[2024-01-24 13:08:58,313] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:08:58,315] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:08:58,316] [INFO] DQC Reference Directory: /var/lib/cwl/stg6264ab38-411b-4ab2-9cf7-d4310de3471b/dqc_reference
[2024-01-24 13:08:59,512] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:08:59,513] [INFO] Task started: Prodigal
[2024-01-24 13:08:59,513] [INFO] Running command: gunzip -c /var/lib/cwl/stgf2ca23ff-1633-4b7a-b3c8-896c1d4c3c6f/GCF_900113155.1_IMG-taxon_2593339147_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900113155.1_IMG-taxon_2593339147_annotated_assembly_genomic.fna/cds.fna -a GCF_900113155.1_IMG-taxon_2593339147_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:09:13,619] [INFO] Task succeeded: Prodigal
[2024-01-24 13:09:13,619] [INFO] Task started: HMMsearch
[2024-01-24 13:09:13,620] [INFO] Running command: hmmsearch --tblout GCF_900113155.1_IMG-taxon_2593339147_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6264ab38-411b-4ab2-9cf7-d4310de3471b/dqc_reference/reference_markers.hmm GCF_900113155.1_IMG-taxon_2593339147_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:09:13,940] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:09:13,942] [INFO] Found 6/6 markers.
[2024-01-24 13:09:13,992] [INFO] Query marker FASTA was written to GCF_900113155.1_IMG-taxon_2593339147_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:09:13,993] [INFO] Task started: Blastn
[2024-01-24 13:09:13,993] [INFO] Running command: blastn -query GCF_900113155.1_IMG-taxon_2593339147_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg6264ab38-411b-4ab2-9cf7-d4310de3471b/dqc_reference/reference_markers.fasta -out GCF_900113155.1_IMG-taxon_2593339147_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:09:14,625] [INFO] Task succeeded: Blastn
[2024-01-24 13:09:14,629] [INFO] Selected 10 target genomes.
[2024-01-24 13:09:14,629] [INFO] Target genome list was writen to GCF_900113155.1_IMG-taxon_2593339147_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:09:14,639] [INFO] Task started: fastANI
[2024-01-24 13:09:14,639] [INFO] Running command: fastANI --query /var/lib/cwl/stgf2ca23ff-1633-4b7a-b3c8-896c1d4c3c6f/GCF_900113155.1_IMG-taxon_2593339147_annotated_assembly_genomic.fna.gz --refList GCF_900113155.1_IMG-taxon_2593339147_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900113155.1_IMG-taxon_2593339147_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:09:25,909] [INFO] Task succeeded: fastANI
[2024-01-24 13:09:25,909] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6264ab38-411b-4ab2-9cf7-d4310de3471b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:09:25,909] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6264ab38-411b-4ab2-9cf7-d4310de3471b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:09:25,918] [INFO] Found 9 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:09:25,918] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:09:25,918] [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
Enterocloster clostridioformis	strain=ATCC 25537	GCA_900113155.1	1531	1531	type	True	100.0	1730	1743	95	conclusive
Enterocloster clostridioformis	strain=NCTC11224	GCA_900447015.1	1531	1531	suspected-type	True	97.723	1342	1743	95	conclusive
Enterocloster clostridioformis	strain=FDAARGOS_1529	GCA_020297485.1	1531	1531	suspected-type	True	97.6349	1353	1743	95	conclusive
Enterocloster bolteae	strain=ATCC BAA-613	GCA_000154365.1	208479	208479	type	True	91.4566	1196	1743	95	below_threshold
Enterocloster bolteae	strain=ATCC BAA-613	GCA_002959675.1	208479	208479	type	True	91.3978	1213	1743	95	below_threshold
Eisenbergiella massiliensis	strain=AT11	GCA_900243045.1	1720294	1720294	type	True	78.61	120	1743	95	below_threshold
Enterocloster asparagiformis	strain=DSM 15981	GCA_025149125.1	333367	333367	type	True	78.1571	391	1743	95	below_threshold
Hungatella hathewayi	strain=DSM 13479	GCA_025149285.1	154046	154046	suspected-type	True	78.0114	199	1743	95	below_threshold
