[2024-01-25 17:36:20,667] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:36:20,669] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:36:20,669] [INFO] DQC Reference Directory: /var/lib/cwl/stg735fcee4-f323-4f51-96c8-7aa2a21ca5f5/dqc_reference
[2024-01-25 17:36:21,796] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:36:21,797] [INFO] Task started: Prodigal
[2024-01-25 17:36:21,797] [INFO] Running command: gunzip -c /var/lib/cwl/stgb13f1089-63d8-4bdd-9d9e-58477607f90d/GCF_014195575.1_ASM1419557v1_genomic.fna.gz | prodigal -d GCF_014195575.1_ASM1419557v1_genomic.fna/cds.fna -a GCF_014195575.1_ASM1419557v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:36:43,384] [INFO] Task succeeded: Prodigal
[2024-01-25 17:36:43,385] [INFO] Task started: HMMsearch
[2024-01-25 17:36:43,385] [INFO] Running command: hmmsearch --tblout GCF_014195575.1_ASM1419557v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg735fcee4-f323-4f51-96c8-7aa2a21ca5f5/dqc_reference/reference_markers.hmm GCF_014195575.1_ASM1419557v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:36:43,711] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:36:43,712] [INFO] Found 6/6 markers.
[2024-01-25 17:36:43,766] [INFO] Query marker FASTA was written to GCF_014195575.1_ASM1419557v1_genomic.fna/markers.fasta
[2024-01-25 17:36:43,766] [INFO] Task started: Blastn
[2024-01-25 17:36:43,766] [INFO] Running command: blastn -query GCF_014195575.1_ASM1419557v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg735fcee4-f323-4f51-96c8-7aa2a21ca5f5/dqc_reference/reference_markers.fasta -out GCF_014195575.1_ASM1419557v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:36:44,325] [INFO] Task succeeded: Blastn
[2024-01-25 17:36:44,328] [INFO] Selected 8 target genomes.
[2024-01-25 17:36:44,328] [INFO] Target genome list was writen to GCF_014195575.1_ASM1419557v1_genomic.fna/target_genomes.txt
[2024-01-25 17:36:44,331] [INFO] Task started: fastANI
[2024-01-25 17:36:44,331] [INFO] Running command: fastANI --query /var/lib/cwl/stgb13f1089-63d8-4bdd-9d9e-58477607f90d/GCF_014195575.1_ASM1419557v1_genomic.fna.gz --refList GCF_014195575.1_ASM1419557v1_genomic.fna/target_genomes.txt --output GCF_014195575.1_ASM1419557v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:36:55,337] [INFO] Task succeeded: fastANI
[2024-01-25 17:36:55,337] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg735fcee4-f323-4f51-96c8-7aa2a21ca5f5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:36:55,337] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg735fcee4-f323-4f51-96c8-7aa2a21ca5f5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:36:55,343] [INFO] Found 6 fastANI hits (3 hits with ANI > threshold)
[2024-01-25 17:36:55,343] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:36:55,343] [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
Flammeovirga yaeyamensis	strain=DSM 25626	GCA_014195575.1	367791	367791	type	True	100.0	2445	2447	95	conclusive
Flammeovirga yaeyamensis	strain=NBRC:100898	GCA_018736045.1	367791	367791	type	True	99.9958	2446	2447	95	conclusive
Flammeovirga yaeyamensis	strain=NBRC 100898	GCA_012844325.1	367791	367791	type	True	99.992	2430	2447	95	conclusive
Flammeovirga pacifica	strain=WPAGA1	GCA_000807855.2	915059	915059	type	True	81.5944	1260	2447	95	below_threshold
Flammeovirga agarivorans	strain=SR4	GCA_012641475.1	2726742	2726742	type	True	79.2142	727	2447	95	below_threshold
Flammeovirga pectinis	strain=L12M1	GCA_003970675.1	2494373	2494373	type	True	77.9901	537	2447	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:36:55,345] [INFO] DFAST Taxonomy check result was written to GCF_014195575.1_ASM1419557v1_genomic.fna/tc_result.tsv
[2024-01-25 17:36:55,346] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:36:55,346] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:36:55,346] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg735fcee4-f323-4f51-96c8-7aa2a21ca5f5/dqc_reference/checkm_data
[2024-01-25 17:36:55,347] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:36:55,419] [INFO] Task started: CheckM
