[2023-06-08 17:48:00,956] [INFO] DFAST_QC pipeline started.
[2023-06-08 17:48:00,959] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 17:48:00,959] [INFO] DQC Reference Directory: /var/lib/cwl/stg7fde51fa-3775-4841-bafb-17bc62ba2297/dqc_reference
[2023-06-08 17:48:02,195] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 17:48:02,196] [INFO] Task started: Prodigal
[2023-06-08 17:48:02,196] [INFO] Running command: gunzip -c /var/lib/cwl/stgaba8dba3-cb5d-4d19-a023-eb68616dc7ad/GCA_947074795.1_SRR13169514_bin.13_metawrap_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_947074795.1_SRR13169514_bin.13_metawrap_v1.3_MAG_genomic.fna/cds.fna -a GCA_947074795.1_SRR13169514_bin.13_metawrap_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 17:48:17,845] [INFO] Task succeeded: Prodigal
[2023-06-08 17:48:17,845] [INFO] Task started: HMMsearch
[2023-06-08 17:48:17,846] [INFO] Running command: hmmsearch --tblout GCA_947074795.1_SRR13169514_bin.13_metawrap_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7fde51fa-3775-4841-bafb-17bc62ba2297/dqc_reference/reference_markers.hmm GCA_947074795.1_SRR13169514_bin.13_metawrap_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 17:48:18,043] [INFO] Task succeeded: HMMsearch
[2023-06-08 17:48:18,044] [INFO] Found 6/6 markers.
[2023-06-08 17:48:18,071] [INFO] Query marker FASTA was written to GCA_947074795.1_SRR13169514_bin.13_metawrap_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 17:48:18,071] [INFO] Task started: Blastn
[2023-06-08 17:48:18,071] [INFO] Running command: blastn -query GCA_947074795.1_SRR13169514_bin.13_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg7fde51fa-3775-4841-bafb-17bc62ba2297/dqc_reference/reference_markers.fasta -out GCA_947074795.1_SRR13169514_bin.13_metawrap_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 17:48:18,644] [INFO] Task succeeded: Blastn
[2023-06-08 17:48:18,648] [INFO] Selected 22 target genomes.
[2023-06-08 17:48:18,648] [INFO] Target genome list was writen to GCA_947074795.1_SRR13169514_bin.13_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 17:48:18,649] [INFO] Task started: fastANI
[2023-06-08 17:48:18,650] [INFO] Running command: fastANI --query /var/lib/cwl/stgaba8dba3-cb5d-4d19-a023-eb68616dc7ad/GCA_947074795.1_SRR13169514_bin.13_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947074795.1_SRR13169514_bin.13_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_947074795.1_SRR13169514_bin.13_metawrap_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 17:48:30,579] [INFO] Task succeeded: fastANI
[2023-06-08 17:48:30,579] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7fde51fa-3775-4841-bafb-17bc62ba2297/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 17:48:30,579] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7fde51fa-3775-4841-bafb-17bc62ba2297/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 17:48:30,587] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 17:48:30,587] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 17:48:30,587] [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
Duncaniella dubosii	strain=H5	GCA_004803915.1	2518971	2518971	type	True	80.035	66	945	95	below_threshold
Duncaniella muris	strain=DSM 103720	GCA_003024805.1	2094150	2094150	type	True	79.1786	74	945	95	below_threshold
Muribaculum intestinale	strain=YL27	GCA_016696845.1	1796646	1796646	type	True	79.1691	72	945	95	below_threshold
Muribaculum intestinale	strain=YL27	GCA_001688845.2	1796646	1796646	type	True	79.0538	74	945	95	below_threshold
Muribaculum intestinale	strain=YL27	GCA_002201515.1	1796646	1796646	type	True	78.9909	72	945	95	below_threshold
Muribaculum gordoncarteri	strain=TLL-A4	GCA_004803695.1	2530390	2530390	type	True	78.5831	51	945	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 17:48:30,606] [INFO] DFAST Taxonomy check result was written to GCA_947074795.1_SRR13169514_bin.13_metawrap_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 17:48:30,606] [INFO] ===== Taxonomy check completed =====
[2023-06-08 17:48:30,607] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 17:48:30,607] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7fde51fa-3775-4841-bafb-17bc62ba2297/dqc_reference/checkm_data
