[2023-06-05 18:05:12,123] [INFO] DFAST_QC pipeline started.
[2023-06-05 18:05:12,128] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 18:05:12,129] [INFO] DQC Reference Directory: /var/lib/cwl/stgd1459e0e-d7d8-40ef-af56-9d2371808b62/dqc_reference
[2023-06-05 18:05:14,302] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 18:05:14,305] [INFO] Task started: Prodigal
[2023-06-05 18:05:14,305] [INFO] Running command: gunzip -c /var/lib/cwl/stgda5e5ca6-35e8-41c2-9c8e-ea21bac86993/GCA_902767545.1_Rumen_uncultured_genome_RUG11277_genomic.fna.gz | prodigal -d GCA_902767545.1_Rumen_uncultured_genome_RUG11277_genomic.fna/cds.fna -a GCA_902767545.1_Rumen_uncultured_genome_RUG11277_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 18:05:28,867] [INFO] Task succeeded: Prodigal
[2023-06-05 18:05:28,868] [INFO] Task started: HMMsearch
[2023-06-05 18:05:28,868] [INFO] Running command: hmmsearch --tblout GCA_902767545.1_Rumen_uncultured_genome_RUG11277_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd1459e0e-d7d8-40ef-af56-9d2371808b62/dqc_reference/reference_markers.hmm GCA_902767545.1_Rumen_uncultured_genome_RUG11277_genomic.fna/protein.faa > /dev/null
[2023-06-05 18:05:29,095] [INFO] Task succeeded: HMMsearch
[2023-06-05 18:05:29,098] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgda5e5ca6-35e8-41c2-9c8e-ea21bac86993/GCA_902767545.1_Rumen_uncultured_genome_RUG11277_genomic.fna.gz]
[2023-06-05 18:05:29,124] [INFO] Query marker FASTA was written to GCA_902767545.1_Rumen_uncultured_genome_RUG11277_genomic.fna/markers.fasta
[2023-06-05 18:05:29,124] [INFO] Task started: Blastn
[2023-06-05 18:05:29,125] [INFO] Running command: blastn -query GCA_902767545.1_Rumen_uncultured_genome_RUG11277_genomic.fna/markers.fasta -db /var/lib/cwl/stgd1459e0e-d7d8-40ef-af56-9d2371808b62/dqc_reference/reference_markers.fasta -out GCA_902767545.1_Rumen_uncultured_genome_RUG11277_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:05:29,832] [INFO] Task succeeded: Blastn
[2023-06-05 18:05:29,838] [INFO] Selected 23 target genomes.
[2023-06-05 18:05:29,838] [INFO] Target genome list was writen to GCA_902767545.1_Rumen_uncultured_genome_RUG11277_genomic.fna/target_genomes.txt
[2023-06-05 18:05:29,846] [INFO] Task started: fastANI
[2023-06-05 18:05:29,847] [INFO] Running command: fastANI --query /var/lib/cwl/stgda5e5ca6-35e8-41c2-9c8e-ea21bac86993/GCA_902767545.1_Rumen_uncultured_genome_RUG11277_genomic.fna.gz --refList GCA_902767545.1_Rumen_uncultured_genome_RUG11277_genomic.fna/target_genomes.txt --output GCA_902767545.1_Rumen_uncultured_genome_RUG11277_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 18:05:43,617] [INFO] Task succeeded: fastANI
[2023-06-05 18:05:43,618] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd1459e0e-d7d8-40ef-af56-9d2371808b62/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 18:05:43,618] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd1459e0e-d7d8-40ef-af56-9d2371808b62/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 18:05:43,637] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 18:05:43,637] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 18:05:43,637] [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 stercorea	strain=DSM 18206	GCA_000235885.1	363265	363265	suspected-type	True	77.0301	113	541	95	below_threshold
Prevotella dentalis	strain=DSM 3688	GCA_000220215.1	52227	52227	type	True	76.8334	115	541	95	below_threshold
Prevotella dentalis	strain=DSM 3688	GCA_000242335.3	52227	52227	type	True	76.8291	115	541	95	below_threshold
Hallella faecis	strain=CLA-AA-H145	GCA_018789675.1	2841596	2841596	type	True	76.7725	96	541	95	below_threshold
Prevotella baroniae	strain=DSM 16972	GCA_000426585.1	305719	305719	type	True	76.6055	85	541	95	below_threshold
Prevotella buccae	strain=ATCC 33574	GCA_000184945.1	28126	28126	type	True	76.581	108	541	95	below_threshold
Prevotella mizrahii	strain=LKV-178-WT-2A	GCA_009695775.1	2606637	2606637	type	True	76.5564	65	541	95	below_threshold
Prevotella multiformis	strain=DSM 16608	GCA_000191065.1	282402	282402	type	True	76.5239	69	541	95	below_threshold
Prevotella baroniae	strain=JCM 13447	GCA_000613565.1	305719	305719	type	True	76.5127	88	541	95	below_threshold
Prevotella denticola	strain=NCTC13067	GCA_900454835.1	28129	28129	type	True	76.4949	72	541	95	below_threshold
Prevotella denticola	strain=DSM 20614	GCA_000421205.1	28129	28129	type	True	76.4367	73	541	95	below_threshold
Prevotella illustrans	strain=A2931	GCA_017426725.1	2800387	2800387	type	True	76.2562	53	541	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 18:05:43,641] [INFO] DFAST Taxonomy check result was written to GCA_902767545.1_Rumen_uncultured_genome_RUG11277_genomic.fna/tc_result.tsv
[2023-06-05 18:05:43,642] [INFO] ===== Taxonomy check completed =====
[2023-06-05 18:05:43,642] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 18:05:43,642] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd1459e0e-d7d8-40ef-af56-9d2371808b62/dqc_reference/checkm_data
[2023-06-05 18:05:43,643] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 18:05:43,667] [INFO] Task started: CheckM
[2023-06-05 18:05:43,668] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902767545.1_Rumen_uncultured_genome_RUG11277_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902767545.1_Rumen_uncultured_genome_RUG11277_genomic.fna/checkm_input GCA_902767545.1_Rumen_uncultured_genome_RUG11277_genomic.fna/checkm_result
[2023-06-05 18:06:34,000] [INFO] Task succeeded: CheckM
[2023-06-05 18:06:34,001] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 18:06:34,109] [INFO] ===== Completeness check finished =====
[2023-06-05 18:06:34,110] [INFO] ===== Start GTDB Search =====
[2023-06-05 18:06:34,110] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902767545.1_Rumen_uncultured_genome_RUG11277_genomic.fna/markers.fasta)
[2023-06-05 18:06:34,110] [INFO] Task started: Blastn
[2023-06-05 18:06:34,111] [INFO] Running command: blastn -query GCA_902767545.1_Rumen_uncultured_genome_RUG11277_genomic.fna/markers.fasta -db /var/lib/cwl/stgd1459e0e-d7d8-40ef-af56-9d2371808b62/dqc_reference/reference_markers_gtdb.fasta -out GCA_902767545.1_Rumen_uncultured_genome_RUG11277_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:06:35,123] [INFO] Task succeeded: Blastn
[2023-06-05 18:06:35,128] [INFO] Selected 25 target genomes.
