[2023-06-08 17:52:10,301] [INFO] DFAST_QC pipeline started.
[2023-06-08 17:52:10,303] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 17:52:10,303] [INFO] DQC Reference Directory: /var/lib/cwl/stg19901dda-c5f4-4528-9021-f5f9cf2bd176/dqc_reference
[2023-06-08 17:52:11,518] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 17:52:11,519] [INFO] Task started: Prodigal
[2023-06-08 17:52:11,519] [INFO] Running command: gunzip -c /var/lib/cwl/stg22a4e1ea-f11e-4aec-9d57-9ec67b41621a/GCA_902757795.1_Rumen_uncultured_genome_RUG10300_genomic.fna.gz | prodigal -d GCA_902757795.1_Rumen_uncultured_genome_RUG10300_genomic.fna/cds.fna -a GCA_902757795.1_Rumen_uncultured_genome_RUG10300_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 17:52:38,023] [INFO] Task succeeded: Prodigal
[2023-06-08 17:52:38,024] [INFO] Task started: HMMsearch
[2023-06-08 17:52:38,024] [INFO] Running command: hmmsearch --tblout GCA_902757795.1_Rumen_uncultured_genome_RUG10300_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg19901dda-c5f4-4528-9021-f5f9cf2bd176/dqc_reference/reference_markers.hmm GCA_902757795.1_Rumen_uncultured_genome_RUG10300_genomic.fna/protein.faa > /dev/null
[2023-06-08 17:52:38,302] [INFO] Task succeeded: HMMsearch
[2023-06-08 17:52:38,303] [INFO] Found 6/6 markers.
[2023-06-08 17:52:38,340] [INFO] Query marker FASTA was written to GCA_902757795.1_Rumen_uncultured_genome_RUG10300_genomic.fna/markers.fasta
[2023-06-08 17:52:38,340] [INFO] Task started: Blastn
[2023-06-08 17:52:38,340] [INFO] Running command: blastn -query GCA_902757795.1_Rumen_uncultured_genome_RUG10300_genomic.fna/markers.fasta -db /var/lib/cwl/stg19901dda-c5f4-4528-9021-f5f9cf2bd176/dqc_reference/reference_markers.fasta -out GCA_902757795.1_Rumen_uncultured_genome_RUG10300_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 17:52:38,929] [INFO] Task succeeded: Blastn
[2023-06-08 17:52:38,934] [INFO] Selected 34 target genomes.
[2023-06-08 17:52:38,934] [INFO] Target genome list was writen to GCA_902757795.1_Rumen_uncultured_genome_RUG10300_genomic.fna/target_genomes.txt
[2023-06-08 17:52:38,936] [INFO] Task started: fastANI
[2023-06-08 17:52:38,936] [INFO] Running command: fastANI --query /var/lib/cwl/stg22a4e1ea-f11e-4aec-9d57-9ec67b41621a/GCA_902757795.1_Rumen_uncultured_genome_RUG10300_genomic.fna.gz --refList GCA_902757795.1_Rumen_uncultured_genome_RUG10300_genomic.fna/target_genomes.txt --output GCA_902757795.1_Rumen_uncultured_genome_RUG10300_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 17:52:54,903] [INFO] Task succeeded: fastANI
[2023-06-08 17:52:54,904] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg19901dda-c5f4-4528-9021-f5f9cf2bd176/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 17:52:54,904] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg19901dda-c5f4-4528-9021-f5f9cf2bd176/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 17:52:54,924] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 17:52:54,924] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 17:52:54,925] [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 albensis	strain=DSM 11370	GCA_000426565.1	77768	77768	type	True	77.0097	59	1447	95	below_threshold
Prevotella albensis	strain=JCM 12258	GCA_000613525.1	77768	77768	type	True	76.9342	59	1447	95	below_threshold
Prevotella pectinovora	strain=P4-76	GCA_000834015.1	1602169	1602169	type	True	76.7791	84	1447	95	below_threshold
Prevotella buccae	strain=ATCC 33574	GCA_000184945.1	28126	28126	type	True	76.6763	91	1447	95	below_threshold
Prevotella dentalis	strain=DSM 3688	GCA_000242335.3	52227	52227	type	True	76.4829	69	1447	95	below_threshold
