[2023-06-05 18:57:36,544] [INFO] DFAST_QC pipeline started.
[2023-06-05 18:57:36,547] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 18:57:36,547] [INFO] DQC Reference Directory: /var/lib/cwl/stga49773fe-1b11-4fc0-a792-52a91bf24c5d/dqc_reference
[2023-06-05 18:57:37,849] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 18:57:37,851] [INFO] Task started: Prodigal
[2023-06-05 18:57:37,851] [INFO] Running command: gunzip -c /var/lib/cwl/stg47b4a9ea-e173-4c6c-8790-4f35470c7e7d/GCA_902758485.1_Rumen_uncultured_genome_RUG10369_genomic.fna.gz | prodigal -d GCA_902758485.1_Rumen_uncultured_genome_RUG10369_genomic.fna/cds.fna -a GCA_902758485.1_Rumen_uncultured_genome_RUG10369_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 18:57:59,011] [INFO] Task succeeded: Prodigal
[2023-06-05 18:57:59,011] [INFO] Task started: HMMsearch
[2023-06-05 18:57:59,011] [INFO] Running command: hmmsearch --tblout GCA_902758485.1_Rumen_uncultured_genome_RUG10369_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga49773fe-1b11-4fc0-a792-52a91bf24c5d/dqc_reference/reference_markers.hmm GCA_902758485.1_Rumen_uncultured_genome_RUG10369_genomic.fna/protein.faa > /dev/null
[2023-06-05 18:57:59,309] [INFO] Task succeeded: HMMsearch
[2023-06-05 18:57:59,310] [INFO] Found 6/6 markers.
[2023-06-05 18:57:59,355] [INFO] Query marker FASTA was written to GCA_902758485.1_Rumen_uncultured_genome_RUG10369_genomic.fna/markers.fasta
[2023-06-05 18:57:59,355] [INFO] Task started: Blastn
[2023-06-05 18:57:59,356] [INFO] Running command: blastn -query GCA_902758485.1_Rumen_uncultured_genome_RUG10369_genomic.fna/markers.fasta -db /var/lib/cwl/stga49773fe-1b11-4fc0-a792-52a91bf24c5d/dqc_reference/reference_markers.fasta -out GCA_902758485.1_Rumen_uncultured_genome_RUG10369_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:58:00,049] [INFO] Task succeeded: Blastn
[2023-06-05 18:58:00,062] [INFO] Selected 28 target genomes.
[2023-06-05 18:58:00,063] [INFO] Target genome list was writen to GCA_902758485.1_Rumen_uncultured_genome_RUG10369_genomic.fna/target_genomes.txt
[2023-06-05 18:58:00,065] [INFO] Task started: fastANI
[2023-06-05 18:58:00,066] [INFO] Running command: fastANI --query /var/lib/cwl/stg47b4a9ea-e173-4c6c-8790-4f35470c7e7d/GCA_902758485.1_Rumen_uncultured_genome_RUG10369_genomic.fna.gz --refList GCA_902758485.1_Rumen_uncultured_genome_RUG10369_genomic.fna/target_genomes.txt --output GCA_902758485.1_Rumen_uncultured_genome_RUG10369_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 18:58:16,369] [INFO] Task succeeded: fastANI
[2023-06-05 18:58:16,369] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga49773fe-1b11-4fc0-a792-52a91bf24c5d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 18:58:16,370] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga49773fe-1b11-4fc0-a792-52a91bf24c5d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 18:58:16,389] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 18:58:16,389] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 18:58:16,389] [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=ATCC 19189	GCA_900108375.1	839	839	type	True	79.3125	326	1214	95	below_threshold
Prevotella ruminicola	strain=Bryant 23	GCA_000025925.1	839	839	type	True	79.2745	335	1214	95	below_threshold
