[2023-06-29 19:20:04,346] [INFO] DFAST_QC pipeline started.
[2023-06-29 19:20:04,350] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 19:20:04,351] [INFO] DQC Reference Directory: /var/lib/cwl/stg85ed261f-f766-4e7f-9e7e-6eaa6bec49fe/dqc_reference
[2023-06-29 19:20:05,957] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 19:20:05,958] [INFO] Task started: Prodigal
[2023-06-29 19:20:05,958] [INFO] Running command: gunzip -c /var/lib/cwl/stg242047c8-fde2-477d-ac8f-e48fdb857670/GCA_021621745.1_ASM2162174v1_genomic.fna.gz | prodigal -d GCA_021621745.1_ASM2162174v1_genomic.fna/cds.fna -a GCA_021621745.1_ASM2162174v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 19:20:19,073] [INFO] Task succeeded: Prodigal
[2023-06-29 19:20:19,073] [INFO] Task started: HMMsearch
[2023-06-29 19:20:19,073] [INFO] Running command: hmmsearch --tblout GCA_021621745.1_ASM2162174v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg85ed261f-f766-4e7f-9e7e-6eaa6bec49fe/dqc_reference/reference_markers.hmm GCA_021621745.1_ASM2162174v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 19:20:19,316] [INFO] Task succeeded: HMMsearch
[2023-06-29 19:20:19,317] [INFO] Found 6/6 markers.
[2023-06-29 19:20:19,343] [INFO] Query marker FASTA was written to GCA_021621745.1_ASM2162174v1_genomic.fna/markers.fasta
[2023-06-29 19:20:19,344] [INFO] Task started: Blastn
[2023-06-29 19:20:19,344] [INFO] Running command: blastn -query GCA_021621745.1_ASM2162174v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg85ed261f-f766-4e7f-9e7e-6eaa6bec49fe/dqc_reference/reference_markers.fasta -out GCA_021621745.1_ASM2162174v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 19:20:20,028] [INFO] Task succeeded: Blastn
[2023-06-29 19:20:20,041] [INFO] Selected 30 target genomes.
[2023-06-29 19:20:20,042] [INFO] Target genome list was writen to GCA_021621745.1_ASM2162174v1_genomic.fna/target_genomes.txt
[2023-06-29 19:20:20,049] [INFO] Task started: fastANI
[2023-06-29 19:20:20,050] [INFO] Running command: fastANI --query /var/lib/cwl/stg242047c8-fde2-477d-ac8f-e48fdb857670/GCA_021621745.1_ASM2162174v1_genomic.fna.gz --refList GCA_021621745.1_ASM2162174v1_genomic.fna/target_genomes.txt --output GCA_021621745.1_ASM2162174v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 19:20:39,085] [INFO] Task succeeded: fastANI
[2023-06-29 19:20:39,086] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg85ed261f-f766-4e7f-9e7e-6eaa6bec49fe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 19:20:39,086] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg85ed261f-f766-4e7f-9e7e-6eaa6bec49fe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 19:20:39,093] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2023-06-29 19:20:39,093] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-29 19:20:39,093] [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
Prevotellamassilia timonensis	strain=Marseille-P2831	GCA_900106785.1	1852370	1852370	type	True	97.031	277	297	95	conclusive
--------------------------------------------------------------------------------
[2023-06-29 19:20:39,096] [INFO] DFAST Taxonomy check result was written to GCA_021621745.1_ASM2162174v1_genomic.fna/tc_result.tsv
[2023-06-29 19:20:39,097] [INFO] ===== Taxonomy check completed =====
[2023-06-29 19:20:39,097] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 19:20:39,098] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg85ed261f-f766-4e7f-9e7e-6eaa6bec49fe/dqc_reference/checkm_data
[2023-06-29 19:20:39,100] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 19:20:39,137] [INFO] Task started: CheckM
[2023-06-29 19:20:39,137] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_021621745.1_ASM2162174v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_021621745.1_ASM2162174v1_genomic.fna/checkm_input GCA_021621745.1_ASM2162174v1_genomic.fna/checkm_result
[2023-06-29 19:21:19,497] [INFO] Task succeeded: CheckM
[2023-06-29 19:21:19,499] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 59.56%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 19:21:19,519] [INFO] ===== Completeness check finished =====
[2023-06-29 19:21:19,519] [INFO] ===== Start GTDB Search =====
[2023-06-29 19:21:19,520] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_021621745.1_ASM2162174v1_genomic.fna/markers.fasta)
[2023-06-29 19:21:19,520] [INFO] Task started: Blastn
[2023-06-29 19:21:19,520] [INFO] Running command: blastn -query GCA_021621745.1_ASM2162174v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg85ed261f-f766-4e7f-9e7e-6eaa6bec49fe/dqc_reference/reference_markers_gtdb.fasta -out GCA_021621745.1_ASM2162174v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 19:21:20,390] [INFO] Task succeeded: Blastn
[2023-06-29 19:21:20,395] [INFO] Selected 24 target genomes.
