[2023-06-08 20:36:34,017] [INFO] DFAST_QC pipeline started.
[2023-06-08 20:36:34,020] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 20:36:34,020] [INFO] DQC Reference Directory: /var/lib/cwl/stg52d05d04-eeae-463b-8328-2de36daf32d9/dqc_reference
[2023-06-08 20:36:35,372] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 20:36:35,373] [INFO] Task started: Prodigal
[2023-06-08 20:36:35,373] [INFO] Running command: gunzip -c /var/lib/cwl/stg91f6b963-4e4d-4c79-a307-dd87a467f89f/GCA_902765795.1_Rumen_uncultured_genome_RUG11105_genomic.fna.gz | prodigal -d GCA_902765795.1_Rumen_uncultured_genome_RUG11105_genomic.fna/cds.fna -a GCA_902765795.1_Rumen_uncultured_genome_RUG11105_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 20:36:48,720] [INFO] Task succeeded: Prodigal
[2023-06-08 20:36:48,720] [INFO] Task started: HMMsearch
[2023-06-08 20:36:48,720] [INFO] Running command: hmmsearch --tblout GCA_902765795.1_Rumen_uncultured_genome_RUG11105_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg52d05d04-eeae-463b-8328-2de36daf32d9/dqc_reference/reference_markers.hmm GCA_902765795.1_Rumen_uncultured_genome_RUG11105_genomic.fna/protein.faa > /dev/null
[2023-06-08 20:36:48,983] [INFO] Task succeeded: HMMsearch
[2023-06-08 20:36:48,985] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg91f6b963-4e4d-4c79-a307-dd87a467f89f/GCA_902765795.1_Rumen_uncultured_genome_RUG11105_genomic.fna.gz]
[2023-06-08 20:36:49,020] [INFO] Query marker FASTA was written to GCA_902765795.1_Rumen_uncultured_genome_RUG11105_genomic.fna/markers.fasta
[2023-06-08 20:36:49,021] [INFO] Task started: Blastn
[2023-06-08 20:36:49,021] [INFO] Running command: blastn -query GCA_902765795.1_Rumen_uncultured_genome_RUG11105_genomic.fna/markers.fasta -db /var/lib/cwl/stg52d05d04-eeae-463b-8328-2de36daf32d9/dqc_reference/reference_markers.fasta -out GCA_902765795.1_Rumen_uncultured_genome_RUG11105_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 20:36:49,630] [INFO] Task succeeded: Blastn
[2023-06-08 20:36:49,635] [INFO] Selected 23 target genomes.
[2023-06-08 20:36:49,636] [INFO] Target genome list was writen to GCA_902765795.1_Rumen_uncultured_genome_RUG11105_genomic.fna/target_genomes.txt
[2023-06-08 20:36:49,638] [INFO] Task started: fastANI
[2023-06-08 20:36:49,638] [INFO] Running command: fastANI --query /var/lib/cwl/stg91f6b963-4e4d-4c79-a307-dd87a467f89f/GCA_902765795.1_Rumen_uncultured_genome_RUG11105_genomic.fna.gz --refList GCA_902765795.1_Rumen_uncultured_genome_RUG11105_genomic.fna/target_genomes.txt --output GCA_902765795.1_Rumen_uncultured_genome_RUG11105_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 20:37:03,656] [INFO] Task succeeded: fastANI
[2023-06-08 20:37:03,657] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg52d05d04-eeae-463b-8328-2de36daf32d9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 20:37:03,657] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg52d05d04-eeae-463b-8328-2de36daf32d9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 20:37:03,672] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 20:37:03,673] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 20:37:03,673] [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 ruminicola	strain=Bryant 23	GCA_000025925.1	839	839	type	True	82.449	516	815	95	below_threshold
Prevotella ruminicola	strain=ATCC 19189	GCA_900108375.1	839	839	type	True	82.4389	515	815	95	below_threshold
Prevotella brevis	strain=ATCC 19188	GCA_000621725.1	83231	83231	type	True	78.2522	169	815	95	below_threshold
Prevotella fusca	strain=W1435	GCA_001262015.1	589436	589436	type	True	77.2375	57	815	95	below_threshold
Prevotella fusca	strain=W1435	GCA_018128145.1	589436	589436	type	True	77.2051	61	815	95	below_threshold
Prevotella albensis	strain=DSM 11370	GCA_000426565.1	77768	77768	type	True	77.0746	50	815	95	below_threshold
Prevotella scopos	strain=W2052	GCA_001683355.1	589437	589437	type	True	77.0487	53	815	95	below_threshold
Prevotella melaninogenica	strain=FDAARGOS_1566	GCA_020735785.1	28132	28132	suspected-type	True	76.9706	56	815	95	below_threshold
Prevotella melaninogenica	strain=ATCC 25845	GCA_000144405.1	28132	28132	suspected-type	True	76.9682	56	815	95	below_threshold
Prevotella stercorea	strain=DSM 18206	GCA_000235885.1	363265	363265	suspected-type	True	76.7912	72	815	95	below_threshold
Prevotella buccae	strain=ATCC 33574	GCA_000184945.1	28126	28126	type	True	76.5828	52	815	95	below_threshold
Prevotella mizrahii	strain=LKV-178-WT-2A	GCA_009695775.1	2606637	2606637	type	True	76.4321	54	815	95	below_threshold
Xylanibacter rodentium	strain=PROD	GCA_013166575.1	2736289	2736289	type	True	76.1926	64	815	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 20:37:03,675] [INFO] DFAST Taxonomy check result was written to GCA_902765795.1_Rumen_uncultured_genome_RUG11105_genomic.fna/tc_result.tsv