[2023-06-05 18:06:35,128] [INFO] Target genome list was writen to GCA_902767545.1_Rumen_uncultured_genome_RUG11277_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 18:06:35,141] [INFO] Task started: fastANI
[2023-06-05 18:06:35,141] [INFO] Running command: fastANI --query /var/lib/cwl/stgda5e5ca6-35e8-41c2-9c8e-ea21bac86993/GCA_902767545.1_Rumen_uncultured_genome_RUG11277_genomic.fna.gz --refList GCA_902767545.1_Rumen_uncultured_genome_RUG11277_genomic.fna/target_genomes_gtdb.txt --output GCA_902767545.1_Rumen_uncultured_genome_RUG11277_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 18:06:49,448] [INFO] Task succeeded: fastANI
[2023-06-05 18:06:49,469] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 18:06:49,469] [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_900318625.1	s__Prevotella sp900318625	98.5053	481	541	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.97	97.03	0.86	0.78	43	conclusive
GCA_902776685.1	s__Prevotella sp902776685	77.8928	142	541	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002353555.1	s__Prevotella sp002353555	77.596	143	541	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.61	97.57	0.79	0.77	3	-
GCA_017557185.1	s__Prevotella sp017557185	77.5097	129	541	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902775475.1	s__Prevotella sp902775475	77.4522	159	541	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.69	98.51	0.89	0.87	7	-
GCA_900320585.1	s__Prevotella sp900320585	77.3472	127	541	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.77	98.44	0.87	0.81	6	-
GCA_905233825.1	s__Prevotella sp905233825	77.2887	81	541	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902760315.1	s__Prevotella sp902760315	77.1525	107	541	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905233425.1	s__Prevotella sp905233425	77.1112	134	541	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002392835.1	s__Prevotella sp002392835	77.0759	111	541	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.57	97.57	0.74	0.74	2	-
GCF_019052365.1	s__Prevotella sp000434975	77.0687	110	541	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.22	96.59	0.82	0.74	11	-
GCA_902767045.1	s__Prevotella sp902767045	77.0552	132	541	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.95	96.95	0.81	0.81	2	-
GCA_902771785.1	s__Prevotella sp902771785	77.0447	144	541	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.01	98.01	0.87	0.87	2	-
GCA_017615355.1	s__Prevotella sp017615355	77.0061	98	541	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900199655.1	s__Prevotella sp900199655	76.8884	115	541	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.91	99.91	0.98	0.98	2	-
GCF_002251435.1	s__Prevotella sp002251435	76.783	66	541	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900546575.1	s__Prevotella sp900546575	76.7344	101	541	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.21	95.49	0.86	0.86	4	-
GCA_900547005.1	s__Prevotella sp900547005	76.7341	92	541	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.66	96.14	0.84	0.69	4	-
GCA_900315455.1	s__Prevotella sp900315455	76.7292	127	541	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.41	96.59	0.90	0.86	13	-
GCA_017477435.1	s__Prevotella sp017477435	76.6065	90	541	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.70	96.70	0.87	0.87	2	-
GCA_902792685.1	s__Prevotella sp902792685	76.5931	80	541	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.79	96.68	0.73	0.71	4	-
GCF_000426585.1	s__Prevotella baroniae	76.5797	86	541	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.79	98.01	0.95	0.92	4	-
GCF_000184945.1	s__Prevotella buccae	76.5786	107	541	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.38	98.24	0.91	0.87	7	-
GCF_009695775.1	s__Prevotella mizrahii	76.5564	65	541	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.15	96.87	0.87	0.84	6	-
--------------------------------------------------------------------------------
[2023-06-05 18:06:49,472] [INFO] GTDB search result was written to GCA_902767545.1_Rumen_uncultured_genome_RUG11277_genomic.fna/result_gtdb.tsv
[2023-06-05 18:06:49,472] [INFO] ===== GTDB Search completed =====
[2023-06-05 18:06:49,477] [INFO] DFAST_QC result json was written to GCA_902767545.1_Rumen_uncultured_genome_RUG11277_genomic.fna/dqc_result.json
[2023-06-05 18:06:49,477] [INFO] DFAST_QC completed!
[2023-06-05 18:06:49,477] [INFO] Total running time: 0h1m37s