[2024-01-24 13:57:16,633] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:16,635] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:16,635] [INFO] DQC Reference Directory: /var/lib/cwl/stg1dc99fd7-5036-4afd-9ca9-bee36b86e50a/dqc_reference
[2024-01-24 13:57:17,959] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:17,960] [INFO] Task started: Prodigal
[2024-01-24 13:57:17,961] [INFO] Running command: gunzip -c /var/lib/cwl/stgdcc133df-3adf-4977-adbc-71046177507c/GCF_002076895.1_ASM207689v1_genomic.fna.gz | prodigal -d GCF_002076895.1_ASM207689v1_genomic.fna/cds.fna -a GCF_002076895.1_ASM207689v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:27,161] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:27,162] [INFO] Task started: HMMsearch
[2024-01-24 13:57:27,162] [INFO] Running command: hmmsearch --tblout GCF_002076895.1_ASM207689v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1dc99fd7-5036-4afd-9ca9-bee36b86e50a/dqc_reference/reference_markers.hmm GCF_002076895.1_ASM207689v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:27,505] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:27,507] [INFO] Found 6/6 markers.
[2024-01-24 13:57:27,550] [INFO] Query marker FASTA was written to GCF_002076895.1_ASM207689v1_genomic.fna/markers.fasta
[2024-01-24 13:57:27,550] [INFO] Task started: Blastn
[2024-01-24 13:57:27,551] [INFO] Running command: blastn -query GCF_002076895.1_ASM207689v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1dc99fd7-5036-4afd-9ca9-bee36b86e50a/dqc_reference/reference_markers.fasta -out GCF_002076895.1_ASM207689v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:28,280] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:28,283] [INFO] Selected 17 target genomes.
[2024-01-24 13:57:28,283] [INFO] Target genome list was writen to GCF_002076895.1_ASM207689v1_genomic.fna/target_genomes.txt
[2024-01-24 13:57:28,290] [INFO] Task started: fastANI
[2024-01-24 13:57:28,291] [INFO] Running command: fastANI --query /var/lib/cwl/stgdcc133df-3adf-4977-adbc-71046177507c/GCF_002076895.1_ASM207689v1_genomic.fna.gz --refList GCF_002076895.1_ASM207689v1_genomic.fna/target_genomes.txt --output GCF_002076895.1_ASM207689v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:57:40,615] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:40,615] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1dc99fd7-5036-4afd-9ca9-bee36b86e50a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:57:40,616] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1dc99fd7-5036-4afd-9ca9-bee36b86e50a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:57:40,628] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:57:40,628] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:57:40,628] [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
Cognaticolwellia mytili	strain=KCTC 52417	GCA_002104475.1	1888913	1888913	type	True	80.0436	582	1553	95	below_threshold
Colwellia chukchiensis	strain=CGMCC 1.9127	GCA_002104455.1	641665	641665	type	True	79.2627	495	1553	95	below_threshold
Colwellia chukchiensis	strain=CGMCC 1.9127	GCA_900109795.1	641665	641665	type	True	79.248	490	1553	95	below_threshold
Pseudocolwellia agarivorans	strain=QM50	GCA_002000085.1	1911682	1911682	type	True	78.5028	268	1553	95	below_threshold
Colwellia hornerae	strain=ACAM 607	GCA_007954355.1	89402	89402	type	True	78.4893	374	1553	95	below_threshold
Colwellia echini	strain=A3	GCA_002843355.2	1982103	1982103	type	True	78.2397	251	1553	95	below_threshold
Thalassotalea piscium	strain=DSM 26287	GCA_014207645.1	1230533	1230533	type	True	78.1517	230	1553	95	below_threshold
Colwellia marinimaniae	strain=MTCD1	GCA_002207865.1	1513592	1513592	type	True	78.0961	231	1553	95	below_threshold
Thalassotalea profundi	strain=CGMCC 1.15922	GCA_014653195.1	2036687	2036687	type	True	78.0764	249	1553	95	below_threshold
Photobacterium toruni	strain=CECT 9189	GCA_024529955.1	1935446	1935446	type	True	77.507	65	1553	95	below_threshold
Shewanella psychromarinicola	strain=M2	GCA_003855155.1	2487742	2487742	type	True	77.4534	73	1553	95	below_threshold
Shewanella psychromarinicola	strain=JCM 32090	GCA_023283865.1	2487742	2487742	type	True	76.1813	65	1553	95	below_threshold
