[2023-06-05 01:31:25,876] [INFO] DFAST_QC pipeline started.
[2023-06-05 01:31:25,879] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 01:31:25,879] [INFO] DQC Reference Directory: /var/lib/cwl/stg3be5650d-83e6-4fde-a95f-ffe29549dd61/dqc_reference
[2023-06-05 01:31:28,789] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 01:31:28,790] [INFO] Task started: Prodigal
[2023-06-05 01:31:28,791] [INFO] Running command: gunzip -c /var/lib/cwl/stg0f76d409-1d59-4a8e-b47e-d90234f0a5d8/GCA_934839655.1_MTG230_bin.10.fa_genomic.fna.gz | prodigal -d GCA_934839655.1_MTG230_bin.10.fa_genomic.fna/cds.fna -a GCA_934839655.1_MTG230_bin.10.fa_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 01:31:34,970] [INFO] Task succeeded: Prodigal
[2023-06-05 01:31:34,970] [INFO] Task started: HMMsearch
[2023-06-05 01:31:34,970] [INFO] Running command: hmmsearch --tblout GCA_934839655.1_MTG230_bin.10.fa_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3be5650d-83e6-4fde-a95f-ffe29549dd61/dqc_reference/reference_markers.hmm GCA_934839655.1_MTG230_bin.10.fa_genomic.fna/protein.faa > /dev/null
[2023-06-05 01:31:35,237] [INFO] Task succeeded: HMMsearch
[2023-06-05 01:31:35,238] [INFO] Found 6/6 markers.
[2023-06-05 01:31:35,259] [INFO] Query marker FASTA was written to GCA_934839655.1_MTG230_bin.10.fa_genomic.fna/markers.fasta
[2023-06-05 01:31:35,259] [INFO] Task started: Blastn
[2023-06-05 01:31:35,259] [INFO] Running command: blastn -query GCA_934839655.1_MTG230_bin.10.fa_genomic.fna/markers.fasta -db /var/lib/cwl/stg3be5650d-83e6-4fde-a95f-ffe29549dd61/dqc_reference/reference_markers.fasta -out GCA_934839655.1_MTG230_bin.10.fa_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 01:31:36,017] [INFO] Task succeeded: Blastn
[2023-06-05 01:31:36,020] [INFO] Selected 12 target genomes.
[2023-06-05 01:31:36,021] [INFO] Target genome list was writen to GCA_934839655.1_MTG230_bin.10.fa_genomic.fna/target_genomes.txt
[2023-06-05 01:31:36,023] [INFO] Task started: fastANI
[2023-06-05 01:31:36,023] [INFO] Running command: fastANI --query /var/lib/cwl/stg0f76d409-1d59-4a8e-b47e-d90234f0a5d8/GCA_934839655.1_MTG230_bin.10.fa_genomic.fna.gz --refList GCA_934839655.1_MTG230_bin.10.fa_genomic.fna/target_genomes.txt --output GCA_934839655.1_MTG230_bin.10.fa_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 01:31:41,782] [INFO] Task succeeded: fastANI
[2023-06-05 01:31:41,783] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3be5650d-83e6-4fde-a95f-ffe29549dd61/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 01:31:41,783] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3be5650d-83e6-4fde-a95f-ffe29549dd61/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 01:31:41,794] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 01:31:41,794] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 01:31:41,794] [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=JCM 10188	GCA_010509075.1	74426	74426	type	True	93.2168	554	645	95	below_threshold
