[2023-06-07 18:45:02,797] [INFO] DFAST_QC pipeline started.
[2023-06-07 18:45:02,801] [INFO] DFAST_QC version: 0.5.7
[2023-06-07 18:45:02,801] [INFO] DQC Reference Directory: /var/lib/cwl/stg817f2f37-9ddf-4b6e-9442-aab27f4f07c5/dqc_reference
[2023-06-07 18:45:04,619] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-07 18:45:04,620] [INFO] Task started: Prodigal
[2023-06-07 18:45:04,620] [INFO] Running command: gunzip -c /var/lib/cwl/stg8598e08a-74c7-42f6-8542-981eb5213ba0/GCA_949122875.1_ERR4467353_bin.5_metawrap_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_949122875.1_ERR4467353_bin.5_metawrap_v1.3_MAG_genomic.fna/cds.fna -a GCA_949122875.1_ERR4467353_bin.5_metawrap_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-07 18:45:20,339] [INFO] Task succeeded: Prodigal
[2023-06-07 18:45:20,340] [INFO] Task started: HMMsearch
[2023-06-07 18:45:20,340] [INFO] Running command: hmmsearch --tblout GCA_949122875.1_ERR4467353_bin.5_metawrap_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg817f2f37-9ddf-4b6e-9442-aab27f4f07c5/dqc_reference/reference_markers.hmm GCA_949122875.1_ERR4467353_bin.5_metawrap_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-07 18:45:20,544] [INFO] Task succeeded: HMMsearch
[2023-06-07 18:45:20,545] [INFO] Found 6/6 markers.
[2023-06-07 18:45:20,571] [INFO] Query marker FASTA was written to GCA_949122875.1_ERR4467353_bin.5_metawrap_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-07 18:45:20,571] [INFO] Task started: Blastn
[2023-06-07 18:45:20,571] [INFO] Running command: blastn -query GCA_949122875.1_ERR4467353_bin.5_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg817f2f37-9ddf-4b6e-9442-aab27f4f07c5/dqc_reference/reference_markers.fasta -out GCA_949122875.1_ERR4467353_bin.5_metawrap_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 18:45:21,114] [INFO] Task succeeded: Blastn
[2023-06-07 18:45:21,117] [INFO] Selected 18 target genomes.
[2023-06-07 18:45:21,117] [INFO] Target genome list was writen to GCA_949122875.1_ERR4467353_bin.5_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-07 18:45:21,120] [INFO] Task started: fastANI
[2023-06-07 18:45:21,120] [INFO] Running command: fastANI --query /var/lib/cwl/stg8598e08a-74c7-42f6-8542-981eb5213ba0/GCA_949122875.1_ERR4467353_bin.5_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_949122875.1_ERR4467353_bin.5_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_949122875.1_ERR4467353_bin.5_metawrap_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-07 18:45:32,206] [INFO] Task succeeded: fastANI
[2023-06-07 18:45:32,207] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg817f2f37-9ddf-4b6e-9442-aab27f4f07c5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-07 18:45:32,207] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg817f2f37-9ddf-4b6e-9442-aab27f4f07c5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-07 18:45:32,213] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-06-07 18:45:32,213] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-07 18:45:32,213] [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	78.5589	206	1005	95	below_threshold
Duncaniella muris	strain=DSM 103720	GCA_003024805.1	2094150	2094150	type	True	78.4188	203	1005	95	below_threshold
Duncaniella freteri	strain=TLL-A3	GCA_004766125.1	2530391	2530391	type	True	77.7498	143	1005	95	below_threshold
Muribaculum gordoncarteri	strain=TLL-A4	GCA_004803695.1	2530390	2530390	type	True	77.2612	110	1005	95	below_threshold
Paramuribaculum intestinale	strain=DSM 100749	GCA_003024925.1	2094151	2094151	type	True	76.8431	52	1005	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-07 18:45:32,215] [INFO] DFAST Taxonomy check result was written to GCA_949122875.1_ERR4467353_bin.5_metawrap_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-07 18:45:32,216] [INFO] ===== Taxonomy check completed =====
[2023-06-07 18:45:32,216] [INFO] ===== Start completeness check using CheckM =====
[2023-06-07 18:45:32,216] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg817f2f37-9ddf-4b6e-9442-aab27f4f07c5/dqc_reference/checkm_data
[2023-06-07 18:45:32,218] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-07 18:45:32,247] [INFO] Task started: CheckM
[2023-06-07 18:45:32,247] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_949122875.1_ERR4467353_bin.5_metawrap_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_949122875.1_ERR4467353_bin.5_metawrap_v1.3_MAG_genomic.fna/checkm_input GCA_949122875.1_ERR4467353_bin.5_metawrap_v1.3_MAG_genomic.fna/checkm_result
[2023-06-07 18:46:20,188] [INFO] Task succeeded: CheckM
