[2023-06-28 03:25:03,236] [INFO] DFAST_QC pipeline started.
[2023-06-28 03:25:03,239] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 03:25:03,240] [INFO] DQC Reference Directory: /var/lib/cwl/stgbd70f3ca-b032-45c0-8bd6-d56cbd7bc63b/dqc_reference
[2023-06-28 03:25:04,542] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 03:25:04,543] [INFO] Task started: Prodigal
[2023-06-28 03:25:04,543] [INFO] Running command: gunzip -c /var/lib/cwl/stga35b9015-a0e7-4090-b612-dcd83c4382d4/GCA_944321845.1_E02_bin299_genomic.fna.gz | prodigal -d GCA_944321845.1_E02_bin299_genomic.fna/cds.fna -a GCA_944321845.1_E02_bin299_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 03:25:19,351] [INFO] Task succeeded: Prodigal
[2023-06-28 03:25:19,351] [INFO] Task started: HMMsearch
[2023-06-28 03:25:19,351] [INFO] Running command: hmmsearch --tblout GCA_944321845.1_E02_bin299_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbd70f3ca-b032-45c0-8bd6-d56cbd7bc63b/dqc_reference/reference_markers.hmm GCA_944321845.1_E02_bin299_genomic.fna/protein.faa > /dev/null
[2023-06-28 03:25:19,621] [INFO] Task succeeded: HMMsearch
[2023-06-28 03:25:19,622] [INFO] Found 6/6 markers.
[2023-06-28 03:25:19,649] [INFO] Query marker FASTA was written to GCA_944321845.1_E02_bin299_genomic.fna/markers.fasta
[2023-06-28 03:25:19,649] [INFO] Task started: Blastn
[2023-06-28 03:25:19,649] [INFO] Running command: blastn -query GCA_944321845.1_E02_bin299_genomic.fna/markers.fasta -db /var/lib/cwl/stgbd70f3ca-b032-45c0-8bd6-d56cbd7bc63b/dqc_reference/reference_markers.fasta -out GCA_944321845.1_E02_bin299_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 03:25:20,300] [INFO] Task succeeded: Blastn
[2023-06-28 03:25:20,306] [INFO] Selected 17 target genomes.
[2023-06-28 03:25:20,306] [INFO] Target genome list was writen to GCA_944321845.1_E02_bin299_genomic.fna/target_genomes.txt
[2023-06-28 03:25:20,308] [INFO] Task started: fastANI
[2023-06-28 03:25:20,308] [INFO] Running command: fastANI --query /var/lib/cwl/stga35b9015-a0e7-4090-b612-dcd83c4382d4/GCA_944321845.1_E02_bin299_genomic.fna.gz --refList GCA_944321845.1_E02_bin299_genomic.fna/target_genomes.txt --output GCA_944321845.1_E02_bin299_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 03:25:32,437] [INFO] Task succeeded: fastANI
[2023-06-28 03:25:32,438] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbd70f3ca-b032-45c0-8bd6-d56cbd7bc63b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 03:25:32,438] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbd70f3ca-b032-45c0-8bd6-d56cbd7bc63b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 03:25:32,453] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 03:25:32,453] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 03:25:32,454] [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
Butyricimonas virosa	strain=DSM 23226	GCA_025148635.1	544645	544645	type	True	77.7013	185	866	95	below_threshold
Butyricimonas faecalis	strain=vagina	GCA_900258545.1	2093856	2093856	type	True	77.6286	184	866	95	below_threshold
Butyricimonas virosa	strain=DSM 23226	GCA_000519105.1	544645	544645	type	True	77.6097	182	866	95	below_threshold
Butyricimonas faecalis	strain=H184	GCA_003991565.1	2093856	2093856	type	True	77.5645	180	866	95	below_threshold
Butyricimonas paravirosa	strain=DSM 105722	GCA_011927845.1	1472417	1472417	type	True	77.4997	186	866	95	below_threshold
Butyricimonas synergistica	strain=DSM 23225	GCA_000379665.1	544644	544644	type	True	77.4734	201	866	95	below_threshold
Butyricimonas paravirosa	strain=JCM 18677	GCA_014647355.1	1472417	1472417	type	True	77.4541	186	866	95	below_threshold
Butyricimonas faecihominis	strain=DSM 105721	GCA_014196975.1	1472416	1472416	type	True	77.3989	181	866	95	below_threshold
Butyricimonas faecihominis	strain=JCM 18676	GCA_014647335.1	1472416	1472416	type	True	77.331	181	866	95	below_threshold
Odoribacter splanchnicus	strain=NCTC10825	GCA_900187175.1	28118	28118	type	True	76.3253	72	866	95	below_threshold
Odoribacter splanchnicus	strain=DSM 220712	GCA_000190535.1	28118	28118	type	True	76.3177	71	866	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 03:25:32,456] [INFO] DFAST Taxonomy check result was written to GCA_944321845.1_E02_bin299_genomic.fna/tc_result.tsv
[2023-06-28 03:25:32,456] [INFO] ===== Taxonomy check completed =====
[2023-06-28 03:25:32,456] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 03:25:32,457] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbd70f3ca-b032-45c0-8bd6-d56cbd7bc63b/dqc_reference/checkm_data
