[2023-06-13 19:58:32,347] [INFO] DFAST_QC pipeline started.
[2023-06-13 19:58:32,349] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 19:58:32,349] [INFO] DQC Reference Directory: /var/lib/cwl/stg09f0d6a1-5241-44bb-84f7-09af2ed306ab/dqc_reference
[2023-06-13 19:58:33,469] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 19:58:33,470] [INFO] Task started: Prodigal
[2023-06-13 19:58:33,470] [INFO] Running command: gunzip -c /var/lib/cwl/stg3518fbca-b740-4020-8b40-1749d1b49c75/GCA_022769345.1_ASM2276934v1_genomic.fna.gz | prodigal -d GCA_022769345.1_ASM2276934v1_genomic.fna/cds.fna -a GCA_022769345.1_ASM2276934v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 19:58:45,639] [INFO] Task succeeded: Prodigal
[2023-06-13 19:58:45,639] [INFO] Task started: HMMsearch
[2023-06-13 19:58:45,639] [INFO] Running command: hmmsearch --tblout GCA_022769345.1_ASM2276934v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg09f0d6a1-5241-44bb-84f7-09af2ed306ab/dqc_reference/reference_markers.hmm GCA_022769345.1_ASM2276934v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 19:58:45,866] [INFO] Task succeeded: HMMsearch
[2023-06-13 19:58:45,867] [INFO] Found 6/6 markers.
[2023-06-13 19:58:45,890] [INFO] Query marker FASTA was written to GCA_022769345.1_ASM2276934v1_genomic.fna/markers.fasta
[2023-06-13 19:58:45,890] [INFO] Task started: Blastn
[2023-06-13 19:58:45,890] [INFO] Running command: blastn -query GCA_022769345.1_ASM2276934v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg09f0d6a1-5241-44bb-84f7-09af2ed306ab/dqc_reference/reference_markers.fasta -out GCA_022769345.1_ASM2276934v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 19:58:46,497] [INFO] Task succeeded: Blastn
[2023-06-13 19:58:46,509] [INFO] Selected 28 target genomes.
[2023-06-13 19:58:46,510] [INFO] Target genome list was writen to GCA_022769345.1_ASM2276934v1_genomic.fna/target_genomes.txt
[2023-06-13 19:58:46,511] [INFO] Task started: fastANI
[2023-06-13 19:58:46,511] [INFO] Running command: fastANI --query /var/lib/cwl/stg3518fbca-b740-4020-8b40-1749d1b49c75/GCA_022769345.1_ASM2276934v1_genomic.fna.gz --refList GCA_022769345.1_ASM2276934v1_genomic.fna/target_genomes.txt --output GCA_022769345.1_ASM2276934v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 19:59:00,164] [INFO] Task succeeded: fastANI
[2023-06-13 19:59:00,164] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg09f0d6a1-5241-44bb-84f7-09af2ed306ab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 19:59:00,165] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg09f0d6a1-5241-44bb-84f7-09af2ed306ab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 19:59:00,174] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 19:59:00,174] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 19:59:00,174] [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 pectinovora	strain=P4-76	GCA_000834015.1	1602169	1602169	type	True	77.3457	138	608	95	below_threshold
Prevotella lascolaii	strain=khD1	GCA_900079775.1	1776379	1776379	type	True	77.1218	69	608	95	below_threshold
Prevotella stercorea	strain=DSM 18206	GCA_000235885.1	363265	363265	suspected-type	True	77.1127	93	608	95	below_threshold
Prevotella buccae	strain=ATCC 33574	GCA_000184945.1	28126	28126	type	True	77.0642	110	608	95	below_threshold
Hallella seregens	strain=ATCC 51272	GCA_000518545.1	52229	52229	type	True	77.017	109	608	95	below_threshold
Prevotella multiformis	strain=DSM 16608	GCA_000191065.1	282402	282402	type	True	76.9989	74	608	95	below_threshold
Prevotella dentalis	strain=DSM 3688	GCA_000220215.1	52227	52227	type	True	76.9922	116	608	95	below_threshold
Xylanibacter muris	strain=PMUR	GCA_013166605.1	2736290	2736290	type	True	76.984	59	608	95	below_threshold
Xylanibacter rodentium	strain=PROD	GCA_013166575.1	2736289	2736289	type	True	76.9316	97	608	95	below_threshold
Prevotella dentalis	strain=DSM 3688	GCA_000242335.3	52227	52227	type	True	76.9151	116	608	95	below_threshold
Prevotella baroniae	strain=DSM 16972	GCA_000426585.1	305719	305719	type	True	76.6656	90	608	95	below_threshold
Prevotella illustrans	strain=A2931	GCA_017426725.1	2800387	2800387	type	True	76.6517	60	608	95	below_threshold
Prevotella baroniae	strain=JCM 13447	GCA_000613565.1	305719	305719	type	True	76.6349	90	608	95	below_threshold
Hallella faecis	strain=CLA-AA-H145	GCA_018789675.1	2841596	2841596	type	True	76.6236	113	608	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 19:59:00,176] [INFO] DFAST Taxonomy check result was written to GCA_022769345.1_ASM2276934v1_genomic.fna/tc_result.tsv
[2023-06-13 19:59:00,176] [INFO] ===== Taxonomy check completed =====
[2023-06-13 19:59:00,177] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 19:59:00,177] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg09f0d6a1-5241-44bb-84f7-09af2ed306ab/dqc_reference/checkm_data
[2023-06-13 19:59:00,177] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 19:59:00,201] [INFO] Task started: CheckM
[2023-06-13 19:59:00,202] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022769345.1_ASM2276934v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022769345.1_ASM2276934v1_genomic.fna/checkm_input GCA_022769345.1_ASM2276934v1_genomic.fna/checkm_result
[2023-06-13 19:59:37,933] [INFO] Task succeeded: CheckM
[2023-06-13 19:59:37,934] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 19:59:37,951] [INFO] ===== Completeness check finished =====
[2023-06-13 19:59:37,951] [INFO] ===== Start GTDB Search =====
[2023-06-13 19:59:37,952] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022769345.1_ASM2276934v1_genomic.fna/markers.fasta)
[2023-06-13 19:59:37,952] [INFO] Task started: Blastn
[2023-06-13 19:59:37,952] [INFO] Running command: blastn -query GCA_022769345.1_ASM2276934v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg09f0d6a1-5241-44bb-84f7-09af2ed306ab/dqc_reference/reference_markers_gtdb.fasta -out GCA_022769345.1_ASM2276934v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 19:59:38,838] [INFO] Task succeeded: Blastn
[2023-06-13 19:59:38,842] [INFO] Selected 26 target genomes.