[2023-06-07 18:46:20,189] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-07 18:46:20,205] [INFO] ===== Completeness check finished =====
[2023-06-07 18:46:20,205] [INFO] ===== Start GTDB Search =====
[2023-06-07 18:46:20,205] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_949122875.1_ERR4467353_bin.5_metawrap_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-07 18:46:20,206] [INFO] Task started: Blastn
[2023-06-07 18:46:20,206] [INFO] Running command: blastn -query GCA_949122875.1_ERR4467353_bin.5_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg817f2f37-9ddf-4b6e-9442-aab27f4f07c5/dqc_reference/reference_markers_gtdb.fasta -out GCA_949122875.1_ERR4467353_bin.5_metawrap_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 18:46:21,041] [INFO] Task succeeded: Blastn
[2023-06-07 18:46:21,046] [INFO] Selected 16 target genomes.
[2023-06-07 18:46:21,046] [INFO] Target genome list was writen to GCA_949122875.1_ERR4467353_bin.5_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-07 18:46:21,050] [INFO] Task started: fastANI
[2023-06-07 18:46:21,051] [INFO] Running command: fastANI --query /var/lib/cwl/stg8598e08a-74c7-42f6-8542-981eb5213ba0/GCA_949122875.1_ERR4467353_bin.5_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_949122875.1_ERR4467353_bin.5_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_949122875.1_ERR4467353_bin.5_metawrap_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-07 18:46:28,747] [INFO] Task succeeded: fastANI
[2023-06-07 18:46:28,760] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-07 18:46:28,760] [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_910578515.1	s__Duncaniella sp910578515	99.9838	1002	1005	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Duncaniella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_910577335.1	s__Duncaniella sp910577335	80.6789	435	1005	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Duncaniella	95.0	95.78	95.78	0.86	0.86	2	-
GCA_910577255.1	s__Duncaniella sp910577255	79.2847	278	1005	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Duncaniella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910577345.1	s__Duncaniella sp910577345	78.5717	247	1005	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Duncaniella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004803915.1	s__Duncaniella dubosii	78.5683	205	1005	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Duncaniella	95.0	98.46	96.11	0.91	0.80	8	-
GCF_003024805.1	s__Duncaniella muris	78.4188	203	1005	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Duncaniella	95.0	98.34	97.90	0.87	0.80	17	-
GCA_014802345.1	s__Duncaniella sp014802345	78.3542	166	1005	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Duncaniella	95.0	98.04	97.99	0.90	0.88	3	-
GCA_900544535.1	s__Duncaniella sp900544535	78.1926	180	1005	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Duncaniella	95.0	100.00	100.00	1.00	1.00	2	-
GCA_910589485.1	s__Duncaniella sp910589485	78.1651	167	1005	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Duncaniella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014802015.1	s__Duncaniella sp014802015	77.83	132	1005	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Duncaniella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910576785.1	s__Duncaniella sp910576785	77.8002	171	1005	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Duncaniella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003762875.1	s__Duncaniella sp001689575	77.7794	176	1005	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Duncaniella	95.0	97.25	96.19	0.92	0.80	7	-
GCA_910587165.1	s__Duncaniella sp910587165	77.6071	151	1005	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Duncaniella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910578305.1	s__Paramuribaculum sp910578305	76.5966	55	1005	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Paramuribaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014802425.1	s__CAG-485 sp014802425	76.0444	52	1005	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-07 18:46:28,762] [INFO] GTDB search result was written to GCA_949122875.1_ERR4467353_bin.5_metawrap_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-07 18:46:28,762] [INFO] ===== GTDB Search completed =====
[2023-06-07 18:46:28,765] [INFO] DFAST_QC result json was written to GCA_949122875.1_ERR4467353_bin.5_metawrap_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-07 18:46:28,765] [INFO] DFAST_QC completed!
[2023-06-07 18:46:28,765] [INFO] Total running time: 0h1m26s