[2023-06-28 03:25:32,458] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 03:25:32,488] [INFO] Task started: CheckM
[2023-06-28 03:25:32,489] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_944321845.1_E02_bin299_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_944321845.1_E02_bin299_genomic.fna/checkm_input GCA_944321845.1_E02_bin299_genomic.fna/checkm_result
[2023-06-28 03:26:16,774] [INFO] Task succeeded: CheckM
[2023-06-28 03:26:16,775] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 03:26:16,795] [INFO] ===== Completeness check finished =====
[2023-06-28 03:26:16,796] [INFO] ===== Start GTDB Search =====
[2023-06-28 03:26:16,796] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_944321845.1_E02_bin299_genomic.fna/markers.fasta)
[2023-06-28 03:26:16,796] [INFO] Task started: Blastn
[2023-06-28 03:26:16,796] [INFO] Running command: blastn -query GCA_944321845.1_E02_bin299_genomic.fna/markers.fasta -db /var/lib/cwl/stgbd70f3ca-b032-45c0-8bd6-d56cbd7bc63b/dqc_reference/reference_markers_gtdb.fasta -out GCA_944321845.1_E02_bin299_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 03:26:17,558] [INFO] Task succeeded: Blastn
[2023-06-28 03:26:17,563] [INFO] Selected 17 target genomes.
[2023-06-28 03:26:17,564] [INFO] Target genome list was writen to GCA_944321845.1_E02_bin299_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 03:26:17,611] [INFO] Task started: fastANI
[2023-06-28 03:26:17,611] [INFO] Running command: fastANI --query /var/lib/cwl/stga35b9015-a0e7-4090-b612-dcd83c4382d4/GCA_944321845.1_E02_bin299_genomic.fna.gz --refList GCA_944321845.1_E02_bin299_genomic.fna/target_genomes_gtdb.txt --output GCA_944321845.1_E02_bin299_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 03:26:29,837] [INFO] Task succeeded: fastANI
[2023-06-28 03:26:29,854] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 03:26:29,854] [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_900184685.1	s__Butyricimonas sp900184685	77.6274	182	866	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Butyricimonas	95.0	97.37	96.90	0.86	0.81	4	-
GCF_000519105.1	s__Butyricimonas virosa	77.6097	182	866	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Butyricimonas	95.0	98.30	95.30	0.86	0.78	18	-
GCF_003991565.1	s__Butyricimonas faecalis	77.582	180	866	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Butyricimonas	95.0	98.78	97.96	0.89	0.85	6	-
GCF_011927845.1	s__Butyricimonas paravirosa	77.5164	185	866	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Butyricimonas	95.0	98.86	97.78	0.90	0.83	11	-
GCF_000379665.1	s__Butyricimonas synergistica	77.4887	200	866	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Butyricimonas	95.0	98.02	98.02	0.85	0.85	3	-
GCF_003479425.1	s__Butyricimonas sp003479425	77.4198	191	866	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Butyricimonas	95.0	99.97	99.94	0.99	0.98	3	-
GCA_900761485.1	s__Butyricimonas sp900761485	77.3824	142	866	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Butyricimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014647335.1	s__Butyricimonas faecihominis	77.3455	180	866	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Butyricimonas	95.0	99.47	98.30	0.95	0.86	7	-
GCA_019117165.1	s__Butyricimonas faecavium	77.3141	138	866	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Butyricimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900759925.1	s__Butyricimonas sp900759925	77.306	177	866	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Butyricimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900541415.1	s__Odoribacter sp900541415	76.3422	63	866	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Odoribacter	95.0	99.97	99.97	0.96	0.96	2	-
GCF_000190535.1	s__Odoribacter splanchnicus	76.3151	71	866	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Odoribacter	95.0	98.99	98.34	0.85	0.73	51	-
GCA_910578985.1	s__Odoribacter sp910578985	76.0754	52	866	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Odoribacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 03:26:29,856] [INFO] GTDB search result was written to GCA_944321845.1_E02_bin299_genomic.fna/result_gtdb.tsv
[2023-06-28 03:26:29,857] [INFO] ===== GTDB Search completed =====
[2023-06-28 03:26:29,860] [INFO] DFAST_QC result json was written to GCA_944321845.1_E02_bin299_genomic.fna/dqc_result.json
[2023-06-28 03:26:29,860] [INFO] DFAST_QC completed!
[2023-06-28 03:26:29,861] [INFO] Total running time: 0h1m27s