[2023-06-29 19:21:20,396] [INFO] Target genome list was writen to GCA_021621745.1_ASM2162174v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 19:21:20,409] [INFO] Task started: fastANI
[2023-06-29 19:21:20,409] [INFO] Running command: fastANI --query /var/lib/cwl/stg242047c8-fde2-477d-ac8f-e48fdb857670/GCA_021621745.1_ASM2162174v1_genomic.fna.gz --refList GCA_021621745.1_ASM2162174v1_genomic.fna/target_genomes_gtdb.txt --output GCA_021621745.1_ASM2162174v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 19:21:30,316] [INFO] Task succeeded: fastANI
[2023-06-29 19:21:30,331] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 19:21:30,331] [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_900106785.1	s__Alloprevotella timonensis	97.031	277	297	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Alloprevotella	95.0	97.61	96.80	0.91	0.85	6	conclusive
GCA_900540885.1	s__Alloprevotella sp900540885	79.0042	100	297	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Alloprevotella	95.0	97.94	97.84	0.88	0.83	3	-
GCA_900541575.1	s__Alloprevotella sp900541575	78.8092	70	297	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Alloprevotella	95.0	99.97	99.94	0.96	0.94	3	-
GCA_900542795.1	s__Alloprevotella sp900542795	78.5077	72	297	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Alloprevotella	95.0	97.89	97.87	0.86	0.85	3	-
GCA_900546605.1	s__Alloprevotella sp900546605	78.4839	76	297	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Alloprevotella	95.0	98.64	98.64	0.86	0.86	2	-
GCA_004557185.1	s__Alloprevotella sp004557185	78.2553	78	297	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Alloprevotella	95.0	98.58	98.39	0.90	0.87	3	-
GCA_900543155.1	s__Alloprevotella sp900543155	77.8998	75	297	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Alloprevotella	95.0	98.25	98.25	0.88	0.88	2	-
GCA_004552195.1	s__Alloprevotella sp004552195	77.519	62	297	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Alloprevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000437675.1	s__Alloprevotella sp000437675	77.4941	84	297	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Alloprevotella	95.0	99.30	98.80	0.87	0.84	3	-
GCA_002431845.1	s__Alloprevotella sp002431845	77.3511	62	297	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Alloprevotella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 19:21:30,334] [INFO] GTDB search result was written to GCA_021621745.1_ASM2162174v1_genomic.fna/result_gtdb.tsv
[2023-06-29 19:21:30,335] [INFO] ===== GTDB Search completed =====
[2023-06-29 19:21:30,339] [INFO] DFAST_QC result json was written to GCA_021621745.1_ASM2162174v1_genomic.fna/dqc_result.json
[2023-06-29 19:21:30,340] [INFO] DFAST_QC completed!
[2023-06-29 19:21:30,340] [INFO] Total running time: 0h1m26s