Eisenbergiella porci	strain=WCA-389-WT-23B	GCA_009696275.1	2652274	2652274	type	True	77.8303	130	1743	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:09:25,920] [INFO] DFAST Taxonomy check result was written to GCF_900113155.1_IMG-taxon_2593339147_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:09:25,920] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:09:25,920] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:09:25,920] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6264ab38-411b-4ab2-9cf7-d4310de3471b/dqc_reference/checkm_data
[2024-01-24 13:09:25,922] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:09:25,972] [INFO] Task started: CheckM
[2024-01-24 13:09:25,972] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900113155.1_IMG-taxon_2593339147_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900113155.1_IMG-taxon_2593339147_annotated_assembly_genomic.fna/checkm_input GCF_900113155.1_IMG-taxon_2593339147_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:10:10,190] [INFO] Task succeeded: CheckM
[2024-01-24 13:10:10,192] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:10:10,213] [INFO] ===== Completeness check finished =====
[2024-01-24 13:10:10,214] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:10:10,214] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900113155.1_IMG-taxon_2593339147_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:10:10,215] [INFO] Task started: Blastn
[2024-01-24 13:10:10,215] [INFO] Running command: blastn -query GCF_900113155.1_IMG-taxon_2593339147_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg6264ab38-411b-4ab2-9cf7-d4310de3471b/dqc_reference/reference_markers_gtdb.fasta -out GCF_900113155.1_IMG-taxon_2593339147_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:11,301] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:11,305] [INFO] Selected 8 target genomes.
[2024-01-24 13:10:11,305] [INFO] Target genome list was writen to GCF_900113155.1_IMG-taxon_2593339147_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:10:11,339] [INFO] Task started: fastANI
[2024-01-24 13:10:11,339] [INFO] Running command: fastANI --query /var/lib/cwl/stgf2ca23ff-1633-4b7a-b3c8-896c1d4c3c6f/GCF_900113155.1_IMG-taxon_2593339147_annotated_assembly_genomic.fna.gz --refList GCF_900113155.1_IMG-taxon_2593339147_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900113155.1_IMG-taxon_2593339147_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:10:21,244] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:21,259] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:10:21,259] [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_900113155.1	s__Enterocloster clostridioformis	100.0	1730	1743	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	98.82	97.34	0.84	0.75	45	conclusive
GCF_000424325.1	s__Enterocloster clostridioformis_A	93.5466	1142	1743	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	99.02	99.02	0.92	0.92	2	-
GCF_002234575.2	s__Enterocloster bolteae	91.4373	1215	1743	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	98.46	96.97	0.88	0.78	35	-
GCF_005845215.1	s__Enterocloster sp005845215	88.568	1131	1743	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	99.62	99.13	0.95	0.86	6	-
GCF_003434055.1	s__Enterocloster aldenensis	80.5298	685	1743	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	99.16	97.51	0.89	0.78	13	-
GCA_000155435.1	s__Enterocloster sp000155435	80.3589	690	1743	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	99.08	98.70	0.90	0.83	5	-
GCF_000233455.1	s__Enterocloster citroniae	80.1053	668	1743	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	99.23	99.13	0.87	0.84	10	-
GCA_900547035.1	s__Enterocloster excrementigallinarum	77.5034	208	1743	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	98.35	98.28	0.80	0.77	6	-
--------------------------------------------------------------------------------
[2024-01-24 13:10:21,261] [INFO] GTDB search result was written to GCF_900113155.1_IMG-taxon_2593339147_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:10:21,261] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:10:21,264] [INFO] DFAST_QC result json was written to GCF_900113155.1_IMG-taxon_2593339147_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:10:21,264] [INFO] DFAST_QC completed!
[2024-01-24 13:10:21,264] [INFO] Total running time: 0h1m23s