[2024-01-24 14:22:31,940] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:22:31,942] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:22:31,942] [INFO] DQC Reference Directory: /var/lib/cwl/stg6ba9176b-4912-4843-ba9b-0473301b8ab5/dqc_reference
[2024-01-24 14:22:36,013] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:22:36,015] [INFO] Task started: Prodigal
[2024-01-24 14:22:36,015] [INFO] Running command: gunzip -c /var/lib/cwl/stgbee732b7-fe66-4e22-a042-4b0a04b0a794/GCF_004118265.1_ASM411826v1_genomic.fna.gz | prodigal -d GCF_004118265.1_ASM411826v1_genomic.fna/cds.fna -a GCF_004118265.1_ASM411826v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:23:02,043] [INFO] Task succeeded: Prodigal
[2024-01-24 14:23:02,044] [INFO] Task started: HMMsearch
[2024-01-24 14:23:02,044] [INFO] Running command: hmmsearch --tblout GCF_004118265.1_ASM411826v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6ba9176b-4912-4843-ba9b-0473301b8ab5/dqc_reference/reference_markers.hmm GCF_004118265.1_ASM411826v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:23:02,522] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:23:02,531] [INFO] Found 6/6 markers.
[2024-01-24 14:23:02,579] [INFO] Query marker FASTA was written to GCF_004118265.1_ASM411826v1_genomic.fna/markers.fasta
[2024-01-24 14:23:02,579] [INFO] Task started: Blastn
[2024-01-24 14:23:02,579] [INFO] Running command: blastn -query GCF_004118265.1_ASM411826v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6ba9176b-4912-4843-ba9b-0473301b8ab5/dqc_reference/reference_markers.fasta -out GCF_004118265.1_ASM411826v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:23:06,331] [INFO] Task succeeded: Blastn
[2024-01-24 14:23:06,336] [INFO] Selected 20 target genomes.
[2024-01-24 14:23:06,336] [INFO] Target genome list was writen to GCF_004118265.1_ASM411826v1_genomic.fna/target_genomes.txt
[2024-01-24 14:23:06,348] [INFO] Task started: fastANI
[2024-01-24 14:23:06,348] [INFO] Running command: fastANI --query /var/lib/cwl/stgbee732b7-fe66-4e22-a042-4b0a04b0a794/GCF_004118265.1_ASM411826v1_genomic.fna.gz --refList GCF_004118265.1_ASM411826v1_genomic.fna/target_genomes.txt --output GCF_004118265.1_ASM411826v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:23:28,175] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:28,175] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6ba9176b-4912-4843-ba9b-0473301b8ab5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:23:28,176] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6ba9176b-4912-4843-ba9b-0473301b8ab5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:23:28,301] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:23:28,301] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:23:28,302] [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
Lacibacter luteus	strain=TTM-7	GCA_004118265.1	2508719	2508719	type	True	100.0	1677	1678	95	conclusive
Lacibacter cauensis	strain=CGMCC 1.7271	GCA_007830055.1	510947	510947	type	True	84.4793	1172	1678	95	below_threshold
Ferruginibacter albus	strain=KIS38-8	GCA_020042285.1	2875540	2875540	type	True	76.4367	103	1678	95	below_threshold
Flavisolibacter nicotianae	strain=X7X	GCA_003628535.1	2364882	2364882	type	True	76.3149	53	1678	95	below_threshold
Niastella yeongjuensis	strain=DSM 17621	GCA_002077935.1	354355	354355	type	True	76.2721	104	1678	95	below_threshold
Pinibacter aurantiacus	strain=MAH-26	GCA_019130065.1	2851599	2851599	type	True	76.2556	102	1678	95	below_threshold
Niastella yeongjuensis	strain=DSM 17621	GCA_900110245.1	354355	354355	type	True	76.1129	106	1678	95	below_threshold
Deminuibacter soli	strain=K23C18032701	GCA_003412455.1	2291815	2291815	type	True	76.0912	113	1678	95	below_threshold
Panacibacter microcysteis	strain=DH6	GCA_015831355.1	2793269	2793269	type	True	76.0808	83	1678	95	below_threshold
Flavihumibacter stibioxidans	strain=YS-17	GCA_014332695.1	1834163	1834163	type	True	76.0683	65	1678	95	below_threshold
Pseudobacter ginsenosidimutans	strain=DSM 18116	GCA_004291315.1	661488	661488	type	True	76.016	79	1678	95	below_threshold
Pseudobacter ginsenosidimutans	strain=Gsoil 221	GCA_007970185.1	661488	661488	type	True	75.9972	80	1678	95	below_threshold
Hydrotalea flava	strain=CCUG 51397	GCA_001623405.1	714549	714549	suspected-type	True	75.9741	76	1678	95	below_threshold
Filimonas zeae	strain=CGMCC 1.15290	GCA_014641615.1	1737353	1737353	type	True	75.8649	97	1678	95	below_threshold
Niabella beijingensis	strain=3A5MI-3	GCA_020034665.1	2872700	2872700	type	True	75.8596	59	1678	95	below_threshold
