[2024-01-24 12:36:57,465] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:36:57,469] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:36:57,469] [INFO] DQC Reference Directory: /var/lib/cwl/stg4014fc29-34b2-4c9f-82b8-6964abdfd797/dqc_reference
[2024-01-24 12:36:58,853] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:36:58,854] [INFO] Task started: Prodigal
[2024-01-24 12:36:58,854] [INFO] Running command: gunzip -c /var/lib/cwl/stgf8ff4929-1c01-4bdd-8a52-229807f0260b/GCF_014656435.1_ASM1465643v1_genomic.fna.gz | prodigal -d GCF_014656435.1_ASM1465643v1_genomic.fna/cds.fna -a GCF_014656435.1_ASM1465643v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:37:09,262] [INFO] Task succeeded: Prodigal
[2024-01-24 12:37:09,263] [INFO] Task started: HMMsearch
[2024-01-24 12:37:09,263] [INFO] Running command: hmmsearch --tblout GCF_014656435.1_ASM1465643v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4014fc29-34b2-4c9f-82b8-6964abdfd797/dqc_reference/reference_markers.hmm GCF_014656435.1_ASM1465643v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:37:09,632] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:37:09,633] [INFO] Found 6/6 markers.
[2024-01-24 12:37:09,693] [INFO] Query marker FASTA was written to GCF_014656435.1_ASM1465643v1_genomic.fna/markers.fasta
[2024-01-24 12:37:09,694] [INFO] Task started: Blastn
[2024-01-24 12:37:09,694] [INFO] Running command: blastn -query GCF_014656435.1_ASM1465643v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4014fc29-34b2-4c9f-82b8-6964abdfd797/dqc_reference/reference_markers.fasta -out GCF_014656435.1_ASM1465643v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:10,578] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:10,582] [INFO] Selected 25 target genomes.
[2024-01-24 12:37:10,582] [INFO] Target genome list was writen to GCF_014656435.1_ASM1465643v1_genomic.fna/target_genomes.txt
[2024-01-24 12:37:10,598] [INFO] Task started: fastANI
[2024-01-24 12:37:10,598] [INFO] Running command: fastANI --query /var/lib/cwl/stgf8ff4929-1c01-4bdd-8a52-229807f0260b/GCF_014656435.1_ASM1465643v1_genomic.fna.gz --refList GCF_014656435.1_ASM1465643v1_genomic.fna/target_genomes.txt --output GCF_014656435.1_ASM1465643v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:37:29,567] [INFO] Task succeeded: fastANI
[2024-01-24 12:37:29,567] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4014fc29-34b2-4c9f-82b8-6964abdfd797/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:37:29,568] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4014fc29-34b2-4c9f-82b8-6964abdfd797/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:37:29,583] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:37:29,583] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:37:29,583] [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 marina	strain=KCTC 42731	GCA_014656435.1	1673741	1673741	type	True	100.0	1606	1608	95	conclusive
Colwellia chukchiensis	strain=CGMCC 1.9127	GCA_900109795.1	641665	641665	type	True	79.5779	173	1608	95	below_threshold
Colwellia chukchiensis	strain=CGMCC 1.9127	GCA_002104455.1	641665	641665	type	True	79.5575	179	1608	95	below_threshold
Thalassotalea agarivorans	strain=DSM 19706	GCA_900111755.1	349064	349064	type	True	78.6809	141	1608	95	below_threshold
Thalassotalea algicola	strain=M1531	GCA_012932965.1	2716224	2716224	type	True	78.6567	186	1608	95	below_threshold
Litorilituus sediminis	strain=JCM 17549	GCA_004295665.1	718192	718192	type	True	78.2671	189	1608	95	below_threshold
Thalassotalea profundi	strain=CGMCC 1.15922	GCA_014653195.1	2036687	2036687	type	True	78.1409	210	1608	95	below_threshold
Colwellia echini	strain=A3	GCA_002843355.2	1982103	1982103	type	True	77.8474	143	1608	95	below_threshold
Colwellia ponticola	strain=OISW-25	GCA_005885605.1	2304625	2304625	type	True	77.7588	151	1608	95	below_threshold
Cognaticolwellia mytili	strain=KCTC 52417	GCA_002104475.1	1888913	1888913	type	True	77.7401	205	1608	95	below_threshold
Colwellia demingiae	strain=ACAM 459	GCA_007954275.1	89401	89401	type	True	77.5453	164	1608	95	below_threshold
Pseudocolwellia agarivorans	strain=QM50	GCA_002000085.1	1911682	1911682	type	True	77.4627	184	1608	95	below_threshold
Thalassotalea piscium	strain=DSM 26287	GCA_014207645.1	1230533	1230533	type	True	77.4606	205	1608	95	below_threshold
Colwellia hornerae	strain=ACAM 607	GCA_007954355.1	89402	89402	type	True	77.3499	174	1608	95	below_threshold
Pseudoalteromonas piratica	strain=OCN003	GCA_000788395.1	1348114	1348114	type	True	76.9934	104	1608	95	below_threshold
Photobacterium swingsii	strain=CECT 7576	GCA_024346715.1	680026	680026	type	True	76.9763	52	1608	95	below_threshold
Photobacterium damselae	strain=NCTC11647	GCA_900454585.1	38293	38293	type	True	76.6713	54	1608	95	below_threshold
Aliivibrio fischeri	strain=DSM 507	GCA_023983475.1	668	668	suspected-type	True	76.6577	58	1608	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:37:29,589] [INFO] DFAST Taxonomy check result was written to GCF_014656435.1_ASM1465643v1_genomic.fna/tc_result.tsv