Prevotella brevis	strain=ATCC 19188	GCA_000621725.1	83231	83231	type	True	78.1644	212	1214	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_000157935.1	165179	165179	suspected-type	True	76.8747	113	1214	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_009495405.1	165179	165179	suspected-type	True	76.8162	107	1214	95	below_threshold
Prevotella dentalis	strain=DSM 3688	GCA_000242335.3	52227	52227	type	True	76.7419	80	1214	95	below_threshold
Prevotella dentalis	strain=DSM 3688	GCA_000220215.1	52227	52227	type	True	76.7301	80	1214	95	below_threshold
Hallella seregens	strain=ATCC 51272	GCA_000518545.1	52229	52229	type	True	76.715	76	1214	95	below_threshold
Prevotella buccae	strain=ATCC 33574	GCA_000184945.1	28126	28126	type	True	76.6822	82	1214	95	below_threshold
Prevotella lacticifex	strain=R5019	GCA_019973375.1	2854755	2854755	type	True	76.641	67	1214	95	below_threshold
Hallella faecis	strain=CLA-AA-H145	GCA_018789675.1	2841596	2841596	type	True	76.5009	88	1214	95	below_threshold
Prevotella albensis	strain=JCM 12258	GCA_000613525.1	77768	77768	type	True	76.3407	54	1214	95	below_threshold
Prevotella albensis	strain=DSM 11370	GCA_000426565.1	77768	77768	type	True	76.2912	56	1214	95	below_threshold
Prevotella illustrans	strain=A2931	GCA_017426725.1	2800387	2800387	type	True	76.2221	51	1214	95	below_threshold
Palleniella intestinalis	strain=PINT	GCA_013166595.1	2736291	2736291	type	True	75.8989	51	1214	95	below_threshold
Xylanibacter rodentium	strain=PROD	GCA_013166575.1	2736289	2736289	type	True	75.8711	79	1214	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 18:58:16,401] [INFO] DFAST Taxonomy check result was written to GCA_902758485.1_Rumen_uncultured_genome_RUG10369_genomic.fna/tc_result.tsv
[2023-06-05 18:58:16,403] [INFO] ===== Taxonomy check completed =====
[2023-06-05 18:58:16,404] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 18:58:16,404] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga49773fe-1b11-4fc0-a792-52a91bf24c5d/dqc_reference/checkm_data
[2023-06-05 18:58:16,407] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 18:58:16,474] [INFO] Task started: CheckM
[2023-06-05 18:58:16,475] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902758485.1_Rumen_uncultured_genome_RUG10369_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902758485.1_Rumen_uncultured_genome_RUG10369_genomic.fna/checkm_input GCA_902758485.1_Rumen_uncultured_genome_RUG10369_genomic.fna/checkm_result
[2023-06-05 18:59:16,877] [INFO] Task succeeded: CheckM
[2023-06-05 18:59:16,878] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 84.36%
Contamintation: 2.32%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-05 18:59:16,903] [INFO] ===== Completeness check finished =====
[2023-06-05 18:59:16,903] [INFO] ===== Start GTDB Search =====
[2023-06-05 18:59:16,903] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902758485.1_Rumen_uncultured_genome_RUG10369_genomic.fna/markers.fasta)
[2023-06-05 18:59:16,904] [INFO] Task started: Blastn
[2023-06-05 18:59:16,904] [INFO] Running command: blastn -query GCA_902758485.1_Rumen_uncultured_genome_RUG10369_genomic.fna/markers.fasta -db /var/lib/cwl/stga49773fe-1b11-4fc0-a792-52a91bf24c5d/dqc_reference/reference_markers_gtdb.fasta -out GCA_902758485.1_Rumen_uncultured_genome_RUG10369_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:59:17,804] [INFO] Task succeeded: Blastn
[2023-06-05 18:59:17,808] [INFO] Selected 29 target genomes.
