[2023-06-29 09:02:14,154] [INFO] DFAST_QC pipeline started.
[2023-06-29 09:02:14,155] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 09:02:14,156] [INFO] DQC Reference Directory: /var/lib/cwl/stgcf27956d-7d25-41d7-8d2f-01415fa8816f/dqc_reference
[2023-06-29 09:02:16,045] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 09:02:16,046] [INFO] Task started: Prodigal
[2023-06-29 09:02:16,047] [INFO] Running command: gunzip -c /var/lib/cwl/stg50ed4862-3407-4ec6-88cb-31279e506ee1/GCA_015491035.1_ASM1549103v1_genomic.fna.gz | prodigal -d GCA_015491035.1_ASM1549103v1_genomic.fna/cds.fna -a GCA_015491035.1_ASM1549103v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 09:02:31,408] [INFO] Task succeeded: Prodigal
[2023-06-29 09:02:31,408] [INFO] Task started: HMMsearch
[2023-06-29 09:02:31,409] [INFO] Running command: hmmsearch --tblout GCA_015491035.1_ASM1549103v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcf27956d-7d25-41d7-8d2f-01415fa8816f/dqc_reference/reference_markers.hmm GCA_015491035.1_ASM1549103v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 09:02:31,623] [INFO] Task succeeded: HMMsearch
[2023-06-29 09:02:31,624] [INFO] Found 6/6 markers.
[2023-06-29 09:02:31,657] [INFO] Query marker FASTA was written to GCA_015491035.1_ASM1549103v1_genomic.fna/markers.fasta
[2023-06-29 09:02:31,657] [INFO] Task started: Blastn
[2023-06-29 09:02:31,657] [INFO] Running command: blastn -query GCA_015491035.1_ASM1549103v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcf27956d-7d25-41d7-8d2f-01415fa8816f/dqc_reference/reference_markers.fasta -out GCA_015491035.1_ASM1549103v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 09:02:32,238] [INFO] Task succeeded: Blastn
[2023-06-29 09:02:32,242] [INFO] Selected 30 target genomes.
[2023-06-29 09:02:32,242] [INFO] Target genome list was writen to GCA_015491035.1_ASM1549103v1_genomic.fna/target_genomes.txt
[2023-06-29 09:02:32,280] [INFO] Task started: fastANI
[2023-06-29 09:02:32,280] [INFO] Running command: fastANI --query /var/lib/cwl/stg50ed4862-3407-4ec6-88cb-31279e506ee1/GCA_015491035.1_ASM1549103v1_genomic.fna.gz --refList GCA_015491035.1_ASM1549103v1_genomic.fna/target_genomes.txt --output GCA_015491035.1_ASM1549103v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 09:02:56,371] [INFO] Task succeeded: fastANI
[2023-06-29 09:02:56,372] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcf27956d-7d25-41d7-8d2f-01415fa8816f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 09:02:56,372] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcf27956d-7d25-41d7-8d2f-01415fa8816f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 09:02:56,377] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 09:02:56,377] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 09:02:56,377] [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
Cesiribacter andamanensis	strain=AMV16	GCA_000348925.1	649507	649507	type	True	76.0484	50	853	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 09:02:56,378] [INFO] DFAST Taxonomy check result was written to GCA_015491035.1_ASM1549103v1_genomic.fna/tc_result.tsv
[2023-06-29 09:02:56,379] [INFO] ===== Taxonomy check completed =====
[2023-06-29 09:02:56,379] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 09:02:56,379] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcf27956d-7d25-41d7-8d2f-01415fa8816f/dqc_reference/checkm_data
[2023-06-29 09:02:56,380] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 09:02:56,411] [INFO] Task started: CheckM
[2023-06-29 09:02:56,412] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_015491035.1_ASM1549103v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_015491035.1_ASM1549103v1_genomic.fna/checkm_input GCA_015491035.1_ASM1549103v1_genomic.fna/checkm_result
[2023-06-29 09:03:40,529] [INFO] Task succeeded: CheckM
[2023-06-29 09:03:40,530] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.61%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-29 09:03:40,547] [INFO] ===== Completeness check finished =====
[2023-06-29 09:03:40,548] [INFO] ===== Start GTDB Search =====
[2023-06-29 09:03:40,548] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_015491035.1_ASM1549103v1_genomic.fna/markers.fasta)
[2023-06-29 09:03:40,548] [INFO] Task started: Blastn
[2023-06-29 09:03:40,548] [INFO] Running command: blastn -query GCA_015491035.1_ASM1549103v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcf27956d-7d25-41d7-8d2f-01415fa8816f/dqc_reference/reference_markers_gtdb.fasta -out GCA_015491035.1_ASM1549103v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 09:03:41,416] [INFO] Task succeeded: Blastn
[2023-06-29 09:03:41,421] [INFO] Selected 28 target genomes.
[2023-06-29 09:03:41,421] [INFO] Target genome list was writen to GCA_015491035.1_ASM1549103v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 09:03:41,438] [INFO] Task started: fastANI
[2023-06-29 09:03:41,439] [INFO] Running command: fastANI --query /var/lib/cwl/stg50ed4862-3407-4ec6-88cb-31279e506ee1/GCA_015491035.1_ASM1549103v1_genomic.fna.gz --refList GCA_015491035.1_ASM1549103v1_genomic.fna/target_genomes_gtdb.txt --output GCA_015491035.1_ASM1549103v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 09:04:01,635] [INFO] Task succeeded: fastANI
[2023-06-29 09:04:01,639] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 09:04:01,640] [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_015488485.1	s__S012-113 sp015488485	99.1965	783	853	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__S012-113	95.0	99.09	98.80	0.91	0.89	4	conclusive
GCF_000348925.1	s__Cesiribacter andamanensis	76.0484	50	853	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cesiribacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 09:04:01,642] [INFO] GTDB search result was written to GCA_015491035.1_ASM1549103v1_genomic.fna/result_gtdb.tsv
[2023-06-29 09:04:01,642] [INFO] ===== GTDB Search completed =====
[2023-06-29 09:04:01,644] [INFO] DFAST_QC result json was written to GCA_015491035.1_ASM1549103v1_genomic.fna/dqc_result.json
[2023-06-29 09:04:01,645] [INFO] DFAST_QC completed!
[2023-06-29 09:04:01,645] [INFO] Total running time: 0h1m47s