Prevotella stercorea	strain=DSM 18206	GCA_000235885.1	363265	363265	suspected-type	True	76.4753	73	1447	95	below_threshold
Hallella faecis	strain=CLA-AA-H145	GCA_018789675.1	2841596	2841596	type	True	76.4706	79	1447	95	below_threshold
Prevotella dentalis	strain=DSM 3688	GCA_000220215.1	52227	52227	type	True	76.4431	72	1447	95	below_threshold
Prevotella denticola	strain=NCTC13067	GCA_900454835.1	28129	28129	type	True	76.4398	61	1447	95	below_threshold
Prevotella bergensis	strain=DSM 17361	GCA_000160535.1	242750	242750	type	True	76.4122	50	1447	95	below_threshold
Prevotella denticola	strain=DSM 20614	GCA_000421205.1	28129	28129	type	True	76.4008	62	1447	95	below_threshold
Prevotella lascolaii	strain=khD1	GCA_900079775.1	1776379	1776379	type	True	76.3839	55	1447	95	below_threshold
Hallella seregens	strain=ATCC 51272	GCA_000518545.1	52229	52229	type	True	76.2886	70	1447	95	below_threshold
Xylanibacter rodentium	strain=PROD	GCA_013166575.1	2736289	2736289	type	True	76.2242	75	1447	95	below_threshold
Prevotella koreensis	strain=KCOM 3155	GCA_003977605.1	2490854	2490854	type	True	76.2108	61	1447	95	below_threshold
Prevotella loescheii	strain=DSM 19665	GCA_000378085.1	840	840	type	True	76.2016	55	1447	95	below_threshold
Prevotella loescheii	strain=ATCC 15930	GCA_000698925.1	840	840	type	True	76.1795	53	1447	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_025151535.1	165179	165179	suspected-type	True	76.0758	81	1447	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_009495405.1	165179	165179	suspected-type	True	76.0276	76	1447	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_000157935.1	165179	165179	suspected-type	True	76.0032	81	1447	95	below_threshold
Prevotella hominis	strain=BCRC 81118	GCA_004535825.1	2518605	2518605	type	True	75.9903	68	1447	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 17:52:54,927] [INFO] DFAST Taxonomy check result was written to GCA_902757795.1_Rumen_uncultured_genome_RUG10300_genomic.fna/tc_result.tsv
[2023-06-08 17:52:54,927] [INFO] ===== Taxonomy check completed =====
[2023-06-08 17:52:54,927] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 17:52:54,928] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg19901dda-c5f4-4528-9021-f5f9cf2bd176/dqc_reference/checkm_data
[2023-06-08 17:52:54,928] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 17:52:54,985] [INFO] Task started: CheckM
[2023-06-08 17:52:54,986] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902757795.1_Rumen_uncultured_genome_RUG10300_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902757795.1_Rumen_uncultured_genome_RUG10300_genomic.fna/checkm_input GCA_902757795.1_Rumen_uncultured_genome_RUG10300_genomic.fna/checkm_result
[2023-06-08 17:54:10,337] [INFO] Task succeeded: CheckM
[2023-06-08 17:54:10,339] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 17:54:10,362] [INFO] ===== Completeness check finished =====
[2023-06-08 17:54:10,362] [INFO] ===== Start GTDB Search =====
[2023-06-08 17:54:10,363] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902757795.1_Rumen_uncultured_genome_RUG10300_genomic.fna/markers.fasta)
[2023-06-08 17:54:10,363] [INFO] Task started: Blastn
[2023-06-08 17:54:10,363] [INFO] Running command: blastn -query GCA_902757795.1_Rumen_uncultured_genome_RUG10300_genomic.fna/markers.fasta -db /var/lib/cwl/stg19901dda-c5f4-4528-9021-f5f9cf2bd176/dqc_reference/reference_markers_gtdb.fasta -out GCA_902757795.1_Rumen_uncultured_genome_RUG10300_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 17:54:11,210] [INFO] Task succeeded: Blastn
[2023-06-08 17:54:11,215] [INFO] Selected 21 target genomes.
