[2023-06-12 23:06:17,172] [INFO] DFAST_QC pipeline started.
[2023-06-12 23:06:17,177] [INFO] DFAST_QC version: 0.5.7
[2023-06-12 23:06:17,177] [INFO] DQC Reference Directory: /var/lib/cwl/stg2847267c-7258-4e0d-b3f3-35299b287a77/dqc_reference
[2023-06-12 23:06:18,856] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-12 23:06:18,858] [INFO] Task started: Prodigal
[2023-06-12 23:06:18,858] [INFO] Running command: gunzip -c /var/lib/cwl/stg3e88adb6-c7ca-4afc-ac5a-c795f7bc6edd/GCA_938005455.1_ERR912063_bin.113_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_938005455.1_ERR912063_bin.113_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_938005455.1_ERR912063_bin.113_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-12 23:06:26,560] [INFO] Task succeeded: Prodigal
[2023-06-12 23:06:26,561] [INFO] Task started: HMMsearch
[2023-06-12 23:06:26,561] [INFO] Running command: hmmsearch --tblout GCA_938005455.1_ERR912063_bin.113_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2847267c-7258-4e0d-b3f3-35299b287a77/dqc_reference/reference_markers.hmm GCA_938005455.1_ERR912063_bin.113_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-12 23:06:26,823] [INFO] Task succeeded: HMMsearch
[2023-06-12 23:06:26,824] [INFO] Found 6/6 markers.
[2023-06-12 23:06:26,855] [INFO] Query marker FASTA was written to GCA_938005455.1_ERR912063_bin.113_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-12 23:06:26,855] [INFO] Task started: Blastn
[2023-06-12 23:06:26,856] [INFO] Running command: blastn -query GCA_938005455.1_ERR912063_bin.113_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg2847267c-7258-4e0d-b3f3-35299b287a77/dqc_reference/reference_markers.fasta -out GCA_938005455.1_ERR912063_bin.113_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-12 23:06:27,520] [INFO] Task succeeded: Blastn
[2023-06-12 23:06:27,525] [INFO] Selected 29 target genomes.
[2023-06-12 23:06:27,525] [INFO] Target genome list was writen to GCA_938005455.1_ERR912063_bin.113_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-12 23:06:27,531] [INFO] Task started: fastANI
[2023-06-12 23:06:27,531] [INFO] Running command: fastANI --query /var/lib/cwl/stg3e88adb6-c7ca-4afc-ac5a-c795f7bc6edd/GCA_938005455.1_ERR912063_bin.113_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_938005455.1_ERR912063_bin.113_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_938005455.1_ERR912063_bin.113_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-12 23:06:44,298] [INFO] Task succeeded: fastANI
[2023-06-12 23:06:44,299] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2847267c-7258-4e0d-b3f3-35299b287a77/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-12 23:06:44,300] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2847267c-7258-4e0d-b3f3-35299b287a77/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-12 23:06:44,321] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2023-06-12 23:06:44,321] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-12 23:06:44,321] [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
Blautia intestinalis	strain=27-44	GCA_014297355.1	2763028	2763028	type	True	77.6115	97	992	95	below_threshold
Jingyaoa shaoxingensis	strain=NSJ-46	GCA_014385005.1	2763671	2763671	type	True	77.5923	116	992	95	below_threshold
Blautia massiliensis	strain=GD9	GCA_001487165.1	1737424	1737424	type	True	77.4309	104	992	95	below_threshold
Hominisplanchenecus faecis	strain=CLA-AA-H246	GCA_020687205.1	2885351	2885351	type	True	77.2587	132	992	95	below_threshold
Marvinbryantia formatexigens	strain=DSM 14469	GCA_025148285.1	168384	168384	type	True	77.0453	116	992	95	below_threshold
Marvinbryantia formatexigens	strain=I-52	GCA_900102475.1	168384	168384	type	True	77.0391	117	992	95	below_threshold
Marvinbryantia formatexigens	strain=DSM 14469	GCA_000173815.1	168384	168384	type	True	77.0267	114	992	95	below_threshold
Blautia marasmi	strain=Marseille-P2377	GCA_900258535.1	1917868	1917868	suspected-type	True	76.8589	53	992	95	below_threshold
Coprococcus catus	strain=ATCC 27761	GCA_025289135.1	116085	116085	suspected-type	True	76.8131	56	992	95	below_threshold
Blautia coccoides	strain=NCTC11035	GCA_900461125.1	1532	1532	type	True	76.3237	60	992	95	below_threshold
Coprococcus comes	strain=ATCC 27758	GCA_025149785.1	410072	410072	type	True	76.321	78	992	95	below_threshold
Blautia coccoides	strain=DSM 935	GCA_004340925.1	1532	1532	type	True	76.2798	59	992	95	below_threshold
Murimonas intestini	strain=DSM 26524	GCA_024622195.1	1337051	1337051	type	True	76.2664	65	992	95	below_threshold
Blautia pseudococcoides	strain=YL58	GCA_002221555.2	1796616	1796616	type	True	76.1706	50	992	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_025152275.1	33038	33038	type	True	76.1677	67	992	95	below_threshold
Blautia pseudococcoides	strain=YL58	GCA_016696745.1	1796616	1796616	type	True	76.1622	53	992	95	below_threshold
Blautia pseudococcoides	strain=YL58	GCA_001689125.2	1796616	1796616	type	True	76.1622	53	992	95	below_threshold
Hungatella effluvii	strain=DSM 24995	GCA_003201875.1	1096246	1096246	type	True	76.0059	50	992	95	below_threshold
Blautia producta	strain=ATCC 27340	GCA_000373885.1	33035	33035	suspected-type	True	75.9588	60	992	95	below_threshold
Blautia producta	strain=DSM 2950	GCA_014131715.1	33035	33035	suspected-type	True	75.933	61	992	95	below_threshold
Blautia producta	strain=DSM 2950	GCA_000439125.1	33035	33035	suspected-type	True	75.9176	61	992	95	below_threshold
Roseburia porci	strain=MUC/MUC-530-WT-4D	GCA_009695765.1	2605790	2605790	type	True	75.6807	54	992	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-12 23:06:44,329] [INFO] DFAST Taxonomy check result was written to GCA_938005455.1_ERR912063_bin.113_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-12 23:06:44,329] [INFO] ===== Taxonomy check completed =====
[2023-06-12 23:06:44,330] [INFO] ===== Start completeness check using CheckM =====
