[2023-06-29 12:22:11,467] [INFO] DFAST_QC pipeline started.
[2023-06-29 12:22:11,470] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 12:22:11,471] [INFO] DQC Reference Directory: /var/lib/cwl/stgf1996888-df9e-4cef-94ad-e2817bd87d33/dqc_reference
[2023-06-29 12:22:12,792] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 12:22:12,794] [INFO] Task started: Prodigal
[2023-06-29 12:22:12,794] [INFO] Running command: gunzip -c /var/lib/cwl/stga1641b55-96fc-4e0f-b214-7a619ce9487d/GCA_910579065.1_MGBC109852_genomic.fna.gz | prodigal -d GCA_910579065.1_MGBC109852_genomic.fna/cds.fna -a GCA_910579065.1_MGBC109852_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 12:22:34,947] [INFO] Task succeeded: Prodigal
[2023-06-29 12:22:34,947] [INFO] Task started: HMMsearch
[2023-06-29 12:22:34,947] [INFO] Running command: hmmsearch --tblout GCA_910579065.1_MGBC109852_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf1996888-df9e-4cef-94ad-e2817bd87d33/dqc_reference/reference_markers.hmm GCA_910579065.1_MGBC109852_genomic.fna/protein.faa > /dev/null
[2023-06-29 12:22:35,231] [INFO] Task succeeded: HMMsearch
[2023-06-29 12:22:35,236] [INFO] Found 6/6 markers.
[2023-06-29 12:22:35,272] [INFO] Query marker FASTA was written to GCA_910579065.1_MGBC109852_genomic.fna/markers.fasta
[2023-06-29 12:22:35,272] [INFO] Task started: Blastn
[2023-06-29 12:22:35,272] [INFO] Running command: blastn -query GCA_910579065.1_MGBC109852_genomic.fna/markers.fasta -db /var/lib/cwl/stgf1996888-df9e-4cef-94ad-e2817bd87d33/dqc_reference/reference_markers.fasta -out GCA_910579065.1_MGBC109852_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 12:22:35,862] [INFO] Task succeeded: Blastn
[2023-06-29 12:22:35,866] [INFO] Selected 22 target genomes.
[2023-06-29 12:22:35,866] [INFO] Target genome list was writen to GCA_910579065.1_MGBC109852_genomic.fna/target_genomes.txt
[2023-06-29 12:22:35,868] [INFO] Task started: fastANI
[2023-06-29 12:22:35,868] [INFO] Running command: fastANI --query /var/lib/cwl/stga1641b55-96fc-4e0f-b214-7a619ce9487d/GCA_910579065.1_MGBC109852_genomic.fna.gz --refList GCA_910579065.1_MGBC109852_genomic.fna/target_genomes.txt --output GCA_910579065.1_MGBC109852_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 12:22:48,319] [INFO] Task succeeded: fastANI
[2023-06-29 12:22:48,320] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf1996888-df9e-4cef-94ad-e2817bd87d33/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 12:22:48,320] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf1996888-df9e-4cef-94ad-e2817bd87d33/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 12:22:48,325] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 12:22:48,325] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 12:22:48,325] [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
Muribaculum gordoncarteri	strain=TLL-A4	GCA_004803695.1	2530390	2530390	type	True	76.6982	71	1336	95	below_threshold
Duncaniella muris	strain=DSM 103720	GCA_003024805.1	2094150	2094150	type	True	76.5155	62	1336	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 12:22:48,327] [INFO] DFAST Taxonomy check result was written to GCA_910579065.1_MGBC109852_genomic.fna/tc_result.tsv
[2023-06-29 12:22:48,328] [INFO] ===== Taxonomy check completed =====
[2023-06-29 12:22:48,328] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 12:22:48,328] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf1996888-df9e-4cef-94ad-e2817bd87d33/dqc_reference/checkm_data
[2023-06-29 12:22:48,330] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 12:22:48,379] [INFO] Task started: CheckM
[2023-06-29 12:22:48,379] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_910579065.1_MGBC109852_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_910579065.1_MGBC109852_genomic.fna/checkm_input GCA_910579065.1_MGBC109852_genomic.fna/checkm_result
[2023-06-29 12:23:51,992] [INFO] Task succeeded: CheckM
[2023-06-29 12:23:51,994] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 12:23:52,017] [INFO] ===== Completeness check finished =====
[2023-06-29 12:23:52,018] [INFO] ===== Start GTDB Search =====
[2023-06-29 12:23:52,018] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_910579065.1_MGBC109852_genomic.fna/markers.fasta)
[2023-06-29 12:23:52,018] [INFO] Task started: Blastn
[2023-06-29 12:23:52,019] [INFO] Running command: blastn -query GCA_910579065.1_MGBC109852_genomic.fna/markers.fasta -db /var/lib/cwl/stgf1996888-df9e-4cef-94ad-e2817bd87d33/dqc_reference/reference_markers_gtdb.fasta -out GCA_910579065.1_MGBC109852_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 12:23:52,833] [INFO] Task succeeded: Blastn
[2023-06-29 12:23:52,839] [INFO] Selected 18 target genomes.
