[2024-01-24 13:40:34,790] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:34,796] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:34,797] [INFO] DQC Reference Directory: /var/lib/cwl/stga46dd66d-776d-4bb4-b518-52193f1df4e1/dqc_reference
[2024-01-24 13:40:36,203] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:36,229] [INFO] Task started: Prodigal
[2024-01-24 13:40:36,230] [INFO] Running command: gunzip -c /var/lib/cwl/stg2a121ebe-a162-4ba5-91ac-606d0b7555e8/GCF_016757215.1_ASM1675721v1_genomic.fna.gz | prodigal -d GCF_016757215.1_ASM1675721v1_genomic.fna/cds.fna -a GCF_016757215.1_ASM1675721v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:57,444] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:57,444] [INFO] Task started: HMMsearch
[2024-01-24 13:40:57,445] [INFO] Running command: hmmsearch --tblout GCF_016757215.1_ASM1675721v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga46dd66d-776d-4bb4-b518-52193f1df4e1/dqc_reference/reference_markers.hmm GCF_016757215.1_ASM1675721v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:57,856] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:57,858] [INFO] Found 6/6 markers.
[2024-01-24 13:40:57,910] [INFO] Query marker FASTA was written to GCF_016757215.1_ASM1675721v1_genomic.fna/markers.fasta
[2024-01-24 13:40:57,910] [INFO] Task started: Blastn
[2024-01-24 13:40:57,911] [INFO] Running command: blastn -query GCF_016757215.1_ASM1675721v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga46dd66d-776d-4bb4-b518-52193f1df4e1/dqc_reference/reference_markers.fasta -out GCF_016757215.1_ASM1675721v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:58,494] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:58,497] [INFO] Selected 22 target genomes.
[2024-01-24 13:40:58,498] [INFO] Target genome list was writen to GCF_016757215.1_ASM1675721v1_genomic.fna/target_genomes.txt
[2024-01-24 13:40:58,506] [INFO] Task started: fastANI
[2024-01-24 13:40:58,506] [INFO] Running command: fastANI --query /var/lib/cwl/stg2a121ebe-a162-4ba5-91ac-606d0b7555e8/GCF_016757215.1_ASM1675721v1_genomic.fna.gz --refList GCF_016757215.1_ASM1675721v1_genomic.fna/target_genomes.txt --output GCF_016757215.1_ASM1675721v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:15,656] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:15,656] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga46dd66d-776d-4bb4-b518-52193f1df4e1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:15,657] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga46dd66d-776d-4bb4-b518-52193f1df4e1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:15,665] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:41:15,666] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:15,666] [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
Fulvivirga sediminis	strain=2943	GCA_016757215.1	2803949	2803949	type	True	100.0	1871	1873	95	conclusive
Fulvivirga lutimaris	strain=KCTC 42720	GCA_009711525.1	1819566	1819566	type	True	76.7131	94	1873	95	below_threshold
Fulvivirga marina	strain=29W222	GCA_016775155.1	2494733	2494733	type	True	76.695	140	1873	95	below_threshold
Fulvivirga aurantia	strain=RKSG066	GCA_009711475.1	2529383	2529383	type	True	76.6946	67	1873	95	below_threshold
Fulvivirga kasyanovii	strain=JCM 16186	GCA_009711405.1	396812	396812	type	True	76.6301	130	1873	95	below_threshold
Marivirga lumbricoides	strain=CGMCC 1.10832	GCA_014636295.1	1046115	1046115	type	True	76.6191	54	1873	95	below_threshold
Fulvivirga imtechensis	strain=AK7	GCA_000331535.1	881893	881893	type	True	76.5075	122	1873	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:15,667] [INFO] DFAST Taxonomy check result was written to GCF_016757215.1_ASM1675721v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:15,668] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:15,668] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:15,668] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga46dd66d-776d-4bb4-b518-52193f1df4e1/dqc_reference/checkm_data
[2024-01-24 13:41:15,669] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:15,722] [INFO] Task started: CheckM
[2024-01-24 13:41:15,722] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016757215.1_ASM1675721v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016757215.1_ASM1675721v1_genomic.fna/checkm_input GCF_016757215.1_ASM1675721v1_genomic.fna/checkm_result
[2024-01-24 13:42:16,868] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:16,870] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:16,892] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:16,893] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:16,893] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016757215.1_ASM1675721v1_genomic.fna/markers.fasta)
[2024-01-24 13:42:16,893] [INFO] Task started: Blastn
[2024-01-24 13:42:16,894] [INFO] Running command: blastn -query GCF_016757215.1_ASM1675721v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga46dd66d-776d-4bb4-b518-52193f1df4e1/dqc_reference/reference_markers_gtdb.fasta -out GCF_016757215.1_ASM1675721v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:17,645] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:17,649] [INFO] Selected 26 target genomes.
[2024-01-24 13:42:17,650] [INFO] Target genome list was writen to GCF_016757215.1_ASM1675721v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:17,699] [INFO] Task started: fastANI
[2024-01-24 13:42:17,699] [INFO] Running command: fastANI --query /var/lib/cwl/stg2a121ebe-a162-4ba5-91ac-606d0b7555e8/GCF_016757215.1_ASM1675721v1_genomic.fna.gz --refList GCF_016757215.1_ASM1675721v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016757215.1_ASM1675721v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:38,493] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:38,507] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:38,507] [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_016757215.1	s__Fulvivirga sp016757215	100.0	1871	1873	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fulvivirga	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009711525.1	s__Fulvivirga lutimaris	76.7131	94	1873	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fulvivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016775155.1	s__Fulvivirga sp016775155	76.695	140	1873	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fulvivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009711475.1	s__Fulvivirga aurantia	76.6946	67	1873	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fulvivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009711405.1	s__Fulvivirga kasyanovii	76.6475	129	1873	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fulvivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014636295.1	s__Marivirga lumbricoides	76.6191	54	1873	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Marivirga	95.0	97.82	97.82	0.87	0.87	2	-
GCF_000331535.1	s__Fulvivirga imtechensis	76.5235	121	1873	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fulvivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002338655.1	s__Fulvivirga sp002338655	76.2002	59	1873	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fulvivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007097395.1	s__Fulvivirga sp007097395	75.9822	82	1873	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fulvivirga	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:38,509] [INFO] GTDB search result was written to GCF_016757215.1_ASM1675721v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:38,509] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:38,512] [INFO] DFAST_QC result json was written to GCF_016757215.1_ASM1675721v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:38,513] [INFO] DFAST_QC completed!
[2024-01-24 13:42:38,513] [INFO] Total running time: 0h2m4s