[2023-06-12 23:06:44,330] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2847267c-7258-4e0d-b3f3-35299b287a77/dqc_reference/checkm_data
[2023-06-12 23:06:44,331] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-12 23:06:44,371] [INFO] Task started: CheckM
[2023-06-12 23:06:44,372] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_938005455.1_ERR912063_bin.113_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_938005455.1_ERR912063_bin.113_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_938005455.1_ERR912063_bin.113_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-12 23:07:12,929] [INFO] Task succeeded: CheckM
[2023-06-12 23:07:12,930] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-12 23:07:12,950] [INFO] ===== Completeness check finished =====
[2023-06-12 23:07:12,950] [INFO] ===== Start GTDB Search =====
[2023-06-12 23:07:12,950] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_938005455.1_ERR912063_bin.113_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-12 23:07:12,951] [INFO] Task started: Blastn
[2023-06-12 23:07:12,951] [INFO] Running command: blastn -query GCA_938005455.1_ERR912063_bin.113_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg2847267c-7258-4e0d-b3f3-35299b287a77/dqc_reference/reference_markers_gtdb.fasta -out GCA_938005455.1_ERR912063_bin.113_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-12 23:07:14,017] [INFO] Task succeeded: Blastn
[2023-06-12 23:07:14,022] [INFO] Selected 23 target genomes.
[2023-06-12 23:07:14,022] [INFO] Target genome list was writen to GCA_938005455.1_ERR912063_bin.113_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-12 23:07:14,031] [INFO] Task started: fastANI
[2023-06-12 23:07:14,032] [INFO] Running command: fastANI --query /var/lib/cwl/stg3e88adb6-c7ca-4afc-ac5a-c795f7bc6edd/GCA_938005455.1_ERR912063_bin.113_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_938005455.1_ERR912063_bin.113_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_938005455.1_ERR912063_bin.113_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-12 23:07:26,585] [INFO] Task succeeded: fastANI
[2023-06-12 23:07:26,601] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-12 23:07:26,601] [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_902363665.1	s__Choladousia sp902363665	98.3662	921	992	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Choladousia	95.0	97.59	97.59	0.93	0.93	2	conclusive
GCA_902363135.1	s__Choladousia sp902363135	79.6489	369	992	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Choladousia	95.0	98.66	98.47	0.96	0.95	4	-
GCA_900757145.1	s__Choladousia sp900757145	78.1395	111	992	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Choladousia	95.0	99.16	99.16	0.96	0.96	2	-
GCA_002491565.1	s__Choladousia sp002491565	78.0108	223	992	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Choladousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003612585.1	s__Choladousia sp003612585	77.7919	147	992	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Choladousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902363685.1	s__UMGS1375 sp900066615	77.2372	138	992	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UMGS1375	95.0	98.15	97.87	0.85	0.79	16	-
GCA_018711885.1	s__Choladousia intestinipullorum	77.2298	137	992	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Choladousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018223365.1	s__Choladocola sp018223365	77.1003	91	992	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Choladocola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003480315.1	s__Ventrimonas sp003480315	77.0924	70	992	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	98.62	98.00	0.91	0.88	5	-
GCA_900551235.1	s__UMGS1375 sp900551235	77.0737	107	992	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UMGS1375	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000173815.1	s__Marvinbryantia formatexigens	77.0257	115	992	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Marvinbryantia	95.0	99.98	99.98	0.99	0.99	3	-
GCA_905214955.1	s__Limivivens sp905214955	76.9969	98	992	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Limivivens	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900539525.1	s__CAG-56 sp900539525	76.9897	93	992	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-56	95.0	99.91	99.91	0.93	0.93	2	-
GCA_900539175.1	s__Pelethocola sp900539175	76.9275	50	992	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Pelethocola	95.0	99.69	99.49	0.84	0.76	3	-
GCA_018366495.1	s__JAGZHZ01 sp018366495	76.6622	64	992	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__JAGZHZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905207905.1	s__Merdiplasma sp905207905	76.5423	55	992	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Merdiplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014287615.1	s__Blautia sp001304935	76.2066	61	992	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia	95.0	99.32	98.73	0.92	0.87	9	-
GCA_900771955.1	s__CAG-45 sp900771955	76.1579	61	992	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-45	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900549015.1	s__Blautia_A sp900549015	76.0163	53	992	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	98.81	98.01	0.88	0.88	3	-
--------------------------------------------------------------------------------
[2023-06-12 23:07:26,603] [INFO] GTDB search result was written to GCA_938005455.1_ERR912063_bin.113_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-12 23:07:26,603] [INFO] ===== GTDB Search completed =====
[2023-06-12 23:07:26,608] [INFO] DFAST_QC result json was written to GCA_938005455.1_ERR912063_bin.113_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-12 23:07:26,608] [INFO] DFAST_QC completed!
[2023-06-12 23:07:26,608] [INFO] Total running time: 0h1m9s