[2023-06-05 02:23:05,377] [INFO] DFAST_QC pipeline started.
[2023-06-05 02:23:05,390] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 02:23:05,390] [INFO] DQC Reference Directory: /var/lib/cwl/stgce9c4f77-18ea-47e6-816f-5429a3c8fcc9/dqc_reference
[2023-06-05 02:23:07,106] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 02:23:07,107] [INFO] Task started: Prodigal
[2023-06-05 02:23:07,107] [INFO] Running command: gunzip -c /var/lib/cwl/stgca767e7a-5f52-4cc0-9daa-bf8dbbb0b359/GCA_902406155.1_UHGG_MGYG-HGUT-04274_genomic.fna.gz | prodigal -d GCA_902406155.1_UHGG_MGYG-HGUT-04274_genomic.fna/cds.fna -a GCA_902406155.1_UHGG_MGYG-HGUT-04274_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 02:23:13,415] [INFO] Task succeeded: Prodigal
[2023-06-05 02:23:13,416] [INFO] Task started: HMMsearch
[2023-06-05 02:23:13,416] [INFO] Running command: hmmsearch --tblout GCA_902406155.1_UHGG_MGYG-HGUT-04274_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgce9c4f77-18ea-47e6-816f-5429a3c8fcc9/dqc_reference/reference_markers.hmm GCA_902406155.1_UHGG_MGYG-HGUT-04274_genomic.fna/protein.faa > /dev/null
[2023-06-05 02:23:13,687] [INFO] Task succeeded: HMMsearch
[2023-06-05 02:23:13,689] [INFO] Found 6/6 markers.
[2023-06-05 02:23:13,737] [INFO] Query marker FASTA was written to GCA_902406155.1_UHGG_MGYG-HGUT-04274_genomic.fna/markers.fasta
[2023-06-05 02:23:13,738] [INFO] Task started: Blastn
[2023-06-05 02:23:13,738] [INFO] Running command: blastn -query GCA_902406155.1_UHGG_MGYG-HGUT-04274_genomic.fna/markers.fasta -db /var/lib/cwl/stgce9c4f77-18ea-47e6-816f-5429a3c8fcc9/dqc_reference/reference_markers.fasta -out GCA_902406155.1_UHGG_MGYG-HGUT-04274_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 02:23:14,485] [INFO] Task succeeded: Blastn
[2023-06-05 02:23:14,489] [INFO] Selected 16 target genomes.
[2023-06-05 02:23:14,489] [INFO] Target genome list was writen to GCA_902406155.1_UHGG_MGYG-HGUT-04274_genomic.fna/target_genomes.txt
[2023-06-05 02:23:14,493] [INFO] Task started: fastANI
[2023-06-05 02:23:14,494] [INFO] Running command: fastANI --query /var/lib/cwl/stgca767e7a-5f52-4cc0-9daa-bf8dbbb0b359/GCA_902406155.1_UHGG_MGYG-HGUT-04274_genomic.fna.gz --refList GCA_902406155.1_UHGG_MGYG-HGUT-04274_genomic.fna/target_genomes.txt --output GCA_902406155.1_UHGG_MGYG-HGUT-04274_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 02:23:21,507] [INFO] Task succeeded: fastANI
[2023-06-05 02:23:21,508] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgce9c4f77-18ea-47e6-816f-5429a3c8fcc9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 02:23:21,508] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgce9c4f77-18ea-47e6-816f-5429a3c8fcc9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 02:23:21,519] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 02:23:21,519] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 02:23:21,519] [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
Collinsella aerofaciens	strain=NCTC11838	GCA_900461335.1	74426	74426	type	True	92.3594	515	629	95	below_threshold