[2023-06-08 17:54:11,216] [INFO] Target genome list was writen to GCA_902757795.1_Rumen_uncultured_genome_RUG10300_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 17:54:11,218] [INFO] Task started: fastANI
[2023-06-08 17:54:11,219] [INFO] Running command: fastANI --query /var/lib/cwl/stg22a4e1ea-f11e-4aec-9d57-9ec67b41621a/GCA_902757795.1_Rumen_uncultured_genome_RUG10300_genomic.fna.gz --refList GCA_902757795.1_Rumen_uncultured_genome_RUG10300_genomic.fna/target_genomes_gtdb.txt --output GCA_902757795.1_Rumen_uncultured_genome_RUG10300_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 17:54:25,421] [INFO] Task succeeded: fastANI
[2023-06-08 17:54:25,440] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 17:54:25,440] [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_900315075.1	s__Prevotella sp900315075	100.0	1440	1447	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.96	98.41	0.92	0.87	4	conclusive
GCA_017548385.1	s__Prevotella sp017548385	81.5548	627	1447	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900315745.1	s__Prevotella sp900315745	78.4062	269	1447	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.44	97.86	0.88	0.79	6	-
GCA_900315455.1	s__Prevotella sp900315455	78.3522	359	1447	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.41	96.59	0.90	0.86	13	-
GCA_900317305.1	s__Prevotella sp900317305	78.1109	301	1447	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.38	97.82	0.87	0.83	11	-
GCA_900320585.1	s__Prevotella sp900320585	77.9894	261	1447	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.77	98.44	0.87	0.81	6	-
GCA_902780635.1	s__Prevotella sp902780635	77.8686	311	1447	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.41	97.41	0.85	0.85	2	-
GCA_016281815.1	s__Prevotella sp016281815	77.8478	288	1447	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902767775.1	s__Prevotella sp902767775	77.8347	330	1447	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.97	97.97	0.86	0.86	2	-
GCA_900314995.1	s__Prevotella sp900314995	77.8194	108	1447	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.11	96.50	0.82	0.73	11	-
GCA_017548605.1	s__Prevotella sp017548605	77.6699	163	1447	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017619375.1	s__Prevotella sp017619375	77.4765	284	1447	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900318915.1	s__Prevotella sp900318915	77.4602	197	1447	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.05	95.26	0.87	0.81	11	-
GCA_905235835.1	s__Prevotella sp905235835	77.2825	82	1447	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.69	98.69	0.87	0.87	2	-
GCA_900313615.1	s__Prevotella sp900313615	77.1724	140	1447	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.60	97.61	0.83	0.73	6	-
GCA_902795605.1	s__Prevotella sp902795605	76.9804	258	1447	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902784615.1	s__Prevotella sp902784615	76.881	112	1447	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017547605.1	s__Prevotella sp017547605	76.5303	68	1447	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017471245.1	s__Prevotella sp017471245	76.4524	110	1447	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.04	98.04	0.83	0.83	2	-
GCA_902797505.1	s__Prevotella sp902797505	76.2232	73	1447	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.08	95.72	0.78	0.72	7	-
GCA_900315035.1	s__Prevotella sp900315035	76.2222	108	1447	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.18	98.35	0.94	0.89	3	-
--------------------------------------------------------------------------------
[2023-06-08 17:54:25,442] [INFO] GTDB search result was written to GCA_902757795.1_Rumen_uncultured_genome_RUG10300_genomic.fna/result_gtdb.tsv
[2023-06-08 17:54:25,442] [INFO] ===== GTDB Search completed =====
[2023-06-08 17:54:25,447] [INFO] DFAST_QC result json was written to GCA_902757795.1_Rumen_uncultured_genome_RUG10300_genomic.fna/dqc_result.json
[2023-06-08 17:54:25,447] [INFO] DFAST_QC completed!
[2023-06-08 17:54:25,448] [INFO] Total running time: 0h2m15s