[2023-06-07 20:39:43,443] [INFO] DFAST_QC pipeline started.
[2023-06-07 20:39:43,445] [INFO] DFAST_QC version: 0.5.7
[2023-06-07 20:39:43,446] [INFO] DQC Reference Directory: /var/lib/cwl/stg318f282c-8352-4a87-966e-859a1b2a81b2/dqc_reference
[2023-06-07 20:39:44,752] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-07 20:39:44,753] [INFO] Task started: Prodigal
[2023-06-07 20:39:44,754] [INFO] Running command: gunzip -c /var/lib/cwl/stgddf365c0-dee2-4210-b654-9caccd712234/GCA_947384795.1_ERR6760091_bin.37_metawrap_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_947384795.1_ERR6760091_bin.37_metawrap_v1.3_MAG_genomic.fna/cds.fna -a GCA_947384795.1_ERR6760091_bin.37_metawrap_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-07 20:39:53,533] [INFO] Task succeeded: Prodigal
[2023-06-07 20:39:53,533] [INFO] Task started: HMMsearch
[2023-06-07 20:39:53,534] [INFO] Running command: hmmsearch --tblout GCA_947384795.1_ERR6760091_bin.37_metawrap_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg318f282c-8352-4a87-966e-859a1b2a81b2/dqc_reference/reference_markers.hmm GCA_947384795.1_ERR6760091_bin.37_metawrap_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-07 20:39:53,828] [INFO] Task succeeded: HMMsearch
[2023-06-07 20:39:53,830] [INFO] Found 6/6 markers.
[2023-06-07 20:39:53,864] [INFO] Query marker FASTA was written to GCA_947384795.1_ERR6760091_bin.37_metawrap_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-07 20:39:53,864] [INFO] Task started: Blastn
[2023-06-07 20:39:53,865] [INFO] Running command: blastn -query GCA_947384795.1_ERR6760091_bin.37_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg318f282c-8352-4a87-966e-859a1b2a81b2/dqc_reference/reference_markers.fasta -out GCA_947384795.1_ERR6760091_bin.37_metawrap_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 20:39:54,514] [INFO] Task succeeded: Blastn
[2023-06-07 20:39:54,526] [INFO] Selected 27 target genomes.
[2023-06-07 20:39:54,527] [INFO] Target genome list was writen to GCA_947384795.1_ERR6760091_bin.37_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-07 20:39:54,529] [INFO] Task started: fastANI
[2023-06-07 20:39:54,530] [INFO] Running command: fastANI --query /var/lib/cwl/stgddf365c0-dee2-4210-b654-9caccd712234/GCA_947384795.1_ERR6760091_bin.37_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947384795.1_ERR6760091_bin.37_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_947384795.1_ERR6760091_bin.37_metawrap_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-07 20:40:11,719] [INFO] Task succeeded: fastANI
[2023-06-07 20:40:11,719] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg318f282c-8352-4a87-966e-859a1b2a81b2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-07 20:40:11,719] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg318f282c-8352-4a87-966e-859a1b2a81b2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-07 20:40:11,732] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-06-07 20:40:11,732] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-07 20:40:11,733] [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
Marvinbryantia formatexigens	strain=I-52	GCA_900102475.1	168384	168384	type	True	77.094	53	1145	95	below_threshold
Marvinbryantia formatexigens	strain=DSM 14469	GCA_025148285.1	168384	168384	type	True	77.0554	52	1145	95	below_threshold
Enterocloster asparagiformis	strain=DSM 15981	GCA_000158075.1	333367	333367	type	True	76.4025	105	1145	95	below_threshold
Enterocloster asparagiformis	strain=DSM 15981	GCA_025149125.1	333367	333367	type	True	76.3779	111	1145	95	below_threshold
Hungatella hathewayi	strain=DSM 13479	GCA_025149285.1	154046	154046	suspected-type	True	76.2165	108	1145	95	below_threshold
Hungatella hathewayi	strain=DSM 13479	GCA_000160095.1	154046	154046	suspected-type	True	76.2125	96	1145	95	below_threshold
Lacrimispora sphenoides	strain=ATCC 19403	GCA_900105615.1	29370	29370	type	True	76.2033	75	1145	95	below_threshold
Lacrimispora sphenoides	strain=NCTC507	GCA_900461315.1	29370	29370	type	True	76.1617	75	1145	95	below_threshold
Diplocloster agilis	strain=ASD5720	GCA_019042275.1	2850323	2850323	type	True	76.1597	51	1145	95	below_threshold
Lacrimispora celerecrescens	strain=18A	GCA_002797975.1	29354	29354	type	True	76.1415	72	1145	95	below_threshold
Lacrimispora aerotolerans	strain=DSM 5434	GCA_000687555.1	36832	36832	type	True	76.1021	59	1145	95	below_threshold
Eisenbergiella porci	strain=WCA-389-WT-23B	GCA_009696275.1	2652274	2652274	type	True	75.773	50	1145	95	below_threshold
Blautia pseudococcoides	strain=YL58	GCA_002221555.2	1796616	1796616	type	True	75.3346	54	1145	95	below_threshold
Blautia pseudococcoides	strain=YL58	GCA_016696745.1	1796616	1796616	type	True	75.3331	54	1145	95	below_threshold
Blautia pseudococcoides	strain=YL58	GCA_001689125.2	1796616	1796616	type	True	75.3331	54	1145	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-07 20:40:11,735] [INFO] DFAST Taxonomy check result was written to GCA_947384795.1_ERR6760091_bin.37_metawrap_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-07 20:40:11,735] [INFO] ===== Taxonomy check completed =====
