[2023-06-08 11:22:25,525] [INFO] DFAST_QC pipeline started.
[2023-06-08 11:22:25,527] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 11:22:25,528] [INFO] DQC Reference Directory: /var/lib/cwl/stg78cdf126-f54f-4b25-831d-587594bcd722/dqc_reference
[2023-06-08 11:22:26,730] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 11:22:26,731] [INFO] Task started: Prodigal
[2023-06-08 11:22:26,731] [INFO] Running command: gunzip -c /var/lib/cwl/stge6f3c527-f3dc-494a-a27d-28c411660bb2/GCA_947347385.1_SRR14698350_bin.7_metawrap_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_947347385.1_SRR14698350_bin.7_metawrap_v1.3_MAG_genomic.fna/cds.fna -a GCA_947347385.1_SRR14698350_bin.7_metawrap_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 11:22:40,674] [INFO] Task succeeded: Prodigal
[2023-06-08 11:22:40,674] [INFO] Task started: HMMsearch
[2023-06-08 11:22:40,674] [INFO] Running command: hmmsearch --tblout GCA_947347385.1_SRR14698350_bin.7_metawrap_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg78cdf126-f54f-4b25-831d-587594bcd722/dqc_reference/reference_markers.hmm GCA_947347385.1_SRR14698350_bin.7_metawrap_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 11:22:40,972] [INFO] Task succeeded: HMMsearch
[2023-06-08 11:22:40,974] [INFO] Found 6/6 markers.
[2023-06-08 11:22:41,019] [INFO] Query marker FASTA was written to GCA_947347385.1_SRR14698350_bin.7_metawrap_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 11:22:41,019] [INFO] Task started: Blastn
[2023-06-08 11:22:41,019] [INFO] Running command: blastn -query GCA_947347385.1_SRR14698350_bin.7_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg78cdf126-f54f-4b25-831d-587594bcd722/dqc_reference/reference_markers.fasta -out GCA_947347385.1_SRR14698350_bin.7_metawrap_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 11:22:41,634] [INFO] Task succeeded: Blastn
[2023-06-08 11:22:41,638] [INFO] Selected 20 target genomes.
[2023-06-08 11:22:41,638] [INFO] Target genome list was writen to GCA_947347385.1_SRR14698350_bin.7_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 11:22:41,639] [INFO] Task started: fastANI
[2023-06-08 11:22:41,639] [INFO] Running command: fastANI --query /var/lib/cwl/stge6f3c527-f3dc-494a-a27d-28c411660bb2/GCA_947347385.1_SRR14698350_bin.7_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947347385.1_SRR14698350_bin.7_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_947347385.1_SRR14698350_bin.7_metawrap_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 11:22:53,800] [INFO] Task succeeded: fastANI
[2023-06-08 11:22:53,801] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg78cdf126-f54f-4b25-831d-587594bcd722/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 11:22:53,802] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg78cdf126-f54f-4b25-831d-587594bcd722/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 11:22:53,813] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 11:22:53,814] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 11:22:53,814] [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 muris	strain=DSM 103720	GCA_003024805.1	2094150	2094150	type	True	76.4825	51	754	95	below_threshold
Muribaculum intestinale	strain=YL27	GCA_001688845.2	1796646	1796646	type	True	76.4786	56	754	95	below_threshold
Muribaculum intestinale	strain=YL27	GCA_002201515.1	1796646	1796646	type	True	76.4753	56	754	95	below_threshold
Muribaculum intestinale	strain=YL27	GCA_016696845.1	1796646	1796646	type	True	76.431	56	754	95	below_threshold
Paramuribaculum intestinale	strain=DSM 100749	GCA_003024925.1	2094151	2094151	type	True	76.3326	50	754	95	below_threshold
Muribaculum gordoncarteri	strain=TLL-A4	GCA_004803695.1	2530390	2530390	type	True	76.2848	53	754	95	below_threshold
Duncaniella dubosii	strain=H5	GCA_004803915.1	2518971	2518971	type	True	75.868	57	754	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 11:22:53,817] [INFO] DFAST Taxonomy check result was written to GCA_947347385.1_SRR14698350_bin.7_metawrap_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 11:22:53,819] [INFO] ===== Taxonomy check completed =====
[2023-06-08 11:22:53,819] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 11:22:53,819] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg78cdf126-f54f-4b25-831d-587594bcd722/dqc_reference/checkm_data
[2023-06-08 11:22:53,820] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 11:22:53,863] [INFO] Task started: CheckM
[2023-06-08 11:22:53,864] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947347385.1_SRR14698350_bin.7_metawrap_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947347385.1_SRR14698350_bin.7_metawrap_v1.3_MAG_genomic.fna/checkm_input GCA_947347385.1_SRR14698350_bin.7_metawrap_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 11:23:37,626] [INFO] Task succeeded: CheckM
[2023-06-08 11:23:37,628] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.25%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 11:23:37,649] [INFO] ===== Completeness check finished =====
[2023-06-08 11:23:37,649] [INFO] ===== Start GTDB Search =====
[2023-06-08 11:23:37,650] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947347385.1_SRR14698350_bin.7_metawrap_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 11:23:37,650] [INFO] Task started: Blastn
[2023-06-08 11:23:37,650] [INFO] Running command: blastn -query GCA_947347385.1_SRR14698350_bin.7_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg78cdf126-f54f-4b25-831d-587594bcd722/dqc_reference/reference_markers_gtdb.fasta -out GCA_947347385.1_SRR14698350_bin.7_metawrap_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 11:23:38,482] [INFO] Task succeeded: Blastn
[2023-06-08 11:23:38,486] [INFO] Selected 20 target genomes.
