[2024-01-24 14:22:14,684] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:22:14,689] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:22:14,690] [INFO] DQC Reference Directory: /var/lib/cwl/stgabf792f2-1ce5-42bd-b921-7a83ff5d55b0/dqc_reference
[2024-01-24 14:22:15,938] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:22:15,939] [INFO] Task started: Prodigal
[2024-01-24 14:22:15,939] [INFO] Running command: gunzip -c /var/lib/cwl/stg18dcc08c-1710-4b80-8044-7cc432d486ac/GCF_025909975.1_ASM2590997v1_genomic.fna.gz | prodigal -d GCF_025909975.1_ASM2590997v1_genomic.fna/cds.fna -a GCF_025909975.1_ASM2590997v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:22:25,605] [INFO] Task succeeded: Prodigal
[2024-01-24 14:22:25,605] [INFO] Task started: HMMsearch
[2024-01-24 14:22:25,605] [INFO] Running command: hmmsearch --tblout GCF_025909975.1_ASM2590997v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgabf792f2-1ce5-42bd-b921-7a83ff5d55b0/dqc_reference/reference_markers.hmm GCF_025909975.1_ASM2590997v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:22:25,810] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:22:25,811] [INFO] Found 6/6 markers.
[2024-01-24 14:22:25,836] [INFO] Query marker FASTA was written to GCF_025909975.1_ASM2590997v1_genomic.fna/markers.fasta
[2024-01-24 14:22:25,837] [INFO] Task started: Blastn
[2024-01-24 14:22:25,837] [INFO] Running command: blastn -query GCF_025909975.1_ASM2590997v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgabf792f2-1ce5-42bd-b921-7a83ff5d55b0/dqc_reference/reference_markers.fasta -out GCF_025909975.1_ASM2590997v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:26,533] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:26,537] [INFO] Selected 10 target genomes.
[2024-01-24 14:22:26,537] [INFO] Target genome list was writen to GCF_025909975.1_ASM2590997v1_genomic.fna/target_genomes.txt
[2024-01-24 14:22:26,546] [INFO] Task started: fastANI
[2024-01-24 14:22:26,546] [INFO] Running command: fastANI --query /var/lib/cwl/stg18dcc08c-1710-4b80-8044-7cc432d486ac/GCF_025909975.1_ASM2590997v1_genomic.fna.gz --refList GCF_025909975.1_ASM2590997v1_genomic.fna/target_genomes.txt --output GCF_025909975.1_ASM2590997v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:22:34,762] [INFO] Task succeeded: fastANI
[2024-01-24 14:22:34,762] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgabf792f2-1ce5-42bd-b921-7a83ff5d55b0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:22:34,763] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgabf792f2-1ce5-42bd-b921-7a83ff5d55b0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:22:34,772] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:22:34,772] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:22:34,773] [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
Flavobacterium cheniae	strain=CGMCC 1.6844	GCA_007830415.1	295428	295428	type	True	93.0328	742	937	95	below_threshold
Flavobacterium cheniae	strain=DSM 22462	GCA_004363695.1	295428	295428	type	True	93.0326	743	937	95	below_threshold
Flavobacterium proteolyticum	strain=1Y8A	GCA_015223105.1	2911683	2911683	type	True	88.7519	771	937	95	below_threshold
Flavobacterium sasangense	strain=DSM 21067	GCA_000686885.1	503361	503361	type	True	88.5071	744	937	95	below_threshold
Flavobacterium aquaticum	strain=CGMCC 1.12398	GCA_003259835.1	1236486	1236486	type	True	88.3907	705	937	95	below_threshold
Flavobacterium cyclinae	strain=KSM-R2A25	GCA_021172145.1	2895947	2895947	type	True	85.4393	673	937	95	below_threshold
Flavobacterium channae	strain=KSM-R2A30	GCA_021172165.1	2897181	2897181	type	True	85.113	695	937	95	below_threshold
Flavobacterium celericrescens	strain=TWA-26	GCA_011392075.1	2709780	2709780	type	True	84.6255	628	937	95	below_threshold
Flavobacterium sediminilitoris	strain=YSM-43	GCA_023008245.1	2024526	2024526	type	True	78.185	401	937	95	below_threshold
Flavobacterium branchiophilum	strain=DSM 24789	GCA_006716585.1	55197	55197	type	True	77.0671	142	937	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:22:34,774] [INFO] DFAST Taxonomy check result was written to GCF_025909975.1_ASM2590997v1_genomic.fna/tc_result.tsv
[2024-01-24 14:22:34,775] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:22:34,775] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:22:34,775] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgabf792f2-1ce5-42bd-b921-7a83ff5d55b0/dqc_reference/checkm_data
[2024-01-24 14:22:34,777] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:22:34,806] [INFO] Task started: CheckM
[2024-01-24 14:22:34,806] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025909975.1_ASM2590997v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025909975.1_ASM2590997v1_genomic.fna/checkm_input GCF_025909975.1_ASM2590997v1_genomic.fna/checkm_result
[2024-01-24 14:23:07,921] [INFO] Task succeeded: CheckM
[2024-01-24 14:23:07,922] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:23:07,941] [INFO] ===== Completeness check finished =====
[2024-01-24 14:23:07,941] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:23:07,941] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025909975.1_ASM2590997v1_genomic.fna/markers.fasta)
[2024-01-24 14:23:07,942] [INFO] Task started: Blastn
[2024-01-24 14:23:07,942] [INFO] Running command: blastn -query GCF_025909975.1_ASM2590997v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgabf792f2-1ce5-42bd-b921-7a83ff5d55b0/dqc_reference/reference_markers_gtdb.fasta -out GCF_025909975.1_ASM2590997v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:23:08,921] [INFO] Task succeeded: Blastn
[2024-01-24 14:23:08,925] [INFO] Selected 9 target genomes.
[2024-01-24 14:23:08,925] [INFO] Target genome list was writen to GCF_025909975.1_ASM2590997v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:23:08,934] [INFO] Task started: fastANI
[2024-01-24 14:23:08,934] [INFO] Running command: fastANI --query /var/lib/cwl/stg18dcc08c-1710-4b80-8044-7cc432d486ac/GCF_025909975.1_ASM2590997v1_genomic.fna.gz --refList GCF_025909975.1_ASM2590997v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025909975.1_ASM2590997v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:23:14,814] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:14,822] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 14:23:14,823] [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_004363695.1	s__Flavobacterium cheniae	93.0326	743	937	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCA_003497625.1	s__Flavobacterium sp003497625	90.4456	667	937	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.98	99.98	0.98	0.98	2	-
GCA_002483315.1	s__Flavobacterium sp002483315	90.1994	679	937	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009495755.1	s__Flavobacterium sp009495755	88.7952	676	937	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015223105.1	s__Flavobacterium aquaticum_A	88.7363	772	937	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000686885.1	s__Flavobacterium sasangense	88.5071	744	937	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003259835.1	s__Flavobacterium aquaticum	88.3907	705	937	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002422095.1	s__Flavobacterium sp002422095	86.8618	540	937	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004293165.1	s__Flavobacterium sp004293165	86.5454	632	937	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	97.30	97.30	0.81	0.81	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:23:14,824] [INFO] GTDB search result was written to GCF_025909975.1_ASM2590997v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:23:14,825] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:23:14,828] [INFO] DFAST_QC result json was written to GCF_025909975.1_ASM2590997v1_genomic.fna/dqc_result.json
[2024-01-24 14:23:14,828] [INFO] DFAST_QC completed!
[2024-01-24 14:23:14,828] [INFO] Total running time: 0h1m0s