[2024-01-24 11:12:28,147] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:28,149] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:28,149] [INFO] DQC Reference Directory: /var/lib/cwl/stg1b1ae5ea-da2d-40d4-b9f5-e76327123692/dqc_reference
[2024-01-24 11:12:29,588] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:29,589] [INFO] Task started: Prodigal
[2024-01-24 11:12:29,589] [INFO] Running command: gunzip -c /var/lib/cwl/stg4b5c612c-b602-4a01-bca5-48ee5d1a4b2c/GCF_015351765.1_ASM1535176v1_genomic.fna.gz | prodigal -d GCF_015351765.1_ASM1535176v1_genomic.fna/cds.fna -a GCF_015351765.1_ASM1535176v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:12:37,238] [INFO] Task succeeded: Prodigal
[2024-01-24 11:12:37,239] [INFO] Task started: HMMsearch
[2024-01-24 11:12:37,239] [INFO] Running command: hmmsearch --tblout GCF_015351765.1_ASM1535176v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1b1ae5ea-da2d-40d4-b9f5-e76327123692/dqc_reference/reference_markers.hmm GCF_015351765.1_ASM1535176v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:12:37,579] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:12:37,580] [INFO] Found 6/6 markers.
[2024-01-24 11:12:37,609] [INFO] Query marker FASTA was written to GCF_015351765.1_ASM1535176v1_genomic.fna/markers.fasta
[2024-01-24 11:12:37,610] [INFO] Task started: Blastn
[2024-01-24 11:12:37,610] [INFO] Running command: blastn -query GCF_015351765.1_ASM1535176v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1b1ae5ea-da2d-40d4-b9f5-e76327123692/dqc_reference/reference_markers.fasta -out GCF_015351765.1_ASM1535176v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:12:38,374] [INFO] Task succeeded: Blastn
[2024-01-24 11:12:38,377] [INFO] Selected 27 target genomes.
[2024-01-24 11:12:38,378] [INFO] Target genome list was writen to GCF_015351765.1_ASM1535176v1_genomic.fna/target_genomes.txt
[2024-01-24 11:12:38,388] [INFO] Task started: fastANI
[2024-01-24 11:12:38,388] [INFO] Running command: fastANI --query /var/lib/cwl/stg4b5c612c-b602-4a01-bca5-48ee5d1a4b2c/GCF_015351765.1_ASM1535176v1_genomic.fna.gz --refList GCF_015351765.1_ASM1535176v1_genomic.fna/target_genomes.txt --output GCF_015351765.1_ASM1535176v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:12:54,930] [INFO] Task succeeded: fastANI
[2024-01-24 11:12:54,930] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1b1ae5ea-da2d-40d4-b9f5-e76327123692/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:12:54,930] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1b1ae5ea-da2d-40d4-b9f5-e76327123692/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:12:54,937] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:12:54,937] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:12:54,937] [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
Clostridium vitabionis	strain=YH-T4B42	GCA_015351765.1	2784388	2784388	type	True	100.0	935	937	95	conclusive
Porcincola intestinalis	strain=Oil+RF-744-WCA-WT-11	GCA_009696445.1	2606632	2606632	type	True	78.8303	61	937	95	below_threshold
[Clostridium] aminophilum	strain=F	GCA_900112885.1	1526	1526	type	True	77.5838	140	937	95	below_threshold
[Clostridium] aminophilum	strain=DSM 10710	GCA_000711825.1	1526	1526	type	True	77.5653	139	937	95	below_threshold
Enterocloster bolteae	strain=ATCC BAA-613	GCA_002959675.1	208479	208479	type	True	77.0119	53	937	95	below_threshold
Enterocloster bolteae	strain=ATCC BAA-613	GCA_000154365.1	208479	208479	type	True	77.009	55	937	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:12:54,939] [INFO] DFAST Taxonomy check result was written to GCF_015351765.1_ASM1535176v1_genomic.fna/tc_result.tsv
[2024-01-24 11:12:54,939] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:12:54,940] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:12:54,940] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1b1ae5ea-da2d-40d4-b9f5-e76327123692/dqc_reference/checkm_data
[2024-01-24 11:12:54,941] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:12:54,970] [INFO] Task started: CheckM
[2024-01-24 11:12:54,971] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_015351765.1_ASM1535176v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_015351765.1_ASM1535176v1_genomic.fna/checkm_input GCF_015351765.1_ASM1535176v1_genomic.fna/checkm_result
[2024-01-24 11:13:22,990] [INFO] Task succeeded: CheckM
[2024-01-24 11:13:22,995] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:13:23,018] [INFO] ===== Completeness check finished =====
[2024-01-24 11:13:23,019] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:13:23,019] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_015351765.1_ASM1535176v1_genomic.fna/markers.fasta)
[2024-01-24 11:13:23,020] [INFO] Task started: Blastn
[2024-01-24 11:13:23,020] [INFO] Running command: blastn -query GCF_015351765.1_ASM1535176v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1b1ae5ea-da2d-40d4-b9f5-e76327123692/dqc_reference/reference_markers_gtdb.fasta -out GCF_015351765.1_ASM1535176v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:24,275] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:24,279] [INFO] Selected 28 target genomes.