[2023-06-08 17:48:30,608] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 17:48:30,638] [INFO] Task started: CheckM
[2023-06-08 17:48:30,638] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947074795.1_SRR13169514_bin.13_metawrap_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947074795.1_SRR13169514_bin.13_metawrap_v1.3_MAG_genomic.fna/checkm_input GCA_947074795.1_SRR13169514_bin.13_metawrap_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 17:49:16,215] [INFO] Task succeeded: CheckM
[2023-06-08 17:49:16,216] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 17:49:16,233] [INFO] ===== Completeness check finished =====
[2023-06-08 17:49:16,233] [INFO] ===== Start GTDB Search =====
[2023-06-08 17:49:16,233] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947074795.1_SRR13169514_bin.13_metawrap_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 17:49:16,234] [INFO] Task started: Blastn
[2023-06-08 17:49:16,234] [INFO] Running command: blastn -query GCA_947074795.1_SRR13169514_bin.13_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg7fde51fa-3775-4841-bafb-17bc62ba2297/dqc_reference/reference_markers_gtdb.fasta -out GCA_947074795.1_SRR13169514_bin.13_metawrap_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 17:49:17,032] [INFO] Task succeeded: Blastn
[2023-06-08 17:49:17,036] [INFO] Selected 14 target genomes.
[2023-06-08 17:49:17,036] [INFO] Target genome list was writen to GCA_947074795.1_SRR13169514_bin.13_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 17:49:17,040] [INFO] Task started: fastANI
[2023-06-08 17:49:17,040] [INFO] Running command: fastANI --query /var/lib/cwl/stgaba8dba3-cb5d-4d19-a023-eb68616dc7ad/GCA_947074795.1_SRR13169514_bin.13_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947074795.1_SRR13169514_bin.13_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_947074795.1_SRR13169514_bin.13_metawrap_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 17:49:24,666] [INFO] Task succeeded: fastANI
[2023-06-08 17:49:24,678] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 17:49:24,678] [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_003833075.1	s__CAG-485 sp002362485	98.9641	854	945	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	98.88	97.97	0.89	0.83	18	conclusive
GCA_910585285.1	s__CAG-485 sp910585285	79.3941	362	945	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910584055.1	s__CAG-485 sp910584055	78.8169	370	945	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014802175.1	s__CAG-485 sp014802175	78.6118	178	945	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	97.58	97.46	0.67	0.65	3	-
GCA_910578075.1	s__CAG-485 sp910578075	78.4332	288	945	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900549375.1	s__CAG-485 sp900549375	78.331	171	945	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	96.66	96.66	0.84	0.84	2	-
GCA_910578385.1	s__CAG-485 sp910578385	77.4788	125	945	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014867205.1	s__CAG-485 sp014867205	77.3455	116	945	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910585275.1	s__CAG-485 sp910585275	77.2676	107	945	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910579845.1	s__CAG-485 sp910579845	77.2347	135	945	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002361155.1	s__CAG-485 sp002361155	76.8265	62	945	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	99.36	98.51	0.82	0.74	7	-
GCA_910589425.1	s__CAG-485 sp910589425	76.7377	69	945	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900554845.1	s__CAG-485 sp900554845	75.9918	52	945	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	97.47	97.47	0.85	0.85	2	-
--------------------------------------------------------------------------------
[2023-06-08 17:49:24,680] [INFO] GTDB search result was written to GCA_947074795.1_SRR13169514_bin.13_metawrap_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 17:49:24,681] [INFO] ===== GTDB Search completed =====
[2023-06-08 17:49:24,684] [INFO] DFAST_QC result json was written to GCA_947074795.1_SRR13169514_bin.13_metawrap_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 17:49:24,684] [INFO] DFAST_QC completed!
[2023-06-08 17:49:24,684] [INFO] Total running time: 0h1m24s