[2023-06-13 19:59:38,842] [INFO] Target genome list was writen to GCA_022769345.1_ASM2276934v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 19:59:38,845] [INFO] Task started: fastANI
[2023-06-13 19:59:38,846] [INFO] Running command: fastANI --query /var/lib/cwl/stg3518fbca-b740-4020-8b40-1749d1b49c75/GCA_022769345.1_ASM2276934v1_genomic.fna.gz --refList GCA_022769345.1_ASM2276934v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022769345.1_ASM2276934v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 19:59:51,308] [INFO] Task succeeded: fastANI
[2023-06-13 19:59:51,323] [INFO] Found 26 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 19:59:51,323] [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_004557285.1	s__Prevotella sp004557285	98.3051	438	608	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.35	98.35	0.77	0.77	2	conclusive
GCA_905214625.1	s__Prevotella sp905214625	78.3702	111	608	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000433175.1	s__Prevotella sp000433175	77.9305	129	608	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.10	97.93	0.86	0.84	3	-
GCA_000436695.1	s__Prevotella sp000436695	77.7502	144	608	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.96	98.24	0.85	0.83	3	-
GCF_001275135.1	s__Prevotella rara	77.6808	164	608	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.17	97.70	0.90	0.86	7	-
GCA_900554695.1	s__Prevotella sp900554695	77.6538	52	608	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.93	97.88	0.84	0.83	3	-
GCA_905211345.1	s__Prevotella sp905211345	77.6372	88	608	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016302965.1	s__Prevotella sp016302965	77.6028	140	608	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905215655.1	s__Prevotella sp905215655	77.5294	98	608	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016899855.1	s__Prevotella sp000436595	77.3944	122	608	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.00	97.50	0.84	0.81	5	-
GCF_000834015.1	s__Prevotella pectinovora	77.3639	138	608	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.37	97.34	0.86	0.79	12	-
GCA_905196835.1	s__Prevotella stercoripullorum	77.3435	153	608	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.53	95.99	0.92	0.86	5	-
GCA_902767775.1	s__Prevotella sp902767775	77.2541	114	608	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.97	97.97	0.86	0.86	2	-
GCA_002369515.1	s__Prevotella sp002369515	77.2329	111	608	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016901395.1	s__Prevotella sp016901395	77.1608	101	608	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013166515.1	s__Prevotella sp013166515	77.1389	119	608	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.36	96.74	0.93	0.86	3	-
GCF_900079775.1	s__Prevotella lascolaii	77.1218	69	608	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.26	98.20	0.94	0.92	5	-
GCA_002353525.1	s__Prevotella sp002353525	77.1014	112	608	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900545525.1	s__Prevotella sp900545525	77.0912	127	608	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.81	98.33	0.87	0.76	5	-
GCA_900318915.1	s__Prevotella sp900318915	77.076	139	608	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.05	95.26	0.87	0.81	11	-
GCA_900550365.1	s__Prevotella sp900550365	77.0222	111	608	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900543975.1	s__Prevotella sp900543975	76.7978	106	608	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.48	97.34	0.84	0.79	5	-
GCA_900317685.1	s__Prevotella sp900317685	76.7597	87	608	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.13	96.10	0.84	0.76	12	-
GCA_002437285.1	s__Prevotella sp002437285	76.7151	88	608	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.68	99.38	0.93	0.88	13	-
GCA_900762125.1	s__Prevotella sp900762125	76.6501	83	608	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018789675.1	s__Prevotella sp002300055	76.6458	113	608	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.15	99.02	0.92	0.90	6	-
--------------------------------------------------------------------------------
[2023-06-13 19:59:51,325] [INFO] GTDB search result was written to GCA_022769345.1_ASM2276934v1_genomic.fna/result_gtdb.tsv
[2023-06-13 19:59:51,326] [INFO] ===== GTDB Search completed =====
[2023-06-13 19:59:51,329] [INFO] DFAST_QC result json was written to GCA_022769345.1_ASM2276934v1_genomic.fna/dqc_result.json
[2023-06-13 19:59:51,330] [INFO] DFAST_QC completed!
[2023-06-13 19:59:51,330] [INFO] Total running time: 0h1m19s