[2023-06-29 12:23:52,839] [INFO] Target genome list was writen to GCA_910579065.1_MGBC109852_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 12:23:52,842] [INFO] Task started: fastANI
[2023-06-29 12:23:52,842] [INFO] Running command: fastANI --query /var/lib/cwl/stga1641b55-96fc-4e0f-b214-7a619ce9487d/GCA_910579065.1_MGBC109852_genomic.fna.gz --refList GCA_910579065.1_MGBC109852_genomic.fna/target_genomes_gtdb.txt --output GCA_910579065.1_MGBC109852_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 12:24:03,458] [INFO] Task succeeded: fastANI
[2023-06-29 12:24:03,475] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 12:24:03,475] [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_003762615.1	s__CAG-485 sp002493045	99.8521	1302	1336	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	99.48	99.22	0.95	0.91	14	conclusive
GCA_910583795.1	s__CAG-485 sp910583795	78.3707	271	1336	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	78.2844	227	1336	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_014801605.1	s__CAG-485 sp014801605	78.1538	135	1336	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_009775365.1	s__CAG-485 sp009775365	78.0491	208	1336	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	99.04	99.04	0.86	0.86	2	-
GCA_910588245.1	s__CAG-485 sp910588245	77.9252	229	1336	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	98.72	98.72	0.89	0.89	2	-
GCA_014800245.1	s__CAG-485 sp014800245	77.4746	84	1336	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_009775375.1	s__CAG-485 sp009775375	77.4636	216	1336	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	99.86	99.86	0.92	0.92	2	-
GCA_002493515.1	s__CAG-485 sp002493515	77.3841	123	1336	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	97.64	97.64	0.78	0.78	2	-
GCA_910577585.1	s__CAG-485 sp910577585	77.3034	122	1336	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_014800895.1	s__CAG-485 sp014800895	77.2259	119	1336	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	77.121	87	1336	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_905209725.1	s__CAG-485 sp900556595	77.0021	98	1336	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	99.46	99.46	0.94	0.94	2	-
GCA_910585285.1	s__CAG-485 sp910585285	76.8818	120	1336	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_900761855.1	s__CAG-485 sp900761855	76.7801	79	1336	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_910584545.1	s__CAG-485 sp910584545	76.7477	75	1336	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 12:24:03,477] [INFO] GTDB search result was written to GCA_910579065.1_MGBC109852_genomic.fna/result_gtdb.tsv
[2023-06-29 12:24:03,478] [INFO] ===== GTDB Search completed =====
[2023-06-29 12:24:03,481] [INFO] DFAST_QC result json was written to GCA_910579065.1_MGBC109852_genomic.fna/dqc_result.json
[2023-06-29 12:24:03,481] [INFO] DFAST_QC completed!
[2023-06-29 12:24:03,481] [INFO] Total running time: 0h1m52s