[2024-01-24 11:58:54,415] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:58:54,421] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:58:54,421] [INFO] DQC Reference Directory: /var/lib/cwl/stga3a8ddf9-e660-4134-8cd8-903aee16c1da/dqc_reference
[2024-01-24 11:58:55,674] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:58:55,675] [INFO] Task started: Prodigal
[2024-01-24 11:58:55,675] [INFO] Running command: gunzip -c /var/lib/cwl/stg372eff40-995c-4fb2-8ac4-5dfa2917a7aa/GCF_030161435.1_ASM3016143v1_genomic.fna.gz | prodigal -d GCF_030161435.1_ASM3016143v1_genomic.fna/cds.fna -a GCF_030161435.1_ASM3016143v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:59:04,516] [INFO] Task succeeded: Prodigal
[2024-01-24 11:59:04,516] [INFO] Task started: HMMsearch
[2024-01-24 11:59:04,516] [INFO] Running command: hmmsearch --tblout GCF_030161435.1_ASM3016143v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga3a8ddf9-e660-4134-8cd8-903aee16c1da/dqc_reference/reference_markers.hmm GCF_030161435.1_ASM3016143v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:59:04,859] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:59:04,860] [INFO] Found 6/6 markers.
[2024-01-24 11:59:04,902] [INFO] Query marker FASTA was written to GCF_030161435.1_ASM3016143v1_genomic.fna/markers.fasta
[2024-01-24 11:59:04,903] [INFO] Task started: Blastn
[2024-01-24 11:59:04,903] [INFO] Running command: blastn -query GCF_030161435.1_ASM3016143v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga3a8ddf9-e660-4134-8cd8-903aee16c1da/dqc_reference/reference_markers.fasta -out GCF_030161435.1_ASM3016143v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:05,653] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:05,657] [INFO] Selected 23 target genomes.
[2024-01-24 11:59:05,658] [INFO] Target genome list was writen to GCF_030161435.1_ASM3016143v1_genomic.fna/target_genomes.txt
[2024-01-24 11:59:05,695] [INFO] Task started: fastANI
[2024-01-24 11:59:05,695] [INFO] Running command: fastANI --query /var/lib/cwl/stg372eff40-995c-4fb2-8ac4-5dfa2917a7aa/GCF_030161435.1_ASM3016143v1_genomic.fna.gz --refList GCF_030161435.1_ASM3016143v1_genomic.fna/target_genomes.txt --output GCF_030161435.1_ASM3016143v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:59:20,857] [INFO] Task succeeded: fastANI
[2024-01-24 11:59:20,858] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga3a8ddf9-e660-4134-8cd8-903aee16c1da/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:59:20,858] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga3a8ddf9-e660-4134-8cd8-903aee16c1da/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:59:20,874] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:59:20,874] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:59:20,874] [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
Thalassotalea algicola	strain=M1531	GCA_012932965.1	2716224	2716224	type	True	78.9944	219	1339	95	below_threshold
Colwellia chukchiensis	strain=CGMCC 1.9127	GCA_900109795.1	641665	641665	type	True	78.9246	147	1339	95	below_threshold
Colwellia chukchiensis	strain=CGMCC 1.9127	GCA_002104455.1	641665	641665	type	True	78.8922	146	1339	95	below_threshold
Thalassotalea piscium	strain=DSM 26287	GCA_014207645.1	1230533	1230533	type	True	78.8721	142	1339	95	below_threshold
Litorilituus sediminis	strain=JCM 17549	GCA_004295665.1	718192	718192	type	True	78.6534	176	1339	95	below_threshold
Thalassotalea profundi	strain=CGMCC 1.15922	GCA_014653195.1	2036687	2036687	type	True	78.586	149	1339	95	below_threshold
Thalassotalea crassostreae	strain=LPB0090	GCA_001831495.1	1763536	1763536	type	True	78.5026	133	1339	95	below_threshold
Thalassotalea agarivorans	strain=DSM 19706	GCA_900111755.1	349064	349064	type	True	78.498	143	1339	95	below_threshold
Thalassotalea marina	strain=KCTC 42731	GCA_014656435.1	1673741	1673741	type	True	78.4957	180	1339	95	below_threshold
Thalassotalea crassostreae	strain=LPB0090	GCA_001652445.1	1763536	1763536	type	True	78.3544	131	1339	95	below_threshold
Cognaticolwellia mytili	strain=KCTC 52417	GCA_002104475.1	1888913	1888913	type	True	78.0975	168	1339	95	below_threshold
Colwellia ponticola	strain=OISW-25	GCA_005885605.1	2304625	2304625	type	True	77.9746	135	1339	95	below_threshold
Colwellia demingiae	strain=ACAM 459	GCA_007954275.1	89401	89401	type	True	77.8157	136	1339	95	below_threshold
Colwellia hornerae	strain=ACAM 607	GCA_007954355.1	89402	89402	type	True	77.6299	138	1339	95	below_threshold
Pseudocolwellia agarivorans	strain=QM50	GCA_002000085.1	1911682	1911682	type	True	77.6138	151	1339	95	below_threshold
Colwellia echini	strain=A3	GCA_002843355.2	1982103	1982103	type	True	77.5335	145	1339	95	below_threshold
Colwellia marinimaniae	strain=MTCD1	GCA_002207865.1	1513592	1513592	type	True	77.4323	116	1339	95	below_threshold
Vibrio coralliirubri	strain=DSM 27495	GCA_024347375.1	1516159	1516159	type	True	77.0832	51	1339	95	below_threshold
Vibrio celticus	strain=CECT 7224	GCA_024347335.1	446372	446372	type	True	77.0674	56	1339	95	below_threshold
Vibrio nitrifigilis	strain=NFV-1	GCA_015686695.1	2789781	2789781	type	True	76.9108	53	1339	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:59:20,876] [INFO] DFAST Taxonomy check result was written to GCF_030161435.1_ASM3016143v1_genomic.fna/tc_result.tsv