Niabella pedocola	strain=JCM 31011	GCA_021044425.1	1752077	1752077	type	True	75.7542	66	1678	95	below_threshold
Niastella vici	strain=DJ57	GCA_002077945.1	1703345	1703345	type	True	75.6873	122	1678	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:23:28,382] [INFO] DFAST Taxonomy check result was written to GCF_004118265.1_ASM411826v1_genomic.fna/tc_result.tsv
[2024-01-24 14:23:28,383] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:23:28,384] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:23:28,384] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6ba9176b-4912-4843-ba9b-0473301b8ab5/dqc_reference/checkm_data
[2024-01-24 14:23:28,449] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:23:28,625] [INFO] Task started: CheckM
[2024-01-24 14:23:28,626] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004118265.1_ASM411826v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004118265.1_ASM411826v1_genomic.fna/checkm_input GCF_004118265.1_ASM411826v1_genomic.fna/checkm_result
[2024-01-24 14:24:52,137] [INFO] Task succeeded: CheckM
[2024-01-24 14:24:52,139] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:24:52,160] [INFO] ===== Completeness check finished =====
[2024-01-24 14:24:52,160] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:24:52,161] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004118265.1_ASM411826v1_genomic.fna/markers.fasta)
[2024-01-24 14:24:52,161] [INFO] Task started: Blastn
[2024-01-24 14:24:52,161] [INFO] Running command: blastn -query GCF_004118265.1_ASM411826v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6ba9176b-4912-4843-ba9b-0473301b8ab5/dqc_reference/reference_markers_gtdb.fasta -out GCF_004118265.1_ASM411826v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:24:53,872] [INFO] Task succeeded: Blastn
[2024-01-24 14:24:53,876] [INFO] Selected 10 target genomes.
[2024-01-24 14:24:53,877] [INFO] Target genome list was writen to GCF_004118265.1_ASM411826v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:24:53,887] [INFO] Task started: fastANI
[2024-01-24 14:24:53,887] [INFO] Running command: fastANI --query /var/lib/cwl/stgbee732b7-fe66-4e22-a042-4b0a04b0a794/GCF_004118265.1_ASM411826v1_genomic.fna.gz --refList GCF_004118265.1_ASM411826v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004118265.1_ASM411826v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:25:04,324] [INFO] Task succeeded: fastANI
[2024-01-24 14:25:04,369] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:25:04,369] [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_004118265.1	s__Lacibacter luteus	100.0	1677	1678	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Lacibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_007830055.1	s__Lacibacter cauensis	84.467	1174	1678	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Lacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009996555.1	s__Lacibacter sp009996555	81.7033	634	1678	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Lacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014168535.1	s__Lacibacter sp014168535	80.9867	959	1678	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Lacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002337125.1	s__Lacibacter sp002337125	78.6819	583	1678	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Lacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016713085.1	s__Lacibacter sp016713085	78.4194	591	1678	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Lacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002336115.1	s__Lacibacter sp002336115	78.1282	452	1678	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Lacibacter	95.0	99.94	99.94	0.95	0.95	2	-
GCF_019130065.1	s__Parasegetibacter sp019130065	76.2556	102	1678	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Parasegetibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002390845.1	s__Panacibacter sp002390845	75.7742	129	1678	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Panacibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:25:04,371] [INFO] GTDB search result was written to GCF_004118265.1_ASM411826v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:25:04,371] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:25:04,375] [INFO] DFAST_QC result json was written to GCF_004118265.1_ASM411826v1_genomic.fna/dqc_result.json
[2024-01-24 14:25:04,375] [INFO] DFAST_QC completed!
[2024-01-24 14:25:04,375] [INFO] Total running time: 0h2m32s