[2023-06-27 11:40:27,440] [INFO] DFAST_QC pipeline started.
[2023-06-27 11:40:27,442] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 11:40:27,442] [INFO] DQC Reference Directory: /var/lib/cwl/stgd19387d0-4016-4dfb-8477-c560e9a1420b/dqc_reference
[2023-06-27 11:40:28,633] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 11:40:28,634] [INFO] Task started: Prodigal
[2023-06-27 11:40:28,634] [INFO] Running command: gunzip -c /var/lib/cwl/stgb12e3eb3-68b6-476c-a287-1f8be15276be/GCA_002418045.1_ASM241804v1_genomic.fna.gz | prodigal -d GCA_002418045.1_ASM241804v1_genomic.fna/cds.fna -a GCA_002418045.1_ASM241804v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 11:40:36,497] [INFO] Task succeeded: Prodigal
[2023-06-27 11:40:36,498] [INFO] Task started: HMMsearch
[2023-06-27 11:40:36,498] [INFO] Running command: hmmsearch --tblout GCA_002418045.1_ASM241804v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd19387d0-4016-4dfb-8477-c560e9a1420b/dqc_reference/reference_markers.hmm GCA_002418045.1_ASM241804v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 11:40:36,676] [INFO] Task succeeded: HMMsearch
[2023-06-27 11:40:36,677] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgb12e3eb3-68b6-476c-a287-1f8be15276be/GCA_002418045.1_ASM241804v1_genomic.fna.gz]
[2023-06-27 11:40:36,826] [INFO] Query marker FASTA was written to GCA_002418045.1_ASM241804v1_genomic.fna/markers.fasta
[2023-06-27 11:40:36,826] [INFO] Task started: Blastn
[2023-06-27 11:40:36,827] [INFO] Running command: blastn -query GCA_002418045.1_ASM241804v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd19387d0-4016-4dfb-8477-c560e9a1420b/dqc_reference/reference_markers.fasta -out GCA_002418045.1_ASM241804v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 11:40:37,347] [INFO] Task succeeded: Blastn
[2023-06-27 11:40:37,350] [INFO] Selected 18 target genomes.
[2023-06-27 11:40:37,351] [INFO] Target genome list was writen to GCA_002418045.1_ASM241804v1_genomic.fna/target_genomes.txt
[2023-06-27 11:40:37,353] [INFO] Task started: fastANI
[2023-06-27 11:40:37,353] [INFO] Running command: fastANI --query /var/lib/cwl/stgb12e3eb3-68b6-476c-a287-1f8be15276be/GCA_002418045.1_ASM241804v1_genomic.fna.gz --refList GCA_002418045.1_ASM241804v1_genomic.fna/target_genomes.txt --output GCA_002418045.1_ASM241804v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 11:40:46,861] [INFO] Task succeeded: fastANI
[2023-06-27 11:40:46,861] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd19387d0-4016-4dfb-8477-c560e9a1420b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 11:40:46,861] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd19387d0-4016-4dfb-8477-c560e9a1420b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 11:40:46,867] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 11:40:46,868] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 11:40:46,868] [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
Prevotella albensis	strain=DSM 11370	GCA_000426565.1	77768	77768	type	True	77.9154	66	652	95	below_threshold
Prevotella albensis	strain=JCM 12258	GCA_000613525.1	77768	77768	type	True	77.8639	67	652	95	below_threshold
Prevotella bryantii	strain=B14	GCA_900110745.1	77095	77095	type	True	77.8122	123	652	95	below_threshold
Prevotella bryantii	strain=B14	GCA_022024235.1	77095	77095	type	True	77.7761	122	652	95	below_threshold
Prevotella bryantii	strain=DSM 11371	GCA_019973295.1	77095	77095	type	True	77.6661	121	652	95	below_threshold
Prevotella bryantii	strain=B14	GCA_000179055.1	77095	77095	type	True	77.6487	117	652	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 11:40:46,872] [INFO] DFAST Taxonomy check result was written to GCA_002418045.1_ASM241804v1_genomic.fna/tc_result.tsv
[2023-06-27 11:40:46,873] [INFO] ===== Taxonomy check completed =====
[2023-06-27 11:40:46,873] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 11:40:46,873] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd19387d0-4016-4dfb-8477-c560e9a1420b/dqc_reference/checkm_data
[2023-06-27 11:40:46,874] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 11:40:46,900] [INFO] Task started: CheckM
[2023-06-27 11:40:46,900] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002418045.1_ASM241804v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002418045.1_ASM241804v1_genomic.fna/checkm_input GCA_002418045.1_ASM241804v1_genomic.fna/checkm_result
[2023-06-27 11:41:13,598] [INFO] Task succeeded: CheckM
[2023-06-27 11:41:13,599] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.82%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 11:41:13,624] [INFO] ===== Completeness check finished =====
[2023-06-27 11:41:13,624] [INFO] ===== Start GTDB Search =====
[2023-06-27 11:41:13,625] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002418045.1_ASM241804v1_genomic.fna/markers.fasta)
[2023-06-27 11:41:13,625] [INFO] Task started: Blastn
[2023-06-27 11:41:13,626] [INFO] Running command: blastn -query GCA_002418045.1_ASM241804v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd19387d0-4016-4dfb-8477-c560e9a1420b/dqc_reference/reference_markers_gtdb.fasta -out GCA_002418045.1_ASM241804v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 11:41:14,317] [INFO] Task succeeded: Blastn
[2023-06-27 11:41:14,321] [INFO] Selected 18 target genomes.
[2023-06-27 11:41:14,321] [INFO] Target genome list was writen to GCA_002418045.1_ASM241804v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 11:41:14,328] [INFO] Task started: fastANI
[2023-06-27 11:41:14,328] [INFO] Running command: fastANI --query /var/lib/cwl/stgb12e3eb3-68b6-476c-a287-1f8be15276be/GCA_002418045.1_ASM241804v1_genomic.fna.gz --refList GCA_002418045.1_ASM241804v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002418045.1_ASM241804v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 11:41:22,889] [INFO] Task succeeded: fastANI
[2023-06-27 11:41:22,894] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-27 11:41:22,894] [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_003483565.1	s__Prevotella sp003483565	99.3601	453	652	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.31	99.31	0.72	0.72	2	conclusive
GCF_000426565.1	s__Prevotella albensis	77.9346	65	652	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.96	99.96	1.00	1.00	2	-
GCF_000179055.1	s__Prevotella bryantii	77.6511	116	652	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.02	98.58	0.88	0.73	13	-
GCA_905236755.1	s__Prevotella sp905236755	77.2031	64	652	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.83	97.34	0.84	0.68	4	-
GCA_905236815.1	s__Prevotella sp905236815	76.3336	58	652	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 11:41:23,323] [INFO] GTDB search result was written to GCA_002418045.1_ASM241804v1_genomic.fna/result_gtdb.tsv
[2023-06-27 11:41:23,324] [INFO] ===== GTDB Search completed =====
[2023-06-27 11:41:23,327] [INFO] DFAST_QC result json was written to GCA_002418045.1_ASM241804v1_genomic.fna/dqc_result.json
[2023-06-27 11:41:23,328] [INFO] DFAST_QC completed!
[2023-06-27 11:41:23,328] [INFO] Total running time: 0h0m56s