[2023-06-08 20:37:03,675] [INFO] ===== Taxonomy check completed =====
[2023-06-08 20:37:03,675] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 20:37:03,676] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg52d05d04-eeae-463b-8328-2de36daf32d9/dqc_reference/checkm_data
[2023-06-08 20:37:03,677] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 20:37:03,706] [INFO] Task started: CheckM
[2023-06-08 20:37:03,706] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902765795.1_Rumen_uncultured_genome_RUG11105_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902765795.1_Rumen_uncultured_genome_RUG11105_genomic.fna/checkm_input GCA_902765795.1_Rumen_uncultured_genome_RUG11105_genomic.fna/checkm_result
[2023-06-08 20:37:45,779] [INFO] Task succeeded: CheckM
[2023-06-08 20:37:45,780] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 74.78%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 20:37:45,801] [INFO] ===== Completeness check finished =====
[2023-06-08 20:37:45,801] [INFO] ===== Start GTDB Search =====
[2023-06-08 20:37:45,802] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902765795.1_Rumen_uncultured_genome_RUG11105_genomic.fna/markers.fasta)
[2023-06-08 20:37:45,802] [INFO] Task started: Blastn
[2023-06-08 20:37:45,802] [INFO] Running command: blastn -query GCA_902765795.1_Rumen_uncultured_genome_RUG11105_genomic.fna/markers.fasta -db /var/lib/cwl/stg52d05d04-eeae-463b-8328-2de36daf32d9/dqc_reference/reference_markers_gtdb.fasta -out GCA_902765795.1_Rumen_uncultured_genome_RUG11105_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 20:37:46,658] [INFO] Task succeeded: Blastn
[2023-06-08 20:37:46,663] [INFO] Selected 14 target genomes.
[2023-06-08 20:37:46,663] [INFO] Target genome list was writen to GCA_902765795.1_Rumen_uncultured_genome_RUG11105_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 20:37:46,668] [INFO] Task started: fastANI
[2023-06-08 20:37:46,668] [INFO] Running command: fastANI --query /var/lib/cwl/stg91f6b963-4e4d-4c79-a307-dd87a467f89f/GCA_902765795.1_Rumen_uncultured_genome_RUG11105_genomic.fna.gz --refList GCA_902765795.1_Rumen_uncultured_genome_RUG11105_genomic.fna/target_genomes_gtdb.txt --output GCA_902765795.1_Rumen_uncultured_genome_RUG11105_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 20:37:56,223] [INFO] Task succeeded: fastANI
[2023-06-08 20:37:56,237] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 20:37:56,237] [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_002351725.1	s__Prevotella sp002351725	97.1963	666	815	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.82	95.50	0.81	0.76	9	conclusive
GCA_902800365.1	s__Prevotella sp902800365	94.2138	661	815	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.33	96.33	0.87	0.87	2	-
GCA_900315765.1	s__Prevotella sp900315765	89.7969	641	815	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.26	97.63	0.83	0.78	5	-
GCF_900142525.1	s__Prevotella ruminicola_A	85.0398	572	815	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902761905.1	s__Prevotella sp902761905	83.5462	529	815	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900317405.1	s__Prevotella sp900317405	83.4717	493	815	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.52	98.08	0.89	0.85	6	-
GCF_000687715.1	s__Prevotella ruminicola_B	82.6346	503	815	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000025925.1	s__Prevotella ruminicola	82.4336	517	815	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.74	96.82	0.88	0.80	15	-
GCF_900107775.1	s__Prevotella ruminicola_C	82.2274	508	815	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.61	97.61	0.89	0.89	3	-
GCA_900315525.1	s__Prevotella sp900315525	79.718	231	815	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.95	96.00	0.84	0.76	10	-
GCA_016286575.1	s__Prevotella sp016286575	78.857	253	815	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017430675.1	s__Prevotella sp017430675	77.7882	197	815	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900320045.1	s__Prevotella sp900320045	77.785	125	815	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.65	96.17	0.87	0.75	5	-
GCA_017389705.1	s__Prevotella sp017389705	77.6117	159	815	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 20:37:56,239] [INFO] GTDB search result was written to GCA_902765795.1_Rumen_uncultured_genome_RUG11105_genomic.fna/result_gtdb.tsv
[2023-06-08 20:37:56,239] [INFO] ===== GTDB Search completed =====
[2023-06-08 20:37:56,243] [INFO] DFAST_QC result json was written to GCA_902765795.1_Rumen_uncultured_genome_RUG11105_genomic.fna/dqc_result.json
[2023-06-08 20:37:56,243] [INFO] DFAST_QC completed!
[2023-06-08 20:37:56,243] [INFO] Total running time: 0h1m22s