[2024-01-24 11:35:07,861] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:35:07,864] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:35:07,864] [INFO] DQC Reference Directory: /var/lib/cwl/stg76741574-0e15-46bd-89bd-06197991c0ca/dqc_reference
[2024-01-24 11:35:09,098] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:35:09,099] [INFO] Task started: Prodigal
[2024-01-24 11:35:09,099] [INFO] Running command: gunzip -c /var/lib/cwl/stg4051a518-e9c6-4e4b-967a-e3055fd6b4e4/GCF_014192475.1_ASM1419247v1_genomic.fna.gz | prodigal -d GCF_014192475.1_ASM1419247v1_genomic.fna/cds.fna -a GCF_014192475.1_ASM1419247v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:35:22,631] [INFO] Task succeeded: Prodigal
[2024-01-24 11:35:22,632] [INFO] Task started: HMMsearch
[2024-01-24 11:35:22,632] [INFO] Running command: hmmsearch --tblout GCF_014192475.1_ASM1419247v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg76741574-0e15-46bd-89bd-06197991c0ca/dqc_reference/reference_markers.hmm GCF_014192475.1_ASM1419247v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:35:22,919] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:35:22,921] [INFO] Found 6/6 markers.
[2024-01-24 11:35:22,952] [INFO] Query marker FASTA was written to GCF_014192475.1_ASM1419247v1_genomic.fna/markers.fasta
[2024-01-24 11:35:22,953] [INFO] Task started: Blastn
[2024-01-24 11:35:22,953] [INFO] Running command: blastn -query GCF_014192475.1_ASM1419247v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg76741574-0e15-46bd-89bd-06197991c0ca/dqc_reference/reference_markers.fasta -out GCF_014192475.1_ASM1419247v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:23,753] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:23,756] [INFO] Selected 24 target genomes.
[2024-01-24 11:35:23,757] [INFO] Target genome list was writen to GCF_014192475.1_ASM1419247v1_genomic.fna/target_genomes.txt
[2024-01-24 11:35:23,764] [INFO] Task started: fastANI
[2024-01-24 11:35:23,764] [INFO] Running command: fastANI --query /var/lib/cwl/stg4051a518-e9c6-4e4b-967a-e3055fd6b4e4/GCF_014192475.1_ASM1419247v1_genomic.fna.gz --refList GCF_014192475.1_ASM1419247v1_genomic.fna/target_genomes.txt --output GCF_014192475.1_ASM1419247v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:40,209] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:40,209] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg76741574-0e15-46bd-89bd-06197991c0ca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:40,209] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg76741574-0e15-46bd-89bd-06197991c0ca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:40,221] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:35:40,222] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:35:40,222] [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
Simiduia aestuariiviva	strain=CECT 8571	GCA_014192475.1	1510459	1510459	type	True	100.0	1240	1241	95	conclusive
Simiduia agarivorans	strain=SA1 = DSM 21679	GCA_000305785.2	447471	447471	type	True	78.464	287	1241	95	below_threshold
Simiduia agarivorans	strain=DSM 21679	GCA_000420285.1	447471	447471	type	True	78.4333	272	1241	95	below_threshold
Saccharophagus degradans	strain=2-40	GCA_000013665.1	86304	86304	type	True	77.0197	56	1241	95	below_threshold
Pseudoteredinibacter isoporae	strain=DSM 22368	GCA_011683895.1	570281	570281	type	True	76.7085	67	1241	95	below_threshold
Microbulbifer elongatus	strain=DSM 6810	GCA_022554105.1	86173	86173	type	True	76.6983	60	1241	95	below_threshold
Pseudoteredinibacter isoporae	strain=DSM 22368	GCA_014207695.1	570281	570281	type	True	76.6748	65	1241	95	below_threshold
Pseudoteredinibacter isoporae	strain=LMG 25246	GCA_011602085.1	570281	570281	type	True	76.6748	65	1241	95	below_threshold
Gilvimarinus chinensis	strain=DSM 19667	GCA_000377745.1	396005	396005	type	True	76.6713	64	1241	95	below_threshold
Microbulbifer elongatus	strain=DSM 6810	GCA_021165935.1	86173	86173	type	True	76.6425	63	1241	95	below_threshold
Cellvibrio zantedeschiae	strain=KCTC 32239	GCA_014652535.1	1237077	1237077	type	True	76.636	52	1241	95	below_threshold
Aestuariicella albida	strain=HHU G3-2	GCA_018863235.1	2842452	2842452	type	True	76.4349	73	1241	95	below_threshold
Aestuariicella hydrocarbonica	strain=JCM 30134	GCA_011602365.1	1470433	1470433	type	True	76.2918	89	1241	95	below_threshold
Gilvimarinus polysaccharolyticus	strain=YN3	GCA_001187555.1	863921	863921	type	True	76.0559	63	1241	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:40,224] [INFO] DFAST Taxonomy check result was written to GCF_014192475.1_ASM1419247v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:40,225] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:40,225] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:40,225] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg76741574-0e15-46bd-89bd-06197991c0ca/dqc_reference/checkm_data
