[2023-06-18 20:10:27,410] [INFO] DFAST_QC pipeline started.
[2023-06-18 20:10:27,412] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 20:10:27,412] [INFO] DQC Reference Directory: /var/lib/cwl/stgad16e9b2-744c-439e-a550-8da51a5af37d/dqc_reference
[2023-06-18 20:10:30,698] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 20:10:30,699] [INFO] Task started: Prodigal
[2023-06-18 20:10:30,699] [INFO] Running command: gunzip -c /var/lib/cwl/stgb6faab96-edee-4237-b480-c2f251a56820/GCA_014845815.1_ASM1484581v1_genomic.fna.gz | prodigal -d GCA_014845815.1_ASM1484581v1_genomic.fna/cds.fna -a GCA_014845815.1_ASM1484581v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 20:10:47,788] [INFO] Task succeeded: Prodigal
[2023-06-18 20:10:47,789] [INFO] Task started: HMMsearch
[2023-06-18 20:10:47,789] [INFO] Running command: hmmsearch --tblout GCA_014845815.1_ASM1484581v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgad16e9b2-744c-439e-a550-8da51a5af37d/dqc_reference/reference_markers.hmm GCA_014845815.1_ASM1484581v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 20:10:48,033] [INFO] Task succeeded: HMMsearch
[2023-06-18 20:10:48,034] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgb6faab96-edee-4237-b480-c2f251a56820/GCA_014845815.1_ASM1484581v1_genomic.fna.gz]
[2023-06-18 20:10:48,066] [INFO] Query marker FASTA was written to GCA_014845815.1_ASM1484581v1_genomic.fna/markers.fasta
[2023-06-18 20:10:48,066] [INFO] Task started: Blastn
[2023-06-18 20:10:48,067] [INFO] Running command: blastn -query GCA_014845815.1_ASM1484581v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgad16e9b2-744c-439e-a550-8da51a5af37d/dqc_reference/reference_markers.fasta -out GCA_014845815.1_ASM1484581v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 20:10:48,620] [INFO] Task succeeded: Blastn
[2023-06-18 20:10:48,624] [INFO] Selected 5 target genomes.
[2023-06-18 20:10:48,625] [INFO] Target genome list was writen to GCA_014845815.1_ASM1484581v1_genomic.fna/target_genomes.txt
[2023-06-18 20:10:48,626] [INFO] Task started: fastANI
[2023-06-18 20:10:48,626] [INFO] Running command: fastANI --query /var/lib/cwl/stgb6faab96-edee-4237-b480-c2f251a56820/GCA_014845815.1_ASM1484581v1_genomic.fna.gz --refList GCA_014845815.1_ASM1484581v1_genomic.fna/target_genomes.txt --output GCA_014845815.1_ASM1484581v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 20:10:54,925] [INFO] Task succeeded: fastANI
[2023-06-18 20:10:54,925] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgad16e9b2-744c-439e-a550-8da51a5af37d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 20:10:54,926] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgad16e9b2-744c-439e-a550-8da51a5af37d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 20:10:54,936] [INFO] Found 5 fastANI hits (5 hits with ANI > threshold)
[2023-06-18 20:10:54,936] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-18 20:10:54,936] [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
Bacteroides thetaiotaomicron	strain=NCTC10582	GCA_900445595.1	818	818	type	True	98.8881	999	1139	95	conclusive
Bacteroides thetaiotaomicron	strain=VPI-5482	GCA_000011065.1	818	818	type	True	98.847	1003	1139	95	conclusive
Bacteroides thetaiotaomicron	strain=VPI 5482	GCA_022453665.1	818	818	type	True	98.8428	1000	1139	95	conclusive
Bacteroides thetaiotaomicron	strain=VPI-5482	GCA_020179495.1	818	818	type	True	98.8245	1003	1139	95	conclusive
Bacteroides thetaiotaomicron	strain=VPI-5482	GCA_002959695.1	818	818	type	True	98.8193	1006	1139	95	conclusive
--------------------------------------------------------------------------------
[2023-06-18 20:10:54,939] [INFO] DFAST Taxonomy check result was written to GCA_014845815.1_ASM1484581v1_genomic.fna/tc_result.tsv
[2023-06-18 20:10:54,940] [INFO] ===== Taxonomy check completed =====