[2024-01-25 17:36:55,419] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014195575.1_ASM1419557v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014195575.1_ASM1419557v1_genomic.fna/checkm_input GCF_014195575.1_ASM1419557v1_genomic.fna/checkm_result
[2024-01-25 17:37:56,637] [INFO] Task succeeded: CheckM
[2024-01-25 17:37:56,638] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.08%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:37:56,685] [INFO] ===== Completeness check finished =====
[2024-01-25 17:37:56,685] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:37:56,686] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014195575.1_ASM1419557v1_genomic.fna/markers.fasta)
[2024-01-25 17:37:56,687] [INFO] Task started: Blastn
[2024-01-25 17:37:56,687] [INFO] Running command: blastn -query GCF_014195575.1_ASM1419557v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg735fcee4-f323-4f51-96c8-7aa2a21ca5f5/dqc_reference/reference_markers_gtdb.fasta -out GCF_014195575.1_ASM1419557v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:37:57,505] [INFO] Task succeeded: Blastn
[2024-01-25 17:37:57,509] [INFO] Selected 11 target genomes.
[2024-01-25 17:37:57,509] [INFO] Target genome list was writen to GCF_014195575.1_ASM1419557v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:37:57,516] [INFO] Task started: fastANI
[2024-01-25 17:37:57,516] [INFO] Running command: fastANI --query /var/lib/cwl/stgb13f1089-63d8-4bdd-9d9e-58477607f90d/GCF_014195575.1_ASM1419557v1_genomic.fna.gz --refList GCF_014195575.1_ASM1419557v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014195575.1_ASM1419557v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:38:12,693] [INFO] Task succeeded: fastANI
[2024-01-25 17:38:12,700] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:38:12,700] [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_018736045.1	s__Flammeovirga yaeyamensis	99.9958	2446	2447	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Flammeovirgaceae;g__Flammeovirga	95.0	98.83	96.49	0.96	0.89	4	conclusive
GCF_000807855.2	s__Flammeovirga pacifica	81.6	1259	2447	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Flammeovirgaceae;g__Flammeovirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012641475.1	s__Flammeovirga sp012641475	79.2017	729	2447	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Flammeovirgaceae;g__Flammeovirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012844305.1	s__Flammeovirga aprica	78.9135	642	2447	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Flammeovirgaceae;g__Flammeovirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014534745.1	s__Flammeovirga sp014534745	78.8702	605	2447	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Flammeovirgaceae;g__Flammeovirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000812565.1	s__Flammeovirga sp000812565	78.7631	618	2447	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Flammeovirgaceae;g__Flammeovirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003970675.1	s__Flammeovirga pectinis	77.9899	537	2447	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Flammeovirgaceae;g__Flammeovirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018736065.1	s__Flammeovirga kamogawensis	77.9703	545	2447	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Flammeovirgaceae;g__Flammeovirga	95.0	100.00	100.00	1.00	1.00	3	-
GCF_003149185.1	s__Sediminitomix flava	76.3143	123	2447	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Flammeovirgaceae;g__Sediminitomix	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:38:12,702] [INFO] GTDB search result was written to GCF_014195575.1_ASM1419557v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:38:12,702] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:38:12,705] [INFO] DFAST_QC result json was written to GCF_014195575.1_ASM1419557v1_genomic.fna/dqc_result.json
[2024-01-25 17:38:12,705] [INFO] DFAST_QC completed!
[2024-01-25 17:38:12,705] [INFO] Total running time: 0h1m52s