Collinsella aerofaciens	strain=ATCC 25986	GCA_000169035.1	74426	74426	type	True	92.2998	515	629	95	below_threshold
Collinsella aerofaciens	strain=JCM 10188	GCA_010509075.1	74426	74426	type	True	92.2845	512	629	95	below_threshold
Collinsella bouchesdurhonensis	strain=Marseille-P3296	GCA_900155365.1	1907654	1907654	type	True	80.1867	212	629	95	below_threshold
Collinsella phocaeensis	strain=Marseille-P3245	GCA_900119895.1	1871016	1871016	type	True	80.1306	213	629	95	below_threshold
Collinsella stercoris	strain=DSM 13279	GCA_000156215.1	147206	147206	type	True	80.1123	228	629	95	below_threshold
Collinsella stercoris	strain=DSM 13279	GCA_025149625.1	147206	147206	type	True	80.0065	230	629	95	below_threshold
Collinsella provencensis	strain=Marseille-P3740	GCA_900199705.1	1937461	1937461	type	True	79.8534	160	629	95	below_threshold
Collinsella tanakaei	strain=YIT 12063	GCA_000225705.1	626935	626935	suspected-type	True	79.6684	207	629	95	below_threshold
Enorma burkinafasonensis	strain=Marseille-P9525	GCA_902150035.1	2590867	2590867	type	True	79.5526	216	629	95	below_threshold
Collinsella intestinalis	strain=DSM 13280	GCA_000156175.1	147207	147207	suspected-type	True	79.4288	217	629	95	below_threshold
Enorma timonensis	strain=GD5	GCA_000321165.1	1232436	1232436	type	True	78.6994	213	629	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 02:23:21,545] [INFO] DFAST Taxonomy check result was written to GCA_902406155.1_UHGG_MGYG-HGUT-04274_genomic.fna/tc_result.tsv
[2023-06-05 02:23:21,546] [INFO] ===== Taxonomy check completed =====
[2023-06-05 02:23:21,547] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 02:23:21,547] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgce9c4f77-18ea-47e6-816f-5429a3c8fcc9/dqc_reference/checkm_data
[2023-06-05 02:23:21,550] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 02:23:21,578] [INFO] Task started: CheckM
[2023-06-05 02:23:21,578] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902406155.1_UHGG_MGYG-HGUT-04274_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902406155.1_UHGG_MGYG-HGUT-04274_genomic.fna/checkm_input GCA_902406155.1_UHGG_MGYG-HGUT-04274_genomic.fna/checkm_result
[2023-06-05 02:23:45,759] [INFO] Task succeeded: CheckM
[2023-06-05 02:23:45,761] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 02:23:45,783] [INFO] ===== Completeness check finished =====
[2023-06-05 02:23:45,783] [INFO] ===== Start GTDB Search =====
[2023-06-05 02:23:45,783] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902406155.1_UHGG_MGYG-HGUT-04274_genomic.fna/markers.fasta)
[2023-06-05 02:23:45,784] [INFO] Task started: Blastn
[2023-06-05 02:23:45,784] [INFO] Running command: blastn -query GCA_902406155.1_UHGG_MGYG-HGUT-04274_genomic.fna/markers.fasta -db /var/lib/cwl/stgce9c4f77-18ea-47e6-816f-5429a3c8fcc9/dqc_reference/reference_markers_gtdb.fasta -out GCA_902406155.1_UHGG_MGYG-HGUT-04274_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 02:23:47,187] [INFO] Task succeeded: Blastn
[2023-06-05 02:23:47,192] [INFO] Selected 26 target genomes.
