[2024-01-24 14:06:31,230] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:06:31,232] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:06:31,232] [INFO] DQC Reference Directory: /var/lib/cwl/stgabd4ed44-b6dc-4cc8-8f7a-8fc9d8849063/dqc_reference
[2024-01-24 14:06:32,562] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:06:32,563] [INFO] Task started: Prodigal
[2024-01-24 14:06:32,563] [INFO] Running command: gunzip -c /var/lib/cwl/stgc09ba972-1110-4680-8431-ccdfb26702de/GCF_009363415.1_ASM936341v1_genomic.fna.gz | prodigal -d GCF_009363415.1_ASM936341v1_genomic.fna/cds.fna -a GCF_009363415.1_ASM936341v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:45,658] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:45,658] [INFO] Task started: HMMsearch
[2024-01-24 14:06:45,659] [INFO] Running command: hmmsearch --tblout GCF_009363415.1_ASM936341v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgabd4ed44-b6dc-4cc8-8f7a-8fc9d8849063/dqc_reference/reference_markers.hmm GCF_009363415.1_ASM936341v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:46,002] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:46,004] [INFO] Found 6/6 markers.
[2024-01-24 14:06:46,055] [INFO] Query marker FASTA was written to GCF_009363415.1_ASM936341v1_genomic.fna/markers.fasta
[2024-01-24 14:06:46,056] [INFO] Task started: Blastn
[2024-01-24 14:06:46,056] [INFO] Running command: blastn -query GCF_009363415.1_ASM936341v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgabd4ed44-b6dc-4cc8-8f7a-8fc9d8849063/dqc_reference/reference_markers.fasta -out GCF_009363415.1_ASM936341v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:47,001] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:47,005] [INFO] Selected 18 target genomes.
[2024-01-24 14:06:47,006] [INFO] Target genome list was writen to GCF_009363415.1_ASM936341v1_genomic.fna/target_genomes.txt
[2024-01-24 14:06:47,077] [INFO] Task started: fastANI
[2024-01-24 14:06:47,078] [INFO] Running command: fastANI --query /var/lib/cwl/stgc09ba972-1110-4680-8431-ccdfb26702de/GCF_009363415.1_ASM936341v1_genomic.fna.gz --refList GCF_009363415.1_ASM936341v1_genomic.fna/target_genomes.txt --output GCF_009363415.1_ASM936341v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:07:04,082] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:04,083] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgabd4ed44-b6dc-4cc8-8f7a-8fc9d8849063/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:07:04,083] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgabd4ed44-b6dc-4cc8-8f7a-8fc9d8849063/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:07:04,098] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:07:04,098] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:07:04,098] [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 aquimaris	strain=THAF100	GCA_009363415.1	2587862	2587862	type	True	100.0	1498	1499	95	conclusive
Vibrio pectenicida	strain=LMG 19642	GCA_024347015.1	62763	62763	type	True	81.5025	900	1499	95	below_threshold
Vibrio pectenicida	strain=CAIM 594	GCA_003937805.1	62763	62763	type	True	81.3383	831	1499	95	below_threshold
Vibrio tubiashii	strain=ATCC 19109	GCA_000772105.1	29498	29498	suspected-type	True	80.4413	315	1499	95	below_threshold
Vibrio hippocampi	strain=CECT 8226	GCA_921292975.1	654686	654686	type	True	80.2452	177	1499	95	below_threshold
Vibrio marisflavi	strain=CECT 7928	GCA_921294215.1	1216040	1216040	type	True	80.1846	192	1499	95	below_threshold
Vibrio europaeus	strain=PP-638	GCA_001695575.1	300876	300876	type	True	80.1156	338	1499	95	below_threshold
Vibrio parahaemolyticus	strain=NCTC10903	GCA_900460535.1	670	670	type	True	80.0962	248	1499	95	below_threshold
Vibrio coralliilyticus	strain=ATCC BAA-450	GCA_000176135.1	190893	190893	type	True	80.0363	475	1499	95	below_threshold
Vibrio tubiashii	strain=ATCC 19109	GCA_000222665.2	29498	29498	suspected-type	True	79.8234	298	1499	95	below_threshold
Vibrio penaeicida	strain=IFO 15640	GCA_019977755.1	104609	104609	type	True	79.7356	205	1499	95	below_threshold
Vibrio panuliri	strain=JCM 19500	GCA_009938205.1	1381081	1381081	type	True	79.5888	273	1499	95	below_threshold
Vibrio aquaticus	strain=BEI207	GCA_003970385.1	2496559	2496559	type	True	79.5198	304	1499	95	below_threshold
Vibrio splendidus	strain=LMG 19031	GCA_024347615.1	29497	29497	type	True	79.4027	217	1499	95	below_threshold
Vibrio panuliri	strain=LBS 2	GCA_008830195.1	1381081	1381081	type	True	79.348	267	1499	95	below_threshold
