[2023-06-29 13:36:09,174] [INFO] DFAST_QC pipeline started.
[2023-06-29 13:36:09,176] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 13:36:09,177] [INFO] DQC Reference Directory: /var/lib/cwl/stgc0edb46d-719d-4b1d-bf83-a7c6c13b7506/dqc_reference
[2023-06-29 13:36:12,713] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 13:36:12,714] [INFO] Task started: Prodigal
[2023-06-29 13:36:12,715] [INFO] Running command: gunzip -c /var/lib/cwl/stg4511115b-485d-4d4d-a69f-fcb0d15da5fb/GCA_021740085.1_ASM2174008v1_genomic.fna.gz | prodigal -d GCA_021740085.1_ASM2174008v1_genomic.fna/cds.fna -a GCA_021740085.1_ASM2174008v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 13:36:21,555] [INFO] Task succeeded: Prodigal
[2023-06-29 13:36:21,556] [INFO] Task started: HMMsearch
[2023-06-29 13:36:21,556] [INFO] Running command: hmmsearch --tblout GCA_021740085.1_ASM2174008v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc0edb46d-719d-4b1d-bf83-a7c6c13b7506/dqc_reference/reference_markers.hmm GCA_021740085.1_ASM2174008v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 13:36:21,787] [INFO] Task succeeded: HMMsearch
[2023-06-29 13:36:21,788] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg4511115b-485d-4d4d-a69f-fcb0d15da5fb/GCA_021740085.1_ASM2174008v1_genomic.fna.gz]
[2023-06-29 13:36:21,814] [INFO] Query marker FASTA was written to GCA_021740085.1_ASM2174008v1_genomic.fna/markers.fasta
[2023-06-29 13:36:21,814] [INFO] Task started: Blastn
[2023-06-29 13:36:21,814] [INFO] Running command: blastn -query GCA_021740085.1_ASM2174008v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc0edb46d-719d-4b1d-bf83-a7c6c13b7506/dqc_reference/reference_markers.fasta -out GCA_021740085.1_ASM2174008v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 13:36:22,406] [INFO] Task succeeded: Blastn
[2023-06-29 13:36:22,410] [INFO] Selected 25 target genomes.
[2023-06-29 13:36:22,411] [INFO] Target genome list was writen to GCA_021740085.1_ASM2174008v1_genomic.fna/target_genomes.txt
[2023-06-29 13:36:22,415] [INFO] Task started: fastANI
[2023-06-29 13:36:22,415] [INFO] Running command: fastANI --query /var/lib/cwl/stg4511115b-485d-4d4d-a69f-fcb0d15da5fb/GCA_021740085.1_ASM2174008v1_genomic.fna.gz --refList GCA_021740085.1_ASM2174008v1_genomic.fna/target_genomes.txt --output GCA_021740085.1_ASM2174008v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 13:36:37,195] [INFO] Task succeeded: fastANI
[2023-06-29 13:36:37,196] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc0edb46d-719d-4b1d-bf83-a7c6c13b7506/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 13:36:37,197] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc0edb46d-719d-4b1d-bf83-a7c6c13b7506/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 13:36:37,198] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 13:36:37,198] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 13:36:37,198] [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
--------------------------------------------------------------------------------
[2023-06-29 13:36:37,200] [INFO] DFAST Taxonomy check result was written to GCA_021740085.1_ASM2174008v1_genomic.fna/tc_result.tsv
[2023-06-29 13:36:37,201] [INFO] ===== Taxonomy check completed =====
[2023-06-29 13:36:37,201] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 13:36:37,201] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc0edb46d-719d-4b1d-bf83-a7c6c13b7506/dqc_reference/checkm_data
[2023-06-29 13:36:37,205] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 13:36:37,235] [INFO] Task started: CheckM
[2023-06-29 13:36:37,235] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_021740085.1_ASM2174008v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_021740085.1_ASM2174008v1_genomic.fna/checkm_input GCA_021740085.1_ASM2174008v1_genomic.fna/checkm_result
[2023-06-29 13:37:08,314] [INFO] Task succeeded: CheckM
[2023-06-29 13:37:08,315] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 13:37:08,333] [INFO] ===== Completeness check finished =====
[2023-06-29 13:37:08,334] [INFO] ===== Start GTDB Search =====
[2023-06-29 13:37:08,334] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_021740085.1_ASM2174008v1_genomic.fna/markers.fasta)
[2023-06-29 13:37:08,334] [INFO] Task started: Blastn
[2023-06-29 13:37:08,335] [INFO] Running command: blastn -query GCA_021740085.1_ASM2174008v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc0edb46d-719d-4b1d-bf83-a7c6c13b7506/dqc_reference/reference_markers_gtdb.fasta -out GCA_021740085.1_ASM2174008v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 13:37:09,133] [INFO] Task succeeded: Blastn
[2023-06-29 13:37:09,138] [INFO] Selected 21 target genomes.
[2023-06-29 13:37:09,138] [INFO] Target genome list was writen to GCA_021740085.1_ASM2174008v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 13:37:09,155] [INFO] Task started: fastANI
[2023-06-29 13:37:09,155] [INFO] Running command: fastANI --query /var/lib/cwl/stg4511115b-485d-4d4d-a69f-fcb0d15da5fb/GCA_021740085.1_ASM2174008v1_genomic.fna.gz --refList GCA_021740085.1_ASM2174008v1_genomic.fna/target_genomes_gtdb.txt --output GCA_021740085.1_ASM2174008v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 13:37:18,991] [INFO] Task succeeded: fastANI
[2023-06-29 13:37:18,997] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 13:37:18,997] [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_903939755.1	s__UBA952 sp903939755	89.0037	654	755	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA952	95.0	99.13	98.32	0.94	0.90	3	-
GCA_009923965.1	s__UBA952 sp009923965	79.4445	51	755	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA952	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903935095.1	s__UBA952 sp903935095	76.9339	58	755	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA952	95.0	99.97	99.95	0.99	0.98	5	-
GCA_018883325.1	s__UBA952 sp018883325	76.3508	67	755	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA952	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017984635.1	s__M0103 sp017984635	76.0878	64	755	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__M0103	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 13:37:18,999] [INFO] GTDB search result was written to GCA_021740085.1_ASM2174008v1_genomic.fna/result_gtdb.tsv
[2023-06-29 13:37:19,000] [INFO] ===== GTDB Search completed =====
[2023-06-29 13:37:19,003] [INFO] DFAST_QC result json was written to GCA_021740085.1_ASM2174008v1_genomic.fna/dqc_result.json
[2023-06-29 13:37:19,003] [INFO] DFAST_QC completed!
[2023-06-29 13:37:19,003] [INFO] Total running time: 0h1m10s