[2023-06-05 02:23:47,193] [INFO] Target genome list was writen to GCA_902406155.1_UHGG_MGYG-HGUT-04274_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 02:23:47,251] [INFO] Task started: fastANI
[2023-06-05 02:23:47,251] [INFO] Running command: fastANI --query /var/lib/cwl/stgca767e7a-5f52-4cc0-9daa-bf8dbbb0b359/GCA_902406155.1_UHGG_MGYG-HGUT-04274_genomic.fna.gz --refList GCA_902406155.1_UHGG_MGYG-HGUT-04274_genomic.fna/target_genomes_gtdb.txt --output GCA_902406155.1_UHGG_MGYG-HGUT-04274_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 02:23:58,908] [INFO] Task succeeded: fastANI
[2023-06-05 02:23:58,932] [INFO] Found 26 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 02:23:58,932] [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_902406155.1	s__Collinsella sp900554155	100.0	625	629	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	99.81	99.81	0.90	0.90	2	conclusive
GCA_900542155.1	s__Collinsella sp900542155	94.3272	522	629	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	100.00	100.00	1.00	1.00	2	-
GCA_905197665.1	s__Collinsella sp900556445	94.2398	532	629	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.037	96.72	95.07	0.91	0.87	4	-
GCA_900541685.1	s__Collinsella sp900541685	94.0292	523	629	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.037	96.60	96.60	0.93	0.93	2	-
GCF_003437035.1	s__Collinsella sp003437035	93.9243	542	629	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.081	96.95	95.41	0.92	0.87	4	-
GCF_003471585.1	s__Collinsella sp003471585	93.9198	535	629	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.1851	100.00	100.00	0.99	0.99	2	-
GCA_902405995.1	s__Collinsella sp902405995	93.9087	528	629	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.1886	96.57	95.30	0.89	0.86	5	-
GCF_002232035.1	s__Collinsella sp002232035	93.9078	544	629	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0836	95.49	95.12	0.86	0.82	32	-
GCA_900549715.1	s__Collinsella sp900549715	93.8624	452	629	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.2122	100.00	100.00	1.00	1.00	2	-
GCA_900757495.1	s__Collinsella sp900757495	93.8526	532	629	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905215115.1	s__Collinsella sp905215115	93.798	477	629	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900542945.1	s__Collinsella sp900542945	93.7762	515	629	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.1063	100.00	100.00	0.99	0.99	2	-
GCA_900542325.1	s__Collinsella sp900542325	93.758	526	629	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	100.00	100.00	1.00	1.00	2	-
GCA_905214435.1	s__Collinsella sp905214435	93.7563	504	629	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.174	95.31	95.19	0.87	0.85	5	-
GCA_905214525.1	s__Collinsella sp905214525	93.6578	539	629	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.3232	N/A	N/A	N/A	N/A	1	-
GCF_003459245.1	s__Collinsella sp003459245	93.6349	530	629	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	96.00	95.31	0.88	0.84	13	-
GCF_003470665.1	s__Collinsella sp003470665	93.5668	524	629	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	100.00	100.00	1.00	1.00	2	-
GCA_900756765.1	s__Collinsella sp900756765	93.5615	460	629	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900757285.1	s__Collinsella sp900757285	93.3207	397	629	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900544725.1	s__Collinsella sp900544725	93.1271	491	629	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900547285.1	s__Collinsella sp900547285	93.0621	429	629	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900757385.1	s__Collinsella sp900757385	93.058	399	629	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003462685.1	s__Collinsella sp003462685	92.9898	523	629	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	99.85	99.71	0.99	0.99	3	-
GCA_900553215.1	s__Collinsella sp900553215	92.7641	336	629	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	99.53	99.53	0.82	0.82	2	-
GCA_900541715.1	s__Collinsella sp900541715	92.7551	470	629	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0922	N/A	N/A	N/A	N/A	1	-
GCA_905209455.1	s__Collinsella sp905209455	92.6523	476	629	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.1399	99.94	99.94	0.95	0.95	2	-
--------------------------------------------------------------------------------
[2023-06-05 02:23:58,934] [INFO] GTDB search result was written to GCA_902406155.1_UHGG_MGYG-HGUT-04274_genomic.fna/result_gtdb.tsv
[2023-06-05 02:23:58,935] [INFO] ===== GTDB Search completed =====
[2023-06-05 02:23:58,939] [INFO] DFAST_QC result json was written to GCA_902406155.1_UHGG_MGYG-HGUT-04274_genomic.fna/dqc_result.json
[2023-06-05 02:23:58,939] [INFO] DFAST_QC completed!
[2023-06-05 02:23:58,939] [INFO] Total running time: 0h0m54s