Vibrio marinisediminis	strain=404	GCA_014050145.1	2758441	2758441	type	True	79.2549	240	1499	95	below_threshold
Vibrio ichthyoenteri	strain=ATCC 700023	GCA_000222605.2	142461	142461	type	True	79.1806	222	1499	95	below_threshold
Vibrio sonorensis	strain=CAIM 1076	GCA_001854765.1	1004316	1004316	type	True	78.7992	253	1499	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:07:04,100] [INFO] DFAST Taxonomy check result was written to GCF_009363415.1_ASM936341v1_genomic.fna/tc_result.tsv
[2024-01-24 14:07:04,100] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:07:04,100] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:07:04,101] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgabd4ed44-b6dc-4cc8-8f7a-8fc9d8849063/dqc_reference/checkm_data
[2024-01-24 14:07:04,102] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:07:04,145] [INFO] Task started: CheckM
[2024-01-24 14:07:04,146] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009363415.1_ASM936341v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009363415.1_ASM936341v1_genomic.fna/checkm_input GCF_009363415.1_ASM936341v1_genomic.fna/checkm_result
[2024-01-24 14:07:47,717] [INFO] Task succeeded: CheckM
[2024-01-24 14:07:47,718] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:07:47,738] [INFO] ===== Completeness check finished =====
[2024-01-24 14:07:47,739] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:07:47,740] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009363415.1_ASM936341v1_genomic.fna/markers.fasta)
[2024-01-24 14:07:47,740] [INFO] Task started: Blastn
[2024-01-24 14:07:47,740] [INFO] Running command: blastn -query GCF_009363415.1_ASM936341v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgabd4ed44-b6dc-4cc8-8f7a-8fc9d8849063/dqc_reference/reference_markers_gtdb.fasta -out GCF_009363415.1_ASM936341v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:49,047] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:49,051] [INFO] Selected 13 target genomes.
[2024-01-24 14:07:49,052] [INFO] Target genome list was writen to GCF_009363415.1_ASM936341v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:07:49,063] [INFO] Task started: fastANI
[2024-01-24 14:07:49,063] [INFO] Running command: fastANI --query /var/lib/cwl/stgc09ba972-1110-4680-8431-ccdfb26702de/GCF_009363415.1_ASM936341v1_genomic.fna.gz --refList GCF_009363415.1_ASM936341v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009363415.1_ASM936341v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:08:01,249] [INFO] Task succeeded: fastANI
[2024-01-24 14:08:01,266] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:08:01,267] [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_009363415.1	s__Vibrio aquimaris	100.0	1498	1499	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_003350295.1	s__Vibrio tetraodonis	94.7542	1233	1499	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	95.28	95.28	0.88	0.88	2	-
GCF_018860525.1	s__Vibrio hepatarius_B	81.6102	854	1499	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003937805.1	s__Vibrio pectenicida	81.325	833	1499	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.20	98.20	0.85	0.85	2	-
GCF_000772105.1	s__Vibrio tubiashii	80.4514	314	1499	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	80.1352	337	1499	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.44	98.30	0.92	0.91	4	-
GCF_000176135.1	s__Vibrio coralliilyticus	80.0177	477	1499	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	79.9314	240	1499	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.31	98.31	0.99	0.99	2	-
GCF_013113835.1	s__Vibrio sp013113835	79.6778	463	1499	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000967495.1	s__Vibrio neptunius	79.6637	423	1499	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.83	96.84	0.91	0.89	7	-
GCF_000189275.1	s__Vibrio sinaloensis_B	79.6456	308	1499	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	79.0579	328	1499	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018222805.1	s__Vibrio sp018222805	78.1457	199	1499	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:08:01,269] [INFO] GTDB search result was written to GCF_009363415.1_ASM936341v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:08:01,269] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:08:01,273] [INFO] DFAST_QC result json was written to GCF_009363415.1_ASM936341v1_genomic.fna/dqc_result.json
[2024-01-24 14:08:01,273] [INFO] DFAST_QC completed!
[2024-01-24 14:08:01,273] [INFO] Total running time: 0h1m30s