Collinsella aerofaciens	strain=NCTC11838	GCA_900461335.1	74426	74426	type	True	93.2098	560	645	95	below_threshold
Collinsella aerofaciens	strain=ATCC 25986	GCA_000169035.1	74426	74426	type	True	93.1901	559	645	95	below_threshold
Collinsella bouchesdurhonensis	strain=Marseille-P3296	GCA_900155365.1	1907654	1907654	type	True	80.3529	226	645	95	below_threshold
Collinsella phocaeensis	strain=Marseille-P3245	GCA_900119895.1	1871016	1871016	type	True	80.0398	223	645	95	below_threshold
Collinsella stercoris	strain=DSM 13279	GCA_000156215.1	147206	147206	type	True	79.9328	237	645	95	below_threshold
Collinsella stercoris	strain=DSM 13279	GCA_025149625.1	147206	147206	type	True	79.7962	241	645	95	below_threshold
Collinsella provencensis	strain=Marseille-P3740	GCA_900199705.1	1937461	1937461	type	True	79.5595	168	645	95	below_threshold
Collinsella tanakaei	strain=YIT 12063	GCA_000225705.1	626935	626935	suspected-type	True	79.4415	220	645	95	below_threshold
Enorma burkinafasonensis	strain=Marseille-P9525	GCA_902150035.1	2590867	2590867	type	True	79.2661	215	645	95	below_threshold
Enorma timonensis	strain=GD5	GCA_000321165.1	1232436	1232436	type	True	78.8122	199	645	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 01:31:41,796] [INFO] DFAST Taxonomy check result was written to GCA_934839655.1_MTG230_bin.10.fa_genomic.fna/tc_result.tsv
[2023-06-05 01:31:41,797] [INFO] ===== Taxonomy check completed =====
[2023-06-05 01:31:41,797] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 01:31:41,797] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3be5650d-83e6-4fde-a95f-ffe29549dd61/dqc_reference/checkm_data
[2023-06-05 01:31:41,799] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 01:31:41,825] [INFO] Task started: CheckM
[2023-06-05 01:31:41,825] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934839655.1_MTG230_bin.10.fa_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934839655.1_MTG230_bin.10.fa_genomic.fna/checkm_input GCA_934839655.1_MTG230_bin.10.fa_genomic.fna/checkm_result
[2023-06-05 01:32:05,686] [INFO] Task succeeded: CheckM
[2023-06-05 01:32:05,688] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.04%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 01:32:05,709] [INFO] ===== Completeness check finished =====
[2023-06-05 01:32:05,710] [INFO] ===== Start GTDB Search =====
[2023-06-05 01:32:05,710] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934839655.1_MTG230_bin.10.fa_genomic.fna/markers.fasta)
[2023-06-05 01:32:05,710] [INFO] Task started: Blastn
[2023-06-05 01:32:05,711] [INFO] Running command: blastn -query GCA_934839655.1_MTG230_bin.10.fa_genomic.fna/markers.fasta -db /var/lib/cwl/stg3be5650d-83e6-4fde-a95f-ffe29549dd61/dqc_reference/reference_markers_gtdb.fasta -out GCA_934839655.1_MTG230_bin.10.fa_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 01:32:07,054] [INFO] Task succeeded: Blastn
[2023-06-05 01:32:07,059] [INFO] Selected 32 target genomes.
