[2024-01-24 13:45:46,440] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:45:46,443] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:45:46,443] [INFO] DQC Reference Directory: /var/lib/cwl/stgb3c0b025-3ccc-47c0-a19a-a064140d09c5/dqc_reference
[2024-01-24 13:45:47,844] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:45:47,845] [INFO] Task started: Prodigal
[2024-01-24 13:45:47,846] [INFO] Running command: gunzip -c /var/lib/cwl/stg4c4f7f8b-49a7-4814-9f84-72b8d4ee257f/GCF_000613985.1_ASM61398v1_genomic.fna.gz | prodigal -d GCF_000613985.1_ASM61398v1_genomic.fna/cds.fna -a GCF_000613985.1_ASM61398v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:45:59,868] [INFO] Task succeeded: Prodigal
[2024-01-24 13:45:59,868] [INFO] Task started: HMMsearch
[2024-01-24 13:45:59,868] [INFO] Running command: hmmsearch --tblout GCF_000613985.1_ASM61398v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb3c0b025-3ccc-47c0-a19a-a064140d09c5/dqc_reference/reference_markers.hmm GCF_000613985.1_ASM61398v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:00,209] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:00,210] [INFO] Found 6/6 markers.
[2024-01-24 13:46:00,248] [INFO] Query marker FASTA was written to GCF_000613985.1_ASM61398v1_genomic.fna/markers.fasta
[2024-01-24 13:46:00,249] [INFO] Task started: Blastn
[2024-01-24 13:46:00,249] [INFO] Running command: blastn -query GCF_000613985.1_ASM61398v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb3c0b025-3ccc-47c0-a19a-a064140d09c5/dqc_reference/reference_markers.fasta -out GCF_000613985.1_ASM61398v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:00,918] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:00,922] [INFO] Selected 21 target genomes.
[2024-01-24 13:46:00,922] [INFO] Target genome list was writen to GCF_000613985.1_ASM61398v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:00,938] [INFO] Task started: fastANI
[2024-01-24 13:46:00,939] [INFO] Running command: fastANI --query /var/lib/cwl/stg4c4f7f8b-49a7-4814-9f84-72b8d4ee257f/GCF_000613985.1_ASM61398v1_genomic.fna.gz --refList GCF_000613985.1_ASM61398v1_genomic.fna/target_genomes.txt --output GCF_000613985.1_ASM61398v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:11,149] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:11,150] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb3c0b025-3ccc-47c0-a19a-a064140d09c5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:11,150] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb3c0b025-3ccc-47c0-a19a-a064140d09c5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:11,159] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:46:11,159] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:46:11,160] [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
Prevotella nanceiensis	strain=JCM 15639	GCA_000613985.1	425941	425941	type	True	100.0	872	872	95	conclusive
Prevotella nanceiensis	strain=DSM 19126	GCA_000379965.1	425941	425941	type	True	99.9838	870	872	95	conclusive
Prevotella koreensis	strain=KCOM 3155	GCA_003977605.1	2490854	2490854	type	True	82.4061	50	872	95	below_threshold
Prevotella histicola	strain=JCM 15637	GCA_000613925.1	470565	470565	type	True	82.0091	65	872	95	below_threshold
Prevotella aurantiaca	strain=JCM 15754	GCA_000614025.1	596085	596085	type	True	81.6126	85	872	95	below_threshold
Prevotella enoeca	strain=JCM 12259	GCA_000613405.1	76123	76123	type	True	80.5785	67	872	95	below_threshold
Prevotella bivia	strain=DSM 20514	GCA_000262545.1	28125	28125	type	True	80.4642	85	872	95	below_threshold
Prevotella veroralis	strain=DSM 19559	GCA_000377625.1	28137	28137	type	True	80.2517	80	872	95	below_threshold
Prevotella bivia	strain=JCVIHMP010	GCA_000177315.1	28125	28125	type	True	80.2043	81	872	95	below_threshold
Prevotella veroralis	strain=JCM 6290	GCA_000613325.1	28137	28137	type	True	80.174	70	872	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:11,161] [INFO] DFAST Taxonomy check result was written to GCF_000613985.1_ASM61398v1_genomic.fna/tc_result.tsv
[2024-01-24 13:46:11,162] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:11,162] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:11,162] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb3c0b025-3ccc-47c0-a19a-a064140d09c5/dqc_reference/checkm_data
[2024-01-24 13:46:11,163] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:11,195] [INFO] Task started: CheckM
[2024-01-24 13:46:11,195] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000613985.1_ASM61398v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000613985.1_ASM61398v1_genomic.fna/checkm_input GCF_000613985.1_ASM61398v1_genomic.fna/checkm_result
[2024-01-24 13:46:52,014] [INFO] Task succeeded: CheckM
[2024-01-24 13:46:52,015] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:46:52,042] [INFO] ===== Completeness check finished =====
[2024-01-24 13:46:52,043] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:46:52,043] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000613985.1_ASM61398v1_genomic.fna/markers.fasta)
[2024-01-24 13:46:52,044] [INFO] Task started: Blastn
[2024-01-24 13:46:52,044] [INFO] Running command: blastn -query GCF_000613985.1_ASM61398v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb3c0b025-3ccc-47c0-a19a-a064140d09c5/dqc_reference/reference_markers_gtdb.fasta -out GCF_000613985.1_ASM61398v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:52,829] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:52,832] [INFO] Selected 22 target genomes.
[2024-01-24 13:46:52,832] [INFO] Target genome list was writen to GCF_000613985.1_ASM61398v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:46:52,901] [INFO] Task started: fastANI
[2024-01-24 13:46:52,901] [INFO] Running command: fastANI --query /var/lib/cwl/stg4c4f7f8b-49a7-4814-9f84-72b8d4ee257f/GCF_000613985.1_ASM61398v1_genomic.fna.gz --refList GCF_000613985.1_ASM61398v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000613985.1_ASM61398v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:47:04,371] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:04,383] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:47:04,383] [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_000379965.1	s__Prevotella nanceiensis	99.9838	870	872	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.31	96.77	0.96	0.91	12	conclusive
GCF_000163055.2	s__Prevotella sp000163055	91.7474	677	872	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000613925.1	s__Prevotella histicola	82.1197	63	872	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.82	97.59	0.91	0.86	21	-
GCF_000185845.1	s__Prevotella salivae	82.0981	92	872	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.60	96.70	0.94	0.87	27	-
GCF_000614025.1	s__Prevotella aurantiaca	81.8123	83	872	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.47	98.39	0.93	0.91	4	-
GCF_000262545.1	s__Prevotella bivia	80.5269	84	872	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.82	98.45	0.91	0.86	8	-
GCF_000377625.1	s__Prevotella veroralis	80.3797	78	872	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.76	96.65	0.91	0.86	4	-
GCF_000177075.1	s__Prevotella buccalis	80.0478	76	872	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	95.19	95.19	0.85	0.85	2	-
GCF_000479005.1	s__Prevotella sp000479005	78.1938	58	872	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.86	96.42	0.92	0.87	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:47:04,385] [INFO] GTDB search result was written to GCF_000613985.1_ASM61398v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:47:04,385] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:47:04,388] [INFO] DFAST_QC result json was written to GCF_000613985.1_ASM61398v1_genomic.fna/dqc_result.json
[2024-01-24 13:47:04,388] [INFO] DFAST_QC completed!
[2024-01-24 13:47:04,388] [INFO] Total running time: 0h1m18s