[2024-01-25 19:46:05,995] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:46:05,996] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:46:05,996] [INFO] DQC Reference Directory: /var/lib/cwl/stg44d70195-d230-43c0-a3d2-2613b4261218/dqc_reference
[2024-01-25 19:46:07,130] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:46:07,130] [INFO] Task started: Prodigal
[2024-01-25 19:46:07,131] [INFO] Running command: gunzip -c /var/lib/cwl/stg518f45fd-1aaf-4116-a166-0d3f143e0417/GCF_003634455.1_ASM363445v1_genomic.fna.gz | prodigal -d GCF_003634455.1_ASM363445v1_genomic.fna/cds.fna -a GCF_003634455.1_ASM363445v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:46:20,445] [INFO] Task succeeded: Prodigal
[2024-01-25 19:46:20,445] [INFO] Task started: HMMsearch
[2024-01-25 19:46:20,445] [INFO] Running command: hmmsearch --tblout GCF_003634455.1_ASM363445v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg44d70195-d230-43c0-a3d2-2613b4261218/dqc_reference/reference_markers.hmm GCF_003634455.1_ASM363445v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:46:20,744] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:46:20,746] [INFO] Found 6/6 markers.
[2024-01-25 19:46:20,781] [INFO] Query marker FASTA was written to GCF_003634455.1_ASM363445v1_genomic.fna/markers.fasta
[2024-01-25 19:46:20,782] [INFO] Task started: Blastn
[2024-01-25 19:46:20,782] [INFO] Running command: blastn -query GCF_003634455.1_ASM363445v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg44d70195-d230-43c0-a3d2-2613b4261218/dqc_reference/reference_markers.fasta -out GCF_003634455.1_ASM363445v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:46:21,455] [INFO] Task succeeded: Blastn
[2024-01-25 19:46:21,458] [INFO] Selected 11 target genomes.
[2024-01-25 19:46:21,458] [INFO] Target genome list was writen to GCF_003634455.1_ASM363445v1_genomic.fna/target_genomes.txt
[2024-01-25 19:46:21,464] [INFO] Task started: fastANI
[2024-01-25 19:46:21,464] [INFO] Running command: fastANI --query /var/lib/cwl/stg518f45fd-1aaf-4116-a166-0d3f143e0417/GCF_003634455.1_ASM363445v1_genomic.fna.gz --refList GCF_003634455.1_ASM363445v1_genomic.fna/target_genomes.txt --output GCF_003634455.1_ASM363445v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:46:29,792] [INFO] Task succeeded: fastANI
[2024-01-25 19:46:29,792] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg44d70195-d230-43c0-a3d2-2613b4261218/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:46:29,792] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg44d70195-d230-43c0-a3d2-2613b4261218/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:46:29,804] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:46:29,804] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-25 19:46:29,804] [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 endophyticum	strain=DSM 29537	GCA_003634455.1	1540163	1540163	type	True	100.0	1244	1244	95	inconclusive
Flavobacterium gossypii	strain=DSM 100397	GCA_014138495.1	1646119	1646119	type	True	97.1314	1179	1244	95	inconclusive
Flavobacterium microcysteis	strain=MaA-Y11	GCA_006385255.1	2596891	2596891	type	True	81.7699	851	1244	95	below_threshold
Flavobacterium lindanitolerans	strain=DSM 21886	GCA_003663835.1	428988	428988	type	True	81.4924	831	1244	95	below_threshold
Flavobacterium lindanitolerans	strain=IP-10	GCA_002846575.1	428988	428988	type	True	81.4491	840	1244	95	below_threshold
Flavobacterium macacae	strain=YIM 102600	GCA_003865365.1	2488993	2488993	type	True	79.5482	485	1244	95	below_threshold
Flavobacterium endoglycinae	strain=BB8	GCA_017352115.1	2816357	2816357	type	True	77.8931	206	1244	95	below_threshold
Flavobacterium taihuense	strain=NAS39	GCA_019351435.1	2857508	2857508	type	True	77.8411	171	1244	95	below_threshold
Flavobacterium amniphilum	strain=KYPY10	GCA_023634845.1	1834035	1834035	type	True	77.7508	139	1244	95	below_threshold
Flavobacterium proteolyticum	strain=1Y8A	GCA_015223105.1	2911683	2911683	type	True	77.5833	174	1244	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:46:29,806] [INFO] DFAST Taxonomy check result was written to GCF_003634455.1_ASM363445v1_genomic.fna/tc_result.tsv
