[2023-06-08 02:20:21,233] [INFO] DFAST_QC pipeline started.
[2023-06-08 02:20:21,237] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 02:20:21,238] [INFO] DQC Reference Directory: /var/lib/cwl/stga5f7b13b-a178-4b26-8da1-a6143ffc6265/dqc_reference
[2023-06-08 02:20:23,362] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 02:20:23,363] [INFO] Task started: Prodigal
[2023-06-08 02:20:23,363] [INFO] Running command: gunzip -c /var/lib/cwl/stgade61b3e-5926-47fe-80d6-bde34346175b/GCA_902778255.1_Rumen_uncultured_genome_RUG12354_genomic.fna.gz | prodigal -d GCA_902778255.1_Rumen_uncultured_genome_RUG12354_genomic.fna/cds.fna -a GCA_902778255.1_Rumen_uncultured_genome_RUG12354_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 02:20:42,202] [INFO] Task succeeded: Prodigal
[2023-06-08 02:20:42,202] [INFO] Task started: HMMsearch
[2023-06-08 02:20:42,203] [INFO] Running command: hmmsearch --tblout GCA_902778255.1_Rumen_uncultured_genome_RUG12354_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga5f7b13b-a178-4b26-8da1-a6143ffc6265/dqc_reference/reference_markers.hmm GCA_902778255.1_Rumen_uncultured_genome_RUG12354_genomic.fna/protein.faa > /dev/null
[2023-06-08 02:20:42,496] [INFO] Task succeeded: HMMsearch
[2023-06-08 02:20:42,498] [INFO] Found 6/6 markers.
[2023-06-08 02:20:42,533] [INFO] Query marker FASTA was written to GCA_902778255.1_Rumen_uncultured_genome_RUG12354_genomic.fna/markers.fasta
[2023-06-08 02:20:42,534] [INFO] Task started: Blastn
[2023-06-08 02:20:42,534] [INFO] Running command: blastn -query GCA_902778255.1_Rumen_uncultured_genome_RUG12354_genomic.fna/markers.fasta -db /var/lib/cwl/stga5f7b13b-a178-4b26-8da1-a6143ffc6265/dqc_reference/reference_markers.fasta -out GCA_902778255.1_Rumen_uncultured_genome_RUG12354_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 02:20:43,127] [INFO] Task succeeded: Blastn
[2023-06-08 02:20:43,138] [INFO] Selected 21 target genomes.
[2023-06-08 02:20:43,138] [INFO] Target genome list was writen to GCA_902778255.1_Rumen_uncultured_genome_RUG12354_genomic.fna/target_genomes.txt
[2023-06-08 02:20:43,142] [INFO] Task started: fastANI
[2023-06-08 02:20:43,143] [INFO] Running command: fastANI --query /var/lib/cwl/stgade61b3e-5926-47fe-80d6-bde34346175b/GCA_902778255.1_Rumen_uncultured_genome_RUG12354_genomic.fna.gz --refList GCA_902778255.1_Rumen_uncultured_genome_RUG12354_genomic.fna/target_genomes.txt --output GCA_902778255.1_Rumen_uncultured_genome_RUG12354_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 02:20:54,382] [INFO] Task succeeded: fastANI
[2023-06-08 02:20:54,382] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga5f7b13b-a178-4b26-8da1-a6143ffc6265/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 02:20:54,383] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga5f7b13b-a178-4b26-8da1-a6143ffc6265/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 02:20:54,401] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 02:20:54,401] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 02:20:54,401] [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 brevis	strain=ATCC 19188	GCA_000621725.1	83231	83231	type	True	79.5412	312	1132	95	below_threshold
Prevotella ruminicola	strain=Bryant 23	GCA_000025925.1	839	839	type	True	79.327	228	1132	95	below_threshold
Prevotella ruminicola	strain=ATCC 19189	GCA_900108375.1	839	839	type	True	79.2932	228	1132	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_025151535.1	165179	165179	suspected-type	True	77.1902	101	1132	95	below_threshold
Prevotella multiformis	strain=DSM 16608	GCA_000191065.1	282402	282402	type	True	77.0322	63	1132	95	below_threshold
Prevotella denticola	strain=DSM 20614	GCA_000421205.1	28129	28129	type	True	76.9408	51	1132	95	below_threshold
Prevotella pectinovora	strain=P4-76	GCA_000834015.1	1602169	1602169	type	True	76.8965	91	1132	95	below_threshold
Prevotella denticola	strain=NCTC13067	GCA_900454835.1	28129	28129	type	True	76.8921	52	1132	95	below_threshold
Prevotella dentasini	strain=JCM 15908	GCA_000614065.1	589537	589537	type	True	76.8294	59	1132	95	below_threshold
Hallella faecis	strain=CLA-AA-H145	GCA_018789675.1	2841596	2841596	type	True	76.7468	93	1132	95	below_threshold
Prevotella fusca	strain=W1435	GCA_018128145.1	589436	589436	type	True	76.4211	63	1132	95	below_threshold
Xylanibacter rodentium	strain=PROD	GCA_013166575.1	2736289	2736289	type	True	76.3841	80	1132	95	below_threshold
Prevotella fusca	strain=W1435	GCA_001262015.1	589436	589436	type	True	76.2942	65	1132	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 02:20:54,403] [INFO] DFAST Taxonomy check result was written to GCA_902778255.1_Rumen_uncultured_genome_RUG12354_genomic.fna/tc_result.tsv
