[2023-06-08 17:09:25,830] [INFO] DFAST_QC pipeline started.
[2023-06-08 17:09:25,834] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 17:09:25,834] [INFO] DQC Reference Directory: /var/lib/cwl/stgeddbb33e-efbc-48ae-a4d5-14aaf09a2577/dqc_reference
[2023-06-08 17:09:27,043] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 17:09:27,044] [INFO] Task started: Prodigal
[2023-06-08 17:09:27,044] [INFO] Running command: gunzip -c /var/lib/cwl/stg4309b720-9413-49d5-bfdf-a44be0b712cd/GCA_902800415.1_Rumen_uncultured_genome_RUG14571_genomic.fna.gz | prodigal -d GCA_902800415.1_Rumen_uncultured_genome_RUG14571_genomic.fna/cds.fna -a GCA_902800415.1_Rumen_uncultured_genome_RUG14571_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 17:09:52,725] [INFO] Task succeeded: Prodigal
[2023-06-08 17:09:52,725] [INFO] Task started: HMMsearch
[2023-06-08 17:09:52,725] [INFO] Running command: hmmsearch --tblout GCA_902800415.1_Rumen_uncultured_genome_RUG14571_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgeddbb33e-efbc-48ae-a4d5-14aaf09a2577/dqc_reference/reference_markers.hmm GCA_902800415.1_Rumen_uncultured_genome_RUG14571_genomic.fna/protein.faa > /dev/null
[2023-06-08 17:09:53,068] [INFO] Task succeeded: HMMsearch
[2023-06-08 17:09:53,069] [INFO] Found 6/6 markers.
[2023-06-08 17:09:53,106] [INFO] Query marker FASTA was written to GCA_902800415.1_Rumen_uncultured_genome_RUG14571_genomic.fna/markers.fasta
[2023-06-08 17:09:53,107] [INFO] Task started: Blastn
[2023-06-08 17:09:53,107] [INFO] Running command: blastn -query GCA_902800415.1_Rumen_uncultured_genome_RUG14571_genomic.fna/markers.fasta -db /var/lib/cwl/stgeddbb33e-efbc-48ae-a4d5-14aaf09a2577/dqc_reference/reference_markers.fasta -out GCA_902800415.1_Rumen_uncultured_genome_RUG14571_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 17:09:53,734] [INFO] Task succeeded: Blastn
[2023-06-08 17:09:53,739] [INFO] Selected 29 target genomes.
[2023-06-08 17:09:53,740] [INFO] Target genome list was writen to GCA_902800415.1_Rumen_uncultured_genome_RUG14571_genomic.fna/target_genomes.txt
[2023-06-08 17:09:53,741] [INFO] Task started: fastANI
[2023-06-08 17:09:53,741] [INFO] Running command: fastANI --query /var/lib/cwl/stg4309b720-9413-49d5-bfdf-a44be0b712cd/GCA_902800415.1_Rumen_uncultured_genome_RUG14571_genomic.fna.gz --refList GCA_902800415.1_Rumen_uncultured_genome_RUG14571_genomic.fna/target_genomes.txt --output GCA_902800415.1_Rumen_uncultured_genome_RUG14571_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 17:10:08,664] [INFO] Task succeeded: fastANI
[2023-06-08 17:10:08,665] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgeddbb33e-efbc-48ae-a4d5-14aaf09a2577/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 17:10:08,666] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgeddbb33e-efbc-48ae-a4d5-14aaf09a2577/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 17:10:08,686] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 17:10:08,686] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 17:10:08,687] [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 buccae	strain=ATCC 33574	GCA_000184945.1	28126	28126	type	True	76.9408	153	1253	95	below_threshold
Prevotella pectinovora	strain=P4-76	GCA_000834015.1	1602169	1602169	type	True	76.8713	128	1253	95	below_threshold
Prevotella stercorea	strain=DSM 18206	GCA_000235885.1	363265	363265	suspected-type	True	76.808	109	1253	95	below_threshold
Prevotella dentalis	strain=DSM 3688	GCA_000242335.3	52227	52227	type	True	76.7901	158	1253	95	below_threshold
Prevotella ruminicola	strain=ATCC 19189	GCA_900108375.1	839	839	type	True	76.7809	125	1253	95	below_threshold
Prevotella ruminicola	strain=Bryant 23	GCA_000025925.1	839	839	type	True	76.7796	126	1253	95	below_threshold
Hallella faecis	strain=CLA-AA-H145	GCA_018789675.1	2841596	2841596	type	True	76.7589	127	1253	95	below_threshold
Prevotella dentalis	strain=DSM 3688	GCA_000220215.1	52227	52227	type	True	76.7418	162	1253	95	below_threshold
Prevotella baroniae	strain=JCM 13447	GCA_000613565.1	305719	305719	type	True	76.7219	111	1253	95	below_threshold
Prevotella baroniae	strain=DSM 16972	GCA_000426585.1	305719	305719	type	True	76.6751	111	1253	95	below_threshold
Prevotella mizrahii	strain=LKV-178-WT-2A	GCA_009695775.1	2606637	2606637	type	True	76.6559	114	1253	95	below_threshold
Prevotella multiformis	strain=DSM 16608	GCA_000191065.1	282402	282402	type	True	76.4702	87	1253	95	below_threshold
Xylanibacter rodentium	strain=PROD	GCA_013166575.1	2736289	2736289	type	True	76.4545	100	1253	95	below_threshold
Prevotella maculosa	strain=JCM 15638	GCA_000613965.1	439703	439703	type	True	76.2323	60	1253	95	below_threshold
Prevotella denticola	strain=DSM 20614	GCA_000421205.1	28129	28129	type	True	76.2019	83	1253	95	below_threshold
Prevotella illustrans	strain=A2931	GCA_017426725.1	2800387	2800387	type	True	76.1828	70	1253	95	below_threshold
Prevotella denticola	strain=NCTC13067	GCA_900454835.1	28129	28129	type	True	76.1824	84	1253	95	below_threshold