[2024-01-25 19:46:29,806] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:46:29,807] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:46:29,807] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg44d70195-d230-43c0-a3d2-2613b4261218/dqc_reference/checkm_data
[2024-01-25 19:46:29,808] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:46:29,847] [INFO] Task started: CheckM
[2024-01-25 19:46:29,847] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003634455.1_ASM363445v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003634455.1_ASM363445v1_genomic.fna/checkm_input GCF_003634455.1_ASM363445v1_genomic.fna/checkm_result
[2024-01-25 19:47:10,116] [INFO] Task succeeded: CheckM
[2024-01-25 19:47:10,117] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:47:10,138] [INFO] ===== Completeness check finished =====
[2024-01-25 19:47:10,138] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:47:10,139] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003634455.1_ASM363445v1_genomic.fna/markers.fasta)
[2024-01-25 19:47:10,139] [INFO] Task started: Blastn
[2024-01-25 19:47:10,139] [INFO] Running command: blastn -query GCF_003634455.1_ASM363445v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg44d70195-d230-43c0-a3d2-2613b4261218/dqc_reference/reference_markers_gtdb.fasta -out GCF_003634455.1_ASM363445v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:47:11,111] [INFO] Task succeeded: Blastn
[2024-01-25 19:47:11,114] [INFO] Selected 12 target genomes.
[2024-01-25 19:47:11,114] [INFO] Target genome list was writen to GCF_003634455.1_ASM363445v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:47:11,125] [INFO] Task started: fastANI
[2024-01-25 19:47:11,125] [INFO] Running command: fastANI --query /var/lib/cwl/stg518f45fd-1aaf-4116-a166-0d3f143e0417/GCF_003634455.1_ASM363445v1_genomic.fna.gz --refList GCF_003634455.1_ASM363445v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003634455.1_ASM363445v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:47:19,822] [INFO] Task succeeded: fastANI
[2024-01-25 19:47:19,830] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:47:19,831] [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_003634455.1	s__Flavobacterium endophyticum	100.0	1244	1244	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	97.19	97.19	0.95	0.95	2	conclusive
GCF_006385255.1	s__Flavobacterium microcysteis	81.7699	851	1244	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002846575.1	s__Flavobacterium lindanitolerans	81.4408	841	1244	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	97.86	97.14	0.91	0.85	11	-
GCF_003865365.1	s__Flavobacterium macacae	79.5541	483	1244	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000422705.1	s__Flavobacterium soli	78.5067	293	1244	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003097635.1	s__Flavobacterium psychrotolerans	78.306	145	1244	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009915155.1	s__Flavobacterium sp009915155	78.2208	261	1244	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009909155.2	s__Flavobacterium undicola	78.0164	161	1244	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007341385.1	s__Flavobacterium daemonense	77.8883	211	1244	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007097265.1	s__Flavobacterium gawalongense	77.6852	193	1244	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.69	99.40	0.97	0.94	5	-
GCA_002280815.1	s__Flavobacterium sp002280815	77.6147	147	1244	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003634615.1	s__Flavobacterium sp002482945	77.4974	178	1244	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.37	98.37	0.85	0.85	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:47:19,832] [INFO] GTDB search result was written to GCF_003634455.1_ASM363445v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:47:19,833] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:47:19,835] [INFO] DFAST_QC result json was written to GCF_003634455.1_ASM363445v1_genomic.fna/dqc_result.json
[2024-01-25 19:47:19,835] [INFO] DFAST_QC completed!
[2024-01-25 19:47:19,835] [INFO] Total running time: 0h1m14s