genomic.fna/markers.fasta)
[2023-06-17 05:05:52,740] [INFO] Task started: Blastn
[2023-06-17 05:05:52,740] [INFO] Running command: blastn -query GCA_013214045.1_ASM1321404v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9186347b-01fc-4eb4-b126-c91f44ced18c/dqc_reference/reference_markers_gtdb.fasta -out GCA_013214045.1_ASM1321404v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 05:05:53,850] [INFO] Task succeeded: Blastn
[2023-06-17 05:05:53,854] [INFO] Selected 17 target genomes.
[2023-06-17 05:05:53,854] [INFO] Target genome list was writen to GCA_013214045.1_ASM1321404v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 05:05:53,968] [INFO] Task started: fastANI
[2023-06-17 05:05:53,969] [INFO] Running command: fastANI --query /var/lib/cwl/stg690fed1d-259a-4fa3-ace2-6da33c77ae0e/GCA_013214045.1_ASM1321404v1_genomic.fna.gz --refList GCA_013214045.1_ASM1321404v1_genomic.fna/target_genomes_gtdb.txt --output GCA_013214045.1_ASM1321404v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 05:06:10,309] [INFO] Task succeeded: fastANI
[2023-06-17 05:06:10,322] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 05:06:10,323] [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	97.9667	1486	1662	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	88.5587	1303	1662	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	88.2703	1256	1662	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	81.6519	602	1662	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	81.4376	599	1662	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.44	98.30	0.92	0.91	4	-
GCF_000808535.1	s__Vibrio sinaloensis	81.1169	535	1662	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.52	97.23	0.92	0.89	7	-
GCF_001399455.2	s__Vibrio bivalvicida	81.0649	582	1662	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.39	98.39	0.93	0.93	2	-
GCF_004551525.1	s__Vibrio ouci	80.9475	540	1662	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000189275.1	s__Vibrio sinaloensis_B	80.8011	508	1662	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003970385.1	s__Vibrio aquaticus	80.7256	540	1662	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	80.6955	534	1662	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	80.5814	502	1662	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	80.297	481	1662	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	100.00	100.00	0.99	0.99	2	-
GCA_001048675.1	s__Vibrio diabolicus	80.0639	384	1662	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.98	97.44	0.93	0.90	43	-
GCF_000354175.2	s__Vibrio alginolyticus	80.0024	392	1662	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.52	98.30	0.93	0.90	169	-
GCF_009938205.1	s__Vibrio panuliri	79.7752	374	1662	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	78.8432	321	1662	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.42	96.82	0.87	0.85	7	-
--------------------------------------------------------------------------------
[2023-06-17 05:06:10,325] [INFO] GTDB search result was written to GCA_013214045.1_ASM1321404v1_genomic.fna/result_gtdb.tsv
[2023-06-17 05:06:10,325] [INFO] ===== GTDB Search completed =====
[2023-06-17 05:06:10,329] [INFO] DFAST_QC result json was written to GCA_013214045.1_ASM1321404v1_genomic.fna/dqc_result.json
[2023-06-17 05:06:10,329] [INFO] DFAST_QC completed!
[2023-06-17 05:06:10,329] [INFO] Total running time: 0h1m35s