[2023-06-05 18:59:17,808] [INFO] Target genome list was writen to GCA_902758485.1_Rumen_uncultured_genome_RUG10369_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 18:59:17,821] [INFO] Task started: fastANI
[2023-06-05 18:59:17,822] [INFO] Running command: fastANI --query /var/lib/cwl/stg47b4a9ea-e173-4c6c-8790-4f35470c7e7d/GCA_902758485.1_Rumen_uncultured_genome_RUG10369_genomic.fna.gz --refList GCA_902758485.1_Rumen_uncultured_genome_RUG10369_genomic.fna/target_genomes_gtdb.txt --output GCA_902758485.1_Rumen_uncultured_genome_RUG10369_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 18:59:35,816] [INFO] Task succeeded: fastANI
[2023-06-05 18:59:35,850] [INFO] Found 29 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 18:59:35,850] [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_900314995.1	s__Prevotella sp900314995	96.3537	871	1214	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.11	96.50	0.82	0.73	11	conclusive
GCA_900318395.1	s__Prevotella sp900318395	81.3314	508	1214	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.69	96.89	0.88	0.81	6	-
GCA_016286575.1	s__Prevotella sp016286575	80.8649	409	1214	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900315525.1	s__Prevotella sp900315525	80.7685	458	1214	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.95	96.00	0.84	0.76	10	-
GCF_900110085.1	s__Prevotella sp900110085	80.7107	521	1214	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.96	96.96	0.82	0.82	3	-
GCA_900315035.1	s__Prevotella sp900315035	80.6087	452	1214	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.18	98.35	0.94	0.89	3	-
GCA_017460765.1	s__Prevotella sp017460765	80.3816	374	1214	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	80.3812	424	1214	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002379425.1	s__Prevotella sp002379425	80.3613	290	1214	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017443345.1	s__Prevotella sp017443345	80.2765	440	1214	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017965475.1	s__Prevotella sp017965475	80.2218	446	1214	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902776545.1	s__Prevotella sp902776545	80.2054	479	1214	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.23	97.16	0.83	0.82	3	-
GCA_902800595.1	s__Prevotella sp902800595	80.1551	378	1214	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.22	98.22	0.82	0.82	2	-
GCA_902799765.1	s__Prevotella sp902799765	80.0652	491	1214	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.49	95.44	0.80	0.73	3	-
GCA_900319305.1	s__Prevotella sp900319305	80.0182	409	1214	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.83	97.65	0.87	0.75	3	-
GCA_900315695.1	s__Prevotella sp900315695	79.8667	437	1214	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.90	97.22	0.82	0.74	6	-
GCA_902785945.1	s__Prevotella sp902785945	79.664	360	1214	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902784065.1	s__Prevotella sp902784065	79.6411	388	1214	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905233555.1	s__Prevotella sp905233555	79.1639	336	1214	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017965725.1	s__Prevotella sp017965725	79.1312	312	1214	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902784565.1	s__Prevotella sp902784565	79.1121	328	1214	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.90	96.90	0.76	0.76	2	-
GCA_017650905.1	s__Prevotella sp017650905	79.091	279	1214	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000619825.1	s__Prevotella sp000619825	78.9641	345	1214	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115435.1	s__Prevotella sp900115435	78.8483	230	1214	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.38	96.23	0.89	0.86	8	-
GCA_017551005.1	s__Prevotella sp017551005	78.7817	309	1214	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017518935.1	s__Prevotella sp017518935	78.7314	280	1214	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902769805.1	s__Prevotella sp902769805	78.0101	188	1214	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.56	97.56	0.77	0.77	2	-
GCA_002353225.1	s__Prevotella sp002353225	77.9394	221	1214	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.18	97.50	0.85	0.76	6	-
GCA_900315075.1	s__Prevotella sp900315075	77.421	109	1214	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.96	98.41	0.92	0.87	4	-
--------------------------------------------------------------------------------
[2023-06-05 18:59:35,852] [INFO] GTDB search result was written to GCA_902758485.1_Rumen_uncultured_genome_RUG10369_genomic.fna/result_gtdb.tsv
[2023-06-05 18:59:35,853] [INFO] ===== GTDB Search completed =====
[2023-06-05 18:59:35,858] [INFO] DFAST_QC result json was written to GCA_902758485.1_Rumen_uncultured_genome_RUG10369_genomic.fna/dqc_result.json
[2023-06-05 18:59:35,859] [INFO] DFAST_QC completed!
[2023-06-05 18:59:35,859] [INFO] Total running time: 0h1m59s