Shewanella saliphila	strain=KCTC 62131	GCA_023283695.1	2282698	2282698	type	True	75.9494	70	1553	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:57:40,630] [INFO] DFAST Taxonomy check result was written to GCF_002076895.1_ASM207689v1_genomic.fna/tc_result.tsv
[2024-01-24 13:57:40,631] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:57:40,631] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:57:40,632] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1dc99fd7-5036-4afd-9ca9-bee36b86e50a/dqc_reference/checkm_data
[2024-01-24 13:57:40,634] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:57:40,681] [INFO] Task started: CheckM
[2024-01-24 13:57:40,681] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002076895.1_ASM207689v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002076895.1_ASM207689v1_genomic.fna/checkm_input GCF_002076895.1_ASM207689v1_genomic.fna/checkm_result
[2024-01-24 13:58:14,840] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:14,841] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:14,855] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:14,855] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:14,856] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002076895.1_ASM207689v1_genomic.fna/markers.fasta)
[2024-01-24 13:58:14,856] [INFO] Task started: Blastn
[2024-01-24 13:58:14,856] [INFO] Running command: blastn -query GCF_002076895.1_ASM207689v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1dc99fd7-5036-4afd-9ca9-bee36b86e50a/dqc_reference/reference_markers_gtdb.fasta -out GCF_002076895.1_ASM207689v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:16,001] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:16,004] [INFO] Selected 11 target genomes.
[2024-01-24 13:58:16,004] [INFO] Target genome list was writen to GCF_002076895.1_ASM207689v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:16,012] [INFO] Task started: fastANI
[2024-01-24 13:58:16,012] [INFO] Running command: fastANI --query /var/lib/cwl/stgdcc133df-3adf-4977-adbc-71046177507c/GCF_002076895.1_ASM207689v1_genomic.fna.gz --refList GCF_002076895.1_ASM207689v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002076895.1_ASM207689v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:58:27,733] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:27,748] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:58:27,749] [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_002076895.1	s__Cognaticolwellia beringensis	100.0	1550	1553	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002077175.1	s__Cognaticolwellia sp002077175	90.6166	1252	1553	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	86.2009	1025	1553	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003061515.1	s__Cognaticolwellia sp003061515	84.3899	1027	1553	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	98.05	98.05	0.90	0.90	2	-
GCF_014077005.1	s__Cognaticolwellia sp014077005	82.6145	915	1553	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	98.22	95.22	0.95	0.87	11	-
GCF_007954265.1	s__Cognaticolwellia sp007954265	82.5213	897	1553	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014077095.1	s__Cognaticolwellia sp014077095	82.4856	872	1553	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002104515.1	s__Cognaticolwellia polaris	81.9321	875	1553	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003971255.1	s__Cognaticolwellia sp003971255	81.3652	801	1553	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002104535.1	s__Cognaticolwellia sediminilitoris	81.0264	737	1553	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	80.7615	692	1553	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:58:27,750] [INFO] GTDB search result was written to GCF_002076895.1_ASM207689v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:58:27,751] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:58:27,754] [INFO] DFAST_QC result json was written to GCF_002076895.1_ASM207689v1_genomic.fna/dqc_result.json
[2024-01-24 13:58:27,754] [INFO] DFAST_QC completed!
[2024-01-24 13:58:27,754] [INFO] Total running time: 0h1m11s