[2024-01-24 12:37:29,593] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:37:29,593] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:37:29,594] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4014fc29-34b2-4c9f-82b8-6964abdfd797/dqc_reference/checkm_data
[2024-01-24 12:37:29,595] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:37:29,664] [INFO] Task started: CheckM
[2024-01-24 12:37:29,665] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014656435.1_ASM1465643v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014656435.1_ASM1465643v1_genomic.fna/checkm_input GCF_014656435.1_ASM1465643v1_genomic.fna/checkm_result
[2024-01-24 12:38:05,898] [INFO] Task succeeded: CheckM
[2024-01-24 12:38:05,899] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:38:05,929] [INFO] ===== Completeness check finished =====
[2024-01-24 12:38:05,930] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:38:05,930] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014656435.1_ASM1465643v1_genomic.fna/markers.fasta)
[2024-01-24 12:38:05,931] [INFO] Task started: Blastn
[2024-01-24 12:38:05,931] [INFO] Running command: blastn -query GCF_014656435.1_ASM1465643v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4014fc29-34b2-4c9f-82b8-6964abdfd797/dqc_reference/reference_markers_gtdb.fasta -out GCF_014656435.1_ASM1465643v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:38:07,173] [INFO] Task succeeded: Blastn
[2024-01-24 12:38:07,177] [INFO] Selected 21 target genomes.
[2024-01-24 12:38:07,177] [INFO] Target genome list was writen to GCF_014656435.1_ASM1465643v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:38:07,210] [INFO] Task started: fastANI
[2024-01-24 12:38:07,210] [INFO] Running command: fastANI --query /var/lib/cwl/stgf8ff4929-1c01-4bdd-8a52-229807f0260b/GCF_014656435.1_ASM1465643v1_genomic.fna.gz --refList GCF_014656435.1_ASM1465643v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014656435.1_ASM1465643v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:38:22,022] [INFO] Task succeeded: fastANI
[2024-01-24 12:38:22,037] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:38:22,038] [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_014656435.1	s__Thalassotalea_C marina	100.0	1606	1608	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea_C	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014898095.1	s__Thalassotalea sp014898095	80.6328	183	1608	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	78.8221	182	1608	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	78.6759	185	1608	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	78.5776	183	1608	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	78.4837	173	1608	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002104515.1	s__Cognaticolwellia polaris	78.2828	181	1608	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006439335.1	s__Litorilituus lipolyticus	78.1122	168	1608	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Litorilituus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001913705.1	s__Thalassotalea_C sp001913705	78.1106	325	1608	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_003545765.1	s__Litorilituus sp003545765	78.064	164	1608	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Litorilituus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003061515.1	s__Cognaticolwellia sp003061515	77.85	181	1608	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	98.05	98.05	0.90	0.90	2	-
GCF_002104475.1	s__Cognaticolwellia mytili	77.7581	203	1608	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002000025.1	s__Cognaticolwellia aestuarii	77.6722	191	1608	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_018860915.1	s__Colwellia sp018860915	77.6308	157	1608	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	77.5705	206	1608	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014207645.1	s__Thalassotalea_B piscium	77.4459	206	1608	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014076845.1	s__Colwellia_A sp014076845	77.3249	178	1608	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia_A	95.0	99.15	95.49	0.95	0.86	8	-
GCA_013215295.1	s__Colwellia_A sp013215295	77.2606	183	1608	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003354085.1	s__Cognaticolwellia sp003354085	76.8678	175	1608	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 12:38:22,039] [INFO] GTDB search result was written to GCF_014656435.1_ASM1465643v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:38:22,040] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:38:22,049] [INFO] DFAST_QC result json was written to GCF_014656435.1_ASM1465643v1_genomic.fna/dqc_result.json
[2024-01-24 12:38:22,049] [INFO] DFAST_QC completed!
[2024-01-24 12:38:22,049] [INFO] Total running time: 0h1m25s