[2023-06-08 02:20:54,404] [INFO] ===== Taxonomy check completed =====
[2023-06-08 02:20:54,404] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 02:20:54,405] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga5f7b13b-a178-4b26-8da1-a6143ffc6265/dqc_reference/checkm_data
[2023-06-08 02:20:54,406] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 02:20:54,445] [INFO] Task started: CheckM
[2023-06-08 02:20:54,446] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902778255.1_Rumen_uncultured_genome_RUG12354_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902778255.1_Rumen_uncultured_genome_RUG12354_genomic.fna/checkm_input GCA_902778255.1_Rumen_uncultured_genome_RUG12354_genomic.fna/checkm_result
[2023-06-08 02:21:50,321] [INFO] Task succeeded: CheckM
[2023-06-08 02:21:50,323] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.12%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 02:21:50,346] [INFO] ===== Completeness check finished =====
[2023-06-08 02:21:50,347] [INFO] ===== Start GTDB Search =====
[2023-06-08 02:21:50,347] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902778255.1_Rumen_uncultured_genome_RUG12354_genomic.fna/markers.fasta)
[2023-06-08 02:21:50,347] [INFO] Task started: Blastn
[2023-06-08 02:21:50,348] [INFO] Running command: blastn -query GCA_902778255.1_Rumen_uncultured_genome_RUG12354_genomic.fna/markers.fasta -db /var/lib/cwl/stga5f7b13b-a178-4b26-8da1-a6143ffc6265/dqc_reference/reference_markers_gtdb.fasta -out GCA_902778255.1_Rumen_uncultured_genome_RUG12354_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 02:21:51,232] [INFO] Task succeeded: Blastn
[2023-06-08 02:21:51,245] [INFO] Selected 15 target genomes.
[2023-06-08 02:21:51,246] [INFO] Target genome list was writen to GCA_902778255.1_Rumen_uncultured_genome_RUG12354_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 02:21:51,251] [INFO] Task started: fastANI
[2023-06-08 02:21:51,251] [INFO] Running command: fastANI --query /var/lib/cwl/stgade61b3e-5926-47fe-80d6-bde34346175b/GCA_902778255.1_Rumen_uncultured_genome_RUG12354_genomic.fna.gz --refList GCA_902778255.1_Rumen_uncultured_genome_RUG12354_genomic.fna/target_genomes_gtdb.txt --output GCA_902778255.1_Rumen_uncultured_genome_RUG12354_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 02:21:59,974] [INFO] Task succeeded: fastANI
[2023-06-08 02:21:59,999] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 02:21:59,999] [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
GCA_902778255.1	s__Prevotella sp902778255	100.0	1130	1132	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.79	98.79	0.87	0.87	2	conclusive
GCA_902799975.1	s__Prevotella sp902799975	82.9117	547	1132	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100635.1	s__Prevotella sp900100635	82.3395	592	1132	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.15	96.60	0.86	0.83	10	-
GCA_902785695.1	s__Prevotella sp902785695	81.5064	430	1132	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902788605.1	s__Prevotella sp902788605	80.6184	443	1132	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.22	98.10	0.87	0.84	7	-
GCA_902775605.1	s__Prevotella sp902775605	79.9839	391	1132	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000621725.1	s__Prevotella brevis	79.5341	312	1132	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.58	97.58	0.89	0.89	2	-
GCA_902799905.1	s__Prevotella sp902799905	79.4846	390	1132	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.33	98.29	0.89	0.87	3	-
GCA_017455845.1	s__Prevotella sp017455845	79.2293	309	1132	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017483805.1	s__Prevotella sp017483805	78.7927	366	1132	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110895.1	s__Prevotella sp900110895	78.1095	187	1132	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.50	96.66	0.93	0.90	3	-
GCA_017965725.1	s__Prevotella sp017965725	77.9172	204	1132	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017470055.1	s__Prevotella sp017470055	77.6896	168	1132	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902778265.1	s__Prevotella sp902778265	77.0978	94	1132	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 02:22:00,001] [INFO] GTDB search result was written to GCA_902778255.1_Rumen_uncultured_genome_RUG12354_genomic.fna/result_gtdb.tsv
[2023-06-08 02:22:00,003] [INFO] ===== GTDB Search completed =====
[2023-06-08 02:22:00,009] [INFO] DFAST_QC result json was written to GCA_902778255.1_Rumen_uncultured_genome_RUG12354_genomic.fna/dqc_result.json
[2023-06-08 02:22:00,009] [INFO] DFAST_QC completed!
[2023-06-08 02:22:00,009] [INFO] Total running time: 0h1m39s