[2023-06-05 01:32:07,060] [INFO] Target genome list was writen to GCA_934839655.1_MTG230_bin.10.fa_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 01:32:07,086] [INFO] Task started: fastANI
[2023-06-05 01:32:07,087] [INFO] Running command: fastANI --query /var/lib/cwl/stg0f76d409-1d59-4a8e-b47e-d90234f0a5d8/GCA_934839655.1_MTG230_bin.10.fa_genomic.fna.gz --refList GCA_934839655.1_MTG230_bin.10.fa_genomic.fna/target_genomes_gtdb.txt --output GCA_934839655.1_MTG230_bin.10.fa_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 01:32:20,977] [INFO] Task succeeded: fastANI
[2023-06-05 01:32:21,002] [INFO] Found 32 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 01:32:21,002] [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
GCF_002232035.1	s__Collinsella sp002232035	95.2192	567	645	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0836	95.49	95.12	0.86	0.82	32	conclusive
GCA_905214525.1	s__Collinsella sp905214525	95.0623	544	645	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.3232	N/A	N/A	N/A	N/A	1	-
GCF_003439125.1	s__Collinsella sp003439125	94.9303	545	645	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.74	95.07	0.88	0.85	15	-
GCF_003471585.1	s__Collinsella sp003471585	94.8642	545	645	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.1851	100.00	100.00	0.99	0.99	2	-
GCA_902835305.1	s__Collinsella sp902835305	94.8268	533	645	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	97.56	95.13	0.93	0.87	3	-
GCA_900543945.1	s__Collinsella sp900543945	94.8149	473	645	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.4468	97.82	95.67	0.91	0.87	3	-
GCA_900540855.1	s__Collinsella sp900540855	94.8105	550	645	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	96.88	95.32	0.93	0.90	4	-
GCA_900762345.1	s__Collinsella sp900762345	94.7936	516	645	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	94.7185	523	645	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.1063	100.00	100.00	0.99	0.99	2	-
GCF_015554145.1	s__Collinsella aerofaciens_AA	94.6748	568	645	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900546085.1	s__Collinsella sp900546085	94.6655	459	645	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0166	N/A	N/A	N/A	N/A	1	-
GCA_900542325.1	s__Collinsella sp900542325	94.6477	525	645	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	100.00	100.00	1.00	1.00	2	-
GCA_900768435.1	s__Collinsella sp900768435	94.647	552	645	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900757235.1	s__Collinsella sp900757235	94.6259	428	645	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	94.5988	423	645	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900550835.1	s__Collinsella sp900550835	94.5802	424	645	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	98.40	95.47	0.90	0.85	4	-
GCA_900757205.1	s__Collinsella sp900757205	94.5756	485	645	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.1956	95.24	95.24	0.77	0.77	2	-
GCA_902388345.1	s__Collinsella sp902388345	94.5422	506	645	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	99.98	99.97	0.98	0.97	3	-
GCA_900551205.1	s__Collinsella sp900551205	94.507	411	645	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.45	95.34	0.91	0.90	4	-
GCA_900551195.1	s__Collinsella sp900551195	94.4691	369	645	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0222	96.98	95.23	0.92	0.90	4	-
GCA_900552705.1	s__Collinsella sp900552705	94.4034	432	645	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	94.3286	461	645	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900757265.1	s__Collinsella sp900757265	94.1728	311	645	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900761995.1	s__Collinsella sp900761995	94.1253	490	645	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018373675.1	s__Collinsella sp018373675	93.5976	541	645	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0912	N/A	N/A	N/A	N/A	1	-
GCA_900553705.1	s__Collinsella sp900553705	93.4904	366	645	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0991	N/A	N/A	N/A	N/A	1	-
GCF_015552075.1	s__Collinsella aerofaciens_Y	93.4007	523	645	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900547805.1	s__Collinsella sp900547805	93.3846	438	645	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900539035.1	s__Collinsella sp900539035	93.3191	524	645	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	99.92	99.92	0.95	0.95	2	-
GCA_900544235.1	s__Collinsella sp900544235	93.2917	502	645	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.05	95.01	0.84	0.81	3	-
GCA_900554325.1	s__Collinsella sp900554325	93.0335	440	645	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015557435.1	s__Collinsella aerofaciens_Z	92.9605	525	645	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 01:32:21,005] [INFO] GTDB search result was written to GCA_934839655.1_MTG230_bin.10.fa_genomic.fna/result_gtdb.tsv
[2023-06-05 01:32:21,005] [INFO] ===== GTDB Search completed =====
[2023-06-05 01:32:21,010] [INFO] DFAST_QC result json was written to GCA_934839655.1_MTG230_bin.10.fa_genomic.fna/dqc_result.json
[2023-06-05 01:32:21,011] [INFO] DFAST_QC completed!
[2023-06-05 01:32:21,011] [INFO] Total running time: 0h0m55s