Prevotella lacticifex	strain=R5019	GCA_019973375.1	2854755	2854755	type	True	76.1099	106	1253	95	below_threshold
Prevotella lascolaii	strain=khD1	GCA_900079775.1	1776379	1776379	type	True	76.0684	85	1253	95	below_threshold
Xylanibacter muris	strain=PMUR	GCA_013166605.1	2736290	2736290	type	True	76.0433	57	1253	95	below_threshold
Prevotella loescheii	strain=DSM 19665	GCA_000378085.1	840	840	type	True	76.0378	62	1253	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 17:10:08,689] [INFO] DFAST Taxonomy check result was written to GCA_902800415.1_Rumen_uncultured_genome_RUG14571_genomic.fna/tc_result.tsv
[2023-06-08 17:10:08,690] [INFO] ===== Taxonomy check completed =====
[2023-06-08 17:10:08,691] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 17:10:08,691] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgeddbb33e-efbc-48ae-a4d5-14aaf09a2577/dqc_reference/checkm_data
[2023-06-08 17:10:08,692] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 17:10:08,739] [INFO] Task started: CheckM
[2023-06-08 17:10:08,739] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902800415.1_Rumen_uncultured_genome_RUG14571_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902800415.1_Rumen_uncultured_genome_RUG14571_genomic.fna/checkm_input GCA_902800415.1_Rumen_uncultured_genome_RUG14571_genomic.fna/checkm_result
[2023-06-08 17:11:19,277] [INFO] Task succeeded: CheckM
[2023-06-08 17:11:19,279] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 17:11:19,299] [INFO] ===== Completeness check finished =====
[2023-06-08 17:11:19,300] [INFO] ===== Start GTDB Search =====
[2023-06-08 17:11:19,300] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902800415.1_Rumen_uncultured_genome_RUG14571_genomic.fna/markers.fasta)
[2023-06-08 17:11:19,300] [INFO] Task started: Blastn
[2023-06-08 17:11:19,300] [INFO] Running command: blastn -query GCA_902800415.1_Rumen_uncultured_genome_RUG14571_genomic.fna/markers.fasta -db /var/lib/cwl/stgeddbb33e-efbc-48ae-a4d5-14aaf09a2577/dqc_reference/reference_markers_gtdb.fasta -out GCA_902800415.1_Rumen_uncultured_genome_RUG14571_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 17:11:20,188] [INFO] Task succeeded: Blastn
[2023-06-08 17:11:20,193] [INFO] Selected 12 target genomes.
[2023-06-08 17:11:20,193] [INFO] Target genome list was writen to GCA_902800415.1_Rumen_uncultured_genome_RUG14571_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 17:11:20,197] [INFO] Task started: fastANI
[2023-06-08 17:11:20,197] [INFO] Running command: fastANI --query /var/lib/cwl/stg4309b720-9413-49d5-bfdf-a44be0b712cd/GCA_902800415.1_Rumen_uncultured_genome_RUG14571_genomic.fna.gz --refList GCA_902800415.1_Rumen_uncultured_genome_RUG14571_genomic.fna/target_genomes_gtdb.txt --output GCA_902800415.1_Rumen_uncultured_genome_RUG14571_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 17:11:29,620] [INFO] Task succeeded: fastANI
[2023-06-08 17:11:29,632] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 17:11:29,632] [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_900315455.1	s__Prevotella sp900315455	96.8802	1110	1253	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.41	96.59	0.90	0.86	13	conclusive
GCA_017617615.1	s__Prevotella sp017617615	85.5478	562	1253	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900317305.1	s__Prevotella sp900317305	82.6093	719	1253	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	82.5512	651	1253	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.77	98.44	0.87	0.81	6	-
GCA_902776475.1	s__Prevotella sp902776475	79.6773	466	1253	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.89	97.89	0.91	0.91	2	-
GCA_902786665.1	s__Prevotella sp902786665	79.5794	549	1253	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.72	98.72	0.89	0.89	2	-
GCA_902767775.1	s__Prevotella sp902767775	79.5249	493	1253	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.97	97.97	0.86	0.86	2	-
GCA_016281815.1	s__Prevotella sp016281815	79.4728	446	1253	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902780635.1	s__Prevotella sp902780635	79.1004	411	1253	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.41	97.41	0.85	0.85	2	-
GCA_902792855.1	s__Prevotella sp902792855	78.8325	419	1253	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.67	98.62	0.88	0.82	4	-
GCA_017619755.1	s__Prevotella sp017619755	78.3554	382	1253	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017548605.1	s__Prevotella sp017548605	77.493	240	1253	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 17:11:29,635] [INFO] GTDB search result was written to GCA_902800415.1_Rumen_uncultured_genome_RUG14571_genomic.fna/result_gtdb.tsv
[2023-06-08 17:11:29,636] [INFO] ===== GTDB Search completed =====
[2023-06-08 17:11:29,639] [INFO] DFAST_QC result json was written to GCA_902800415.1_Rumen_uncultured_genome_RUG14571_genomic.fna/dqc_result.json
[2023-06-08 17:11:29,640] [INFO] DFAST_QC completed!
[2023-06-08 17:11:29,640] [INFO] Total running time: 0h2m4s