[2024-01-24 11:59:20,877] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:59:20,877] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:59:20,877] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga3a8ddf9-e660-4134-8cd8-903aee16c1da/dqc_reference/checkm_data
[2024-01-24 11:59:20,878] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:59:20,917] [INFO] Task started: CheckM
[2024-01-24 11:59:20,918] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030161435.1_ASM3016143v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030161435.1_ASM3016143v1_genomic.fna/checkm_input GCF_030161435.1_ASM3016143v1_genomic.fna/checkm_result
[2024-01-24 11:59:52,574] [INFO] Task succeeded: CheckM
[2024-01-24 11:59:52,575] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:59:52,599] [INFO] ===== Completeness check finished =====
[2024-01-24 11:59:52,600] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:59:52,600] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030161435.1_ASM3016143v1_genomic.fna/markers.fasta)
[2024-01-24 11:59:52,600] [INFO] Task started: Blastn
[2024-01-24 11:59:52,600] [INFO] Running command: blastn -query GCF_030161435.1_ASM3016143v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga3a8ddf9-e660-4134-8cd8-903aee16c1da/dqc_reference/reference_markers_gtdb.fasta -out GCF_030161435.1_ASM3016143v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:53,834] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:53,837] [INFO] Selected 23 target genomes.
[2024-01-24 11:59:53,838] [INFO] Target genome list was writen to GCF_030161435.1_ASM3016143v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:59:53,871] [INFO] Task started: fastANI
[2024-01-24 11:59:53,871] [INFO] Running command: fastANI --query /var/lib/cwl/stg372eff40-995c-4fb2-8ac4-5dfa2917a7aa/GCF_030161435.1_ASM3016143v1_genomic.fna.gz --refList GCF_030161435.1_ASM3016143v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030161435.1_ASM3016143v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:00:09,155] [INFO] Task succeeded: fastANI
[2024-01-24 12:00:09,174] [INFO] Found 23 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:00:09,174] [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_014898095.1	s__Thalassotalea sp014898095	81.0687	588	1339	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003390395.1	s__Thalassotalea euphylliae_C	79.6586	188	1339	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003390375.1	s__Thalassotalea euphylliae_A	79.1198	184	1339	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012932965.1	s__Thalassotalea algicola	78.9828	220	1339	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003390335.1	s__Thalassotalea euphylliae_B	78.8818	182	1339	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007097525.1	s__Thalassotalea_A sp007097525	78.7503	139	1339	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014656435.1	s__Thalassotalea_C marina	78.6231	176	1339	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017744155.1	s__Thalassotalea sp017744155	78.5301	170	1339	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111755.1	s__Thalassotalea_D agarivorans	78.5091	142	1339	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002104515.1	s__Cognaticolwellia polaris	78.2113	177	1339	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002104475.1	s__Cognaticolwellia mytili	78.124	166	1339	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014077505.1	s__Cognaticolwellia sp014077505	78.015	140	1339	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005885605.1	s__Colwellia ponticola	77.9746	135	1339	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001913705.1	s__Thalassotalea_C sp001913705	77.8609	132	1339	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009832865.1	s__Colwellia sp009832865	77.8072	141	1339	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002104535.1	s__Cognaticolwellia sediminilitoris	77.7698	162	1339	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002000085.1	s__Pseudocolwellia agarivorans	77.6756	147	1339	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudocolwellia	95.0	95.36	95.36	0.90	0.90	2	-
GCF_000764185.1	s__Colwellia psychrerythraea_B	77.6248	144	1339	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013215385.1	s__Colwellia_A sp013215385	77.5905	148	1339	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002843355.2	s__Colwellia echini	77.5344	144	1339	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014077005.1	s__Cognaticolwellia sp014077005	77.5195	129	1339	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	98.22	95.22	0.95	0.87	11	-
GCA_016765535.1	s__GCA-2401725 sp016765535	77.1476	105	1339	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__GCA-2401725	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003354085.1	s__Cognaticolwellia sp003354085	76.7666	132	1339	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:00:09,178] [INFO] GTDB search result was written to GCF_030161435.1_ASM3016143v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:00:09,178] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:00:09,191] [INFO] DFAST_QC result json was written to GCF_030161435.1_ASM3016143v1_genomic.fna/dqc_result.json
[2024-01-24 12:00:09,191] [INFO] DFAST_QC completed!
[2024-01-24 12:00:09,191] [INFO] Total running time: 0h1m15s