[2024-01-24 11:35:40,226] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:40,272] [INFO] Task started: CheckM
[2024-01-24 11:35:40,272] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014192475.1_ASM1419247v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014192475.1_ASM1419247v1_genomic.fna/checkm_input GCF_014192475.1_ASM1419247v1_genomic.fna/checkm_result
[2024-01-24 11:36:24,354] [INFO] Task succeeded: CheckM
[2024-01-24 11:36:24,356] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:36:24,377] [INFO] ===== Completeness check finished =====
[2024-01-24 11:36:24,377] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:36:24,377] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014192475.1_ASM1419247v1_genomic.fna/markers.fasta)
[2024-01-24 11:36:24,378] [INFO] Task started: Blastn
[2024-01-24 11:36:24,378] [INFO] Running command: blastn -query GCF_014192475.1_ASM1419247v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg76741574-0e15-46bd-89bd-06197991c0ca/dqc_reference/reference_markers_gtdb.fasta -out GCF_014192475.1_ASM1419247v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:36:25,578] [INFO] Task succeeded: Blastn
[2024-01-24 11:36:25,583] [INFO] Selected 24 target genomes.
[2024-01-24 11:36:25,583] [INFO] Target genome list was writen to GCF_014192475.1_ASM1419247v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:36:25,602] [INFO] Task started: fastANI
[2024-01-24 11:36:25,602] [INFO] Running command: fastANI --query /var/lib/cwl/stg4051a518-e9c6-4e4b-967a-e3055fd6b4e4/GCF_014192475.1_ASM1419247v1_genomic.fna.gz --refList GCF_014192475.1_ASM1419247v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014192475.1_ASM1419247v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:36:43,244] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:43,259] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:36:43,260] [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_014192475.1	s__Simiduia aestuariiviva	100.0	1240	1241	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Simiduia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000305785.2	s__Simiduia agarivorans	78.462	288	1241	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Simiduia	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000013665.1	s__Saccharophagus degradans	77.0196	56	1241	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Saccharophagus	95.0	96.22	96.22	0.89	0.89	2	-
GCF_000708675.1	s__Microbulbifer sp000708675	76.7352	63	1241	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011602085.1	s__Pseudoteredinibacter isoporae	76.6748	65	1241	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Pseudoteredinibacter	95.0	100.00	100.00	1.00	0.99	3	-
GCF_002007605.1	s__Cellvibrio sp002007605	76.6421	58	1241	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Cellvibrio	95.0	97.66	97.66	0.90	0.90	2	-
GCF_014652535.1	s__Cellvibrio zantedeschiae	76.636	52	1241	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Cellvibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004363885.1	s__Cellvibrio sp004363885	76.491	57	1241	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Cellvibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011683955.1	s__Pseudomaricurvus alkylphenolicus	76.4781	76	1241	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Pseudomaricurvus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011602365.1	s__Pseudomaricurvus hydrocarbonicus	76.3008	90	1241	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Pseudomaricurvus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002162135.1	s__Cellvibrio sp002162135	76.1995	74	1241	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Cellvibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001187555.1	s__Gilvimarinus polysaccharolyticus	76.0559	63	1241	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Gilvimarinus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014904735.1	s__Microbulbifer hainanensis	76.0318	71	1241	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007004655.1	s__Exilibacterium tricleocarpae	76.0252	68	1241	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Exilibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903858205.1	s__Cellvibrio sp903858205	75.717	56	1241	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Cellvibrio	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:36:43,261] [INFO] GTDB search result was written to GCF_014192475.1_ASM1419247v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:36:43,262] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:36:43,266] [INFO] DFAST_QC result json was written to GCF_014192475.1_ASM1419247v1_genomic.fna/dqc_result.json
[2024-01-24 11:36:43,266] [INFO] DFAST_QC completed!
[2024-01-24 11:36:43,266] [INFO] Total running time: 0h1m35s