[2023-06-18 20:10:54,941] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 20:10:54,941] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgad16e9b2-744c-439e-a550-8da51a5af37d/dqc_reference/checkm_data
[2023-06-18 20:10:54,943] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 20:10:54,991] [INFO] Task started: CheckM
[2023-06-18 20:10:54,991] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_014845815.1_ASM1484581v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_014845815.1_ASM1484581v1_genomic.fna/checkm_input GCA_014845815.1_ASM1484581v1_genomic.fna/checkm_result
[2023-06-18 20:11:46,062] [INFO] Task succeeded: CheckM
[2023-06-18 20:11:46,064] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 38.43%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 20:11:46,085] [INFO] ===== Completeness check finished =====
[2023-06-18 20:11:46,086] [INFO] ===== Start GTDB Search =====
[2023-06-18 20:11:46,086] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_014845815.1_ASM1484581v1_genomic.fna/markers.fasta)
[2023-06-18 20:11:46,086] [INFO] Task started: Blastn
[2023-06-18 20:11:46,087] [INFO] Running command: blastn -query GCA_014845815.1_ASM1484581v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgad16e9b2-744c-439e-a550-8da51a5af37d/dqc_reference/reference_markers_gtdb.fasta -out GCA_014845815.1_ASM1484581v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 20:11:46,734] [INFO] Task succeeded: Blastn
[2023-06-18 20:11:46,738] [INFO] Selected 9 target genomes.
[2023-06-18 20:11:46,738] [INFO] Target genome list was writen to GCA_014845815.1_ASM1484581v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 20:11:46,741] [INFO] Task started: fastANI
[2023-06-18 20:11:46,741] [INFO] Running command: fastANI --query /var/lib/cwl/stgb6faab96-edee-4237-b480-c2f251a56820/GCA_014845815.1_ASM1484581v1_genomic.fna.gz --refList GCA_014845815.1_ASM1484581v1_genomic.fna/target_genomes_gtdb.txt --output GCA_014845815.1_ASM1484581v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 20:11:57,211] [INFO] Task succeeded: fastANI
[2023-06-18 20:11:57,222] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 20:11:57,222] [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_000011065.1	s__Bacteroides thetaiotaomicron	98.847	1003	1139	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.45	97.24	0.84	0.75	121	conclusive
GCF_900106755.1	s__Bacteroides faecis	89.2649	830	1139	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.27	98.92	0.88	0.84	29	-
GCA_900761785.1	s__Bacteroides sp900761785	83.8279	587	1139	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009193295.2	s__Bacteroides luhongzhouii	81.7775	513	1139	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.19	98.73	0.86	0.78	4	-
GCF_903181435.1	s__Bacteroides sp900765785	81.7086	469	1139	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.28	97.12	0.65	0.59	3	-
GCF_012113595.1	s__Bacteroides sp012113595	81.4027	561	1139	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014750685.1	s__Bacteroides sp014750685	81.3309	570	1139	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902362375.1	s__Bacteroides sp902362375	81.2118	536	1139	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.74	98.46	0.82	0.77	13	-
GCF_900130125.1	s__Bacteroides congonensis	81.1772	533	1139	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.81	97.60	0.79	0.75	6	-
--------------------------------------------------------------------------------
[2023-06-18 20:11:57,224] [INFO] GTDB search result was written to GCA_014845815.1_ASM1484581v1_genomic.fna/result_gtdb.tsv
[2023-06-18 20:11:57,225] [INFO] ===== GTDB Search completed =====
[2023-06-18 20:11:57,228] [INFO] DFAST_QC result json was written to GCA_014845815.1_ASM1484581v1_genomic.fna/dqc_result.json
[2023-06-18 20:11:57,228] [INFO] DFAST_QC completed!
[2023-06-18 20:11:57,228] [INFO] Total running time: 0h1m30s