[2024-01-24 13:17:47,462] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:47,464] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:47,465] [INFO] DQC Reference Directory: /var/lib/cwl/stg021f3981-3062-4b88-84e4-5fbcf2973cc0/dqc_reference
[2024-01-24 13:17:48,846] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:48,847] [INFO] Task started: Prodigal
[2024-01-24 13:17:48,848] [INFO] Running command: gunzip -c /var/lib/cwl/stgba1f5362-8a9a-4606-80fc-3aabab2d8e6e/GCF_002104515.1_ASM210451v1_genomic.fna.gz | prodigal -d GCF_002104515.1_ASM210451v1_genomic.fna/cds.fna -a GCF_002104515.1_ASM210451v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:57,280] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:57,280] [INFO] Task started: HMMsearch
[2024-01-24 13:17:57,281] [INFO] Running command: hmmsearch --tblout GCF_002104515.1_ASM210451v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg021f3981-3062-4b88-84e4-5fbcf2973cc0/dqc_reference/reference_markers.hmm GCF_002104515.1_ASM210451v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:57,659] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:57,661] [INFO] Found 6/6 markers.
[2024-01-24 13:17:57,698] [INFO] Query marker FASTA was written to GCF_002104515.1_ASM210451v1_genomic.fna/markers.fasta
[2024-01-24 13:17:57,698] [INFO] Task started: Blastn
[2024-01-24 13:17:57,698] [INFO] Running command: blastn -query GCF_002104515.1_ASM210451v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg021f3981-3062-4b88-84e4-5fbcf2973cc0/dqc_reference/reference_markers.fasta -out GCF_002104515.1_ASM210451v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:58,519] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:58,523] [INFO] Selected 21 target genomes.
[2024-01-24 13:17:58,523] [INFO] Target genome list was writen to GCF_002104515.1_ASM210451v1_genomic.fna/target_genomes.txt
[2024-01-24 13:17:58,532] [INFO] Task started: fastANI
[2024-01-24 13:17:58,532] [INFO] Running command: fastANI --query /var/lib/cwl/stgba1f5362-8a9a-4606-80fc-3aabab2d8e6e/GCF_002104515.1_ASM210451v1_genomic.fna.gz --refList GCF_002104515.1_ASM210451v1_genomic.fna/target_genomes.txt --output GCF_002104515.1_ASM210451v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:18:15,259] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:15,260] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg021f3981-3062-4b88-84e4-5fbcf2973cc0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:18:15,260] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg021f3981-3062-4b88-84e4-5fbcf2973cc0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:18:15,272] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:18:15,272] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:18:15,272] [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	79.7268	550	1463	95	below_threshold
Colwellia chukchiensis	strain=CGMCC 1.9127	GCA_002104455.1	641665	641665	type	True	79.2593	455	1463	95	below_threshold
Colwellia chukchiensis	strain=CGMCC 1.9127	GCA_900109795.1	641665	641665	type	True	79.2037	452	1463	95	below_threshold
Pseudocolwellia agarivorans	strain=QM50	GCA_002000085.1	1911682	1911682	type	True	78.6415	274	1463	95	below_threshold
Thalassotalea marina	strain=KCTC 42731	GCA_014656435.1	1673741	1673741	type	True	78.4983	176	1463	95	below_threshold
Thalassotalea piscium	strain=DSM 26287	GCA_014207645.1	1230533	1230533	type	True	78.4241	245	1463	95	below_threshold
Colwellia echini	strain=A3	GCA_002843355.2	1982103	1982103	type	True	78.4168	246	1463	95	below_threshold
Thalassomonas viridans	strain=XOM25	GCA_000948985.1	137584	137584	type	True	78.3221	99	1463	95	below_threshold
Colwellia hornerae	strain=ACAM 607	GCA_007954355.1	89402	89402	type	True	78.2876	323	1463	95	below_threshold
Colwellia piezophila	strain=ATCC BAA-637	GCA_000378625.1	211668	211668	type	True	78.2335	234	1463	95	below_threshold
Colwellia demingiae	strain=ACAM 459	GCA_007954275.1	89401	89401	type	True	78.1529	256	1463	95	below_threshold
Litorilituus sediminis	strain=JCM 17549	GCA_004295665.1	718192	718192	type	True	78.1317	230	1463	95	below_threshold