[2023-06-08 11:23:38,487] [INFO] Target genome list was writen to GCA_947347385.1_SRR14698350_bin.7_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 11:23:38,489] [INFO] Task started: fastANI
[2023-06-08 11:23:38,489] [INFO] Running command: fastANI --query /var/lib/cwl/stge6f3c527-f3dc-494a-a27d-28c411660bb2/GCA_947347385.1_SRR14698350_bin.7_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947347385.1_SRR14698350_bin.7_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_947347385.1_SRR14698350_bin.7_metawrap_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 11:23:46,827] [INFO] Task succeeded: fastANI
[2023-06-08 11:23:46,847] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 11:23:46,848] [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_910575545.1	s__UBA7173 sp013316675	99.6523	733	754	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__UBA7173	95.0	99.44	98.97	0.94	0.91	3	conclusive
GCA_001689485.1	s__UBA7173 sp001689485	78.1605	196	754	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__UBA7173	95.0	99.04	99.00	0.86	0.84	5	-
GCA_910586565.1	s__UBA7173 sp910586565	77.9794	188	754	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__UBA7173	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013316535.1	s__UBA7173 sp013316535	77.7561	125	754	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__UBA7173	95.0	97.52	97.52	0.95	0.95	2	-
GCA_900540205.1	s__UBA7173 sp900540205	77.3677	144	754	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__UBA7173	95.0	96.71	95.96	0.83	0.74	4	-
GCA_004557825.1	s__UBA7173 sp004557825	77.3293	58	754	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__UBA7173	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900545955.1	s__UBA7173 sp900545955	77.1888	116	754	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__UBA7173	95.0	97.61	97.55	0.88	0.85	4	-
GCA_905207535.1	s__UBA7173 sp905207535	77.1063	120	754	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__UBA7173	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001701135.1	s__UBA7173 sp001701135	77.0802	95	754	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__UBA7173	95.0	97.33	96.66	0.85	0.83	3	-
GCA_900546835.1	s__UBA7173 sp900546835	77.0798	111	754	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__UBA7173	95.0	99.67	99.65	0.91	0.86	3	-
GCA_910583675.1	s__UBA7173 sp910583675	77.0343	124	754	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__UBA7173	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910575615.1	s__UBA7173 sp001689685	76.9482	113	754	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__UBA7173	95.0	99.70	99.58	0.97	0.94	9	-
GCA_910587075.1	s__UBA7173 sp910587075	76.8081	88	754	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__UBA7173	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910578035.1	s__CAG-873 sp910578035	76.6121	51	754	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910584735.1	s__UBA7173 sp910584735	76.6018	94	754	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__UBA7173	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910579105.1	s__UBA7173 sp910579105	76.4248	80	754	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__UBA7173	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910577255.1	s__Duncaniella sp910577255	76.4225	53	754	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Duncaniella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910586665.1	s__Duncaniella sp910586665	75.9723	68	754	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Duncaniella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 11:23:46,850] [INFO] GTDB search result was written to GCA_947347385.1_SRR14698350_bin.7_metawrap_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 11:23:46,850] [INFO] ===== GTDB Search completed =====
[2023-06-08 11:23:46,854] [INFO] DFAST_QC result json was written to GCA_947347385.1_SRR14698350_bin.7_metawrap_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 11:23:46,854] [INFO] DFAST_QC completed!
[2023-06-08 11:23:46,854] [INFO] Total running time: 0h1m21s