[2023-06-07 20:40:11,735] [INFO] ===== Start completeness check using CheckM =====
[2023-06-07 20:40:11,735] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg318f282c-8352-4a87-966e-859a1b2a81b2/dqc_reference/checkm_data
[2023-06-07 20:40:11,737] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-07 20:40:11,776] [INFO] Task started: CheckM
[2023-06-07 20:40:11,777] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947384795.1_ERR6760091_bin.37_metawrap_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947384795.1_ERR6760091_bin.37_metawrap_v1.3_MAG_genomic.fna/checkm_input GCA_947384795.1_ERR6760091_bin.37_metawrap_v1.3_MAG_genomic.fna/checkm_result
[2023-06-07 20:40:43,079] [INFO] Task succeeded: CheckM
[2023-06-07 20:40:43,080] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-07 20:40:43,108] [INFO] ===== Completeness check finished =====
[2023-06-07 20:40:43,109] [INFO] ===== Start GTDB Search =====
[2023-06-07 20:40:43,109] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947384795.1_ERR6760091_bin.37_metawrap_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-07 20:40:43,109] [INFO] Task started: Blastn
[2023-06-07 20:40:43,110] [INFO] Running command: blastn -query GCA_947384795.1_ERR6760091_bin.37_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg318f282c-8352-4a87-966e-859a1b2a81b2/dqc_reference/reference_markers_gtdb.fasta -out GCA_947384795.1_ERR6760091_bin.37_metawrap_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 20:40:44,163] [INFO] Task succeeded: Blastn
[2023-06-07 20:40:44,168] [INFO] Selected 18 target genomes.
[2023-06-07 20:40:44,169] [INFO] Target genome list was writen to GCA_947384795.1_ERR6760091_bin.37_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-07 20:40:44,187] [INFO] Task started: fastANI
[2023-06-07 20:40:44,187] [INFO] Running command: fastANI --query /var/lib/cwl/stgddf365c0-dee2-4210-b654-9caccd712234/GCA_947384795.1_ERR6760091_bin.37_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947384795.1_ERR6760091_bin.37_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_947384795.1_ERR6760091_bin.37_metawrap_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-07 20:40:58,164] [INFO] Task succeeded: fastANI
[2023-06-07 20:40:58,190] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-07 20:40:58,190] [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_910575255.1	s__Ventrimonas sp910575255	99.3266	1058	1145	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	99.31	99.12	0.89	0.88	4	conclusive
GCA_910588875.1	s__Ventrimonas sp910588875	82.5602	518	1145	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910586255.1	s__Ventrimonas sp910586255	80.2093	525	1145	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003669055.1	s__Ventrimonas sp003669055	80.1938	542	1145	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	100.00	100.00	1.00	1.00	2	-
GCA_910586205.1	s__Ventrimonas sp910586205	79.2116	417	1145	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003611875.1	s__Ventrimonas sp003611875	79.1815	456	1145	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	99.50	99.24	0.91	0.86	4	-
GCA_009911065.1	s__Ventrimonas sp009911065	78.5676	337	1145	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	95.78	95.73	0.75	0.73	3	-
GCA_910577655.1	s__Ventrimonas sp910577655	77.4672	239	1145	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018715565.1	s__Ventrimonas merdavium	77.0993	173	1145	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	99.46	99.46	0.97	0.97	2	-
GCA_004554205.1	s__Ventrimonas sp004554205	77.0787	128	1145	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900540335.1	s__Ventrimonas sp900540335	77.0314	178	1145	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	99.37	99.36	0.86	0.81	3	-
GCA_910584785.1	s__Caccovicinus sp910584785	76.783	111	1145	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Caccovicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018715905.1	s__Caccovicinus merdipullorum	76.7573	108	1145	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Caccovicinus	95.0	98.94	98.69	0.87	0.79	3	-
GCA_900770345.1	s__Enterocloster sp900770345	76.4207	119	1145	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000158075.1	s__Enterocloster asparagiformis	76.3808	105	1145	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	98.72	98.33	0.90	0.88	5	-
GCF_003477885.1	s__AF33-28 sp003477885	75.6216	53	1145	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__AF33-28	95.0	99.55	99.29	0.96	0.92	4	-
--------------------------------------------------------------------------------
[2023-06-07 20:40:58,192] [INFO] GTDB search result was written to GCA_947384795.1_ERR6760091_bin.37_metawrap_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-07 20:40:58,193] [INFO] ===== GTDB Search completed =====
[2023-06-07 20:40:58,197] [INFO] DFAST_QC result json was written to GCA_947384795.1_ERR6760091_bin.37_metawrap_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-07 20:40:58,197] [INFO] DFAST_QC completed!
[2023-06-07 20:40:58,197] [INFO] Total running time: 0h1m15s