[2024-01-24 11:13:24,279] [INFO] Target genome list was writen to GCF_015351765.1_ASM1535176v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:13:24,319] [INFO] Task started: fastANI
[2024-01-24 11:13:24,319] [INFO] Running command: fastANI --query /var/lib/cwl/stg4b5c612c-b602-4a01-bca5-48ee5d1a4b2c/GCF_015351765.1_ASM1535176v1_genomic.fna.gz --refList GCF_015351765.1_ASM1535176v1_genomic.fna/target_genomes_gtdb.txt --output GCF_015351765.1_ASM1535176v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:13:39,148] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:39,176] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:13:39,176] [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_015351765.1	s__Clostridium_R vitabionis	100.0	935	937	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Clostridium_R	95.0	98.49	98.47	0.96	0.96	4	conclusive
GCA_900314565.1	s__UBA1066 sp900314565	78.4002	63	937	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1066	95.0	98.26	96.12	0.90	0.66	19	-
GCA_002160535.1	s__Clostridium_Q saccharolyticum_A	78.1726	71	937	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Clostridium_Q	95.0	98.86	98.46	0.90	0.84	10	-
GCA_018223415.1	s__Copromonas sp900541255	77.6119	86	937	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Copromonas	95.0	99.81	99.68	0.96	0.93	4	-
GCF_000711825.1	s__Clostridium_R aminophilum	77.5711	138	937	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Clostridium_R	95.0	100.00	100.00	0.99	0.99	2	-
GCF_900101295.1	s__Clostridium_R aminophilum_A	77.33	129	937	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Clostridium_R	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002160755.1	s__Lachnoclostridium_A sp002160755	77.3085	96	937	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoclostridium_A	95.0	98.32	98.32	0.92	0.92	2	-
GCA_003445895.1	s__Clostridium_R sp003445895	77.1225	100	937	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Clostridium_R	95.0	98.01	97.09	0.80	0.69	11	-
GCA_900321915.1	s__Clostridium_R sp900321915	77.026	121	937	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Clostridium_R	95.0	100.00	100.00	0.98	0.98	2	-
GCF_002234575.2	s__Enterocloster bolteae	77.0126	52	937	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	98.46	96.97	0.88	0.78	35	-
GCA_900315305.1	s__UBA1066 sp900315305	76.9698	59	937	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1066	95.0	99.26	98.90	0.90	0.82	11	-
GCA_004554205.1	s__Ventrimonas sp004554205	76.9425	61	937	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910575795.1	s__Clostridium_Q sp910575795	76.524	89	937	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Clostridium_Q	95.0	99.66	99.05	0.95	0.91	4	-
GCA_017449925.1	s__Stomatobaculum sp017449925	76.3475	55	937	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Stomatobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900317515.1	s__UBA1066 sp900317515	76.183	64	937	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1066	95.0	98.06	96.06	0.86	0.79	9	-
GCA_019119775.1	s__Lachnoclostridium_A pullistercoris	76.1139	71	937	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoclostridium_A	95.0	99.96	99.96	0.95	0.95	2	-
GCA_900547035.1	s__Enterocloster excrementigallinarum	76.1094	51	937	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	98.35	98.28	0.80	0.77	6	-
GCA_018715565.1	s__Ventrimonas merdavium	76.0881	71	937	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	99.46	99.46	0.97	0.97	2	-
GCA_018713185.1	s__Copromonas avistercoris	75.598	57	937	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Copromonas	95.0	98.24	98.19	0.97	0.95	4	-
--------------------------------------------------------------------------------
[2024-01-24 11:13:39,178] [INFO] GTDB search result was written to GCF_015351765.1_ASM1535176v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:13:39,179] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:13:39,182] [INFO] DFAST_QC result json was written to GCF_015351765.1_ASM1535176v1_genomic.fna/dqc_result.json
[2024-01-24 11:13:39,183] [INFO] DFAST_QC completed!
[2024-01-24 11:13:39,183] [INFO] Total running time: 0h1m11s