Thalassotalea profundi	strain=CGMCC 1.15922	GCA_014653195.1	2036687	2036687	type	True	77.8863	261	1463	95	below_threshold
Shewanella inventionis	strain=KCTC 42807	GCA_023283595.1	1738770	1738770	type	True	76.5872	76	1463	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:18:15,274] [INFO] DFAST Taxonomy check result was written to GCF_002104515.1_ASM210451v1_genomic.fna/tc_result.tsv
[2024-01-24 13:18:15,275] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:18:15,275] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:18:15,275] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg021f3981-3062-4b88-84e4-5fbcf2973cc0/dqc_reference/checkm_data
[2024-01-24 13:18:15,276] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:18:15,324] [INFO] Task started: CheckM
[2024-01-24 13:18:15,324] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002104515.1_ASM210451v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002104515.1_ASM210451v1_genomic.fna/checkm_input GCF_002104515.1_ASM210451v1_genomic.fna/checkm_result
[2024-01-24 13:18:46,880] [INFO] Task succeeded: CheckM
[2024-01-24 13:18:46,882] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:18:46,903] [INFO] ===== Completeness check finished =====
[2024-01-24 13:18:46,903] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:18:46,903] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002104515.1_ASM210451v1_genomic.fna/markers.fasta)
[2024-01-24 13:18:46,904] [INFO] Task started: Blastn
[2024-01-24 13:18:46,904] [INFO] Running command: blastn -query GCF_002104515.1_ASM210451v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg021f3981-3062-4b88-84e4-5fbcf2973cc0/dqc_reference/reference_markers_gtdb.fasta -out GCF_002104515.1_ASM210451v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:48,134] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:48,137] [INFO] Selected 10 target genomes.
[2024-01-24 13:18:48,137] [INFO] Target genome list was writen to GCF_002104515.1_ASM210451v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:18:48,159] [INFO] Task started: fastANI
[2024-01-24 13:18:48,159] [INFO] Running command: fastANI --query /var/lib/cwl/stgba1f5362-8a9a-4606-80fc-3aabab2d8e6e/GCF_002104515.1_ASM210451v1_genomic.fna.gz --refList GCF_002104515.1_ASM210451v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002104515.1_ASM210451v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:18:59,714] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:59,726] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:18:59,726] [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_002104515.1	s__Cognaticolwellia polaris	100.0	1462	1463	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_003061515.1	s__Cognaticolwellia sp003061515	83.4584	1032	1463	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	98.05	98.05	0.90	0.90	2	-
GCF_002077175.1	s__Cognaticolwellia sp002077175	82.3863	943	1463	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002076895.1	s__Cognaticolwellia beringensis	81.8303	886	1463	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	81.6101	843	1463	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	80.8348	675	1463	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003971255.1	s__Cognaticolwellia sp003971255	80.6214	729	1463	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007954265.1	s__Cognaticolwellia sp007954265	80.5194	677	1463	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014077005.1	s__Cognaticolwellia sp014077005	80.5118	716	1463	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	98.22	95.22	0.95	0.87	11	-
GCF_014077095.1	s__Cognaticolwellia sp014077095	80.4794	675	1463	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 13:18:59,728] [INFO] GTDB search result was written to GCF_002104515.1_ASM210451v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:18:59,728] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:18:59,733] [INFO] DFAST_QC result json was written to GCF_002104515.1_ASM210451v1_genomic.fna/dqc_result.json
[2024-01-24 13:18:59,733] [INFO] DFAST_QC completed!
[2024-01-24 13:18:59,733] [INFO] Total running time: 0h1m12s