[2023-06-29 14:59:04,552] [INFO] DFAST_QC pipeline started.
[2023-06-29 14:59:04,554] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 14:59:04,554] [INFO] DQC Reference Directory: /var/lib/cwl/stga42e8696-6786-42ec-b1dd-837f6e379602/dqc_reference
[2023-06-29 14:59:05,948] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 14:59:05,949] [INFO] Task started: Prodigal
[2023-06-29 14:59:05,950] [INFO] Running command: gunzip -c /var/lib/cwl/stg753f3592-3520-4c73-9c00-8d2fda01295c/GCA_021828635.1_ASM2182863v1_genomic.fna.gz | prodigal -d GCA_021828635.1_ASM2182863v1_genomic.fna/cds.fna -a GCA_021828635.1_ASM2182863v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 14:59:16,644] [INFO] Task succeeded: Prodigal
[2023-06-29 14:59:16,645] [INFO] Task started: HMMsearch
[2023-06-29 14:59:16,645] [INFO] Running command: hmmsearch --tblout GCA_021828635.1_ASM2182863v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga42e8696-6786-42ec-b1dd-837f6e379602/dqc_reference/reference_markers.hmm GCA_021828635.1_ASM2182863v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 14:59:16,953] [INFO] Task succeeded: HMMsearch
[2023-06-29 14:59:16,954] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg753f3592-3520-4c73-9c00-8d2fda01295c/GCA_021828635.1_ASM2182863v1_genomic.fna.gz]
[2023-06-29 14:59:16,995] [INFO] Query marker FASTA was written to GCA_021828635.1_ASM2182863v1_genomic.fna/markers.fasta
[2023-06-29 14:59:16,996] [INFO] Task started: Blastn
[2023-06-29 14:59:16,996] [INFO] Running command: blastn -query GCA_021828635.1_ASM2182863v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga42e8696-6786-42ec-b1dd-837f6e379602/dqc_reference/reference_markers.fasta -out GCA_021828635.1_ASM2182863v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 14:59:17,542] [INFO] Task succeeded: Blastn
[2023-06-29 14:59:17,546] [INFO] Selected 9 target genomes.
[2023-06-29 14:59:17,546] [INFO] Target genome list was writen to GCA_021828635.1_ASM2182863v1_genomic.fna/target_genomes.txt
[2023-06-29 14:59:17,548] [INFO] Task started: fastANI
[2023-06-29 14:59:17,548] [INFO] Running command: fastANI --query /var/lib/cwl/stg753f3592-3520-4c73-9c00-8d2fda01295c/GCA_021828635.1_ASM2182863v1_genomic.fna.gz --refList GCA_021828635.1_ASM2182863v1_genomic.fna/target_genomes.txt --output GCA_021828635.1_ASM2182863v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 14:59:27,730] [INFO] Task succeeded: fastANI
[2023-06-29 14:59:27,731] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga42e8696-6786-42ec-b1dd-837f6e379602/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 14:59:27,731] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga42e8696-6786-42ec-b1dd-837f6e379602/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 14:59:27,736] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 14:59:27,737] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 14:59:27,737] [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
Dictyobacter kobayashii	strain=Uno11	GCA_003967555.1	2014872	2014872	type	True	76.4034	57	1067	95	below_threshold
Ktedonosporobacter rubrisoli	strain=SCAWS-G2	GCA_004208415.1	2509675	2509675	type	True	76.0505	57	1067	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 14:59:27,740] [INFO] DFAST Taxonomy check result was written to GCA_021828635.1_ASM2182863v1_genomic.fna/tc_result.tsv
[2023-06-29 14:59:27,740] [INFO] ===== Taxonomy check completed =====
[2023-06-29 14:59:27,741] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 14:59:27,741] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga42e8696-6786-42ec-b1dd-837f6e379602/dqc_reference/checkm_data
[2023-06-29 14:59:27,742] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 14:59:27,792] [INFO] Task started: CheckM
[2023-06-29 14:59:27,792] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_021828635.1_ASM2182863v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_021828635.1_ASM2182863v1_genomic.fna/checkm_input GCA_021828635.1_ASM2182863v1_genomic.fna/checkm_result
[2023-06-29 15:00:03,974] [INFO] Task succeeded: CheckM
[2023-06-29 15:00:03,975] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 74.62%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 15:00:03,999] [INFO] ===== Completeness check finished =====
[2023-06-29 15:00:03,999] [INFO] ===== Start GTDB Search =====
[2023-06-29 15:00:04,000] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_021828635.1_ASM2182863v1_genomic.fna/markers.fasta)
[2023-06-29 15:00:04,000] [INFO] Task started: Blastn
[2023-06-29 15:00:04,000] [INFO] Running command: blastn -query GCA_021828635.1_ASM2182863v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga42e8696-6786-42ec-b1dd-837f6e379602/dqc_reference/reference_markers_gtdb.fasta -out GCA_021828635.1_ASM2182863v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 15:00:04,470] [INFO] Task succeeded: Blastn
[2023-06-29 15:00:04,476] [INFO] Selected 13 target genomes.
[2023-06-29 15:00:04,476] [INFO] Target genome list was writen to GCA_021828635.1_ASM2182863v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 15:00:04,484] [INFO] Task started: fastANI
[2023-06-29 15:00:04,485] [INFO] Running command: fastANI --query /var/lib/cwl/stg753f3592-3520-4c73-9c00-8d2fda01295c/GCA_021828635.1_ASM2182863v1_genomic.fna.gz --refList GCA_021828635.1_ASM2182863v1_genomic.fna/target_genomes_gtdb.txt --output GCA_021828635.1_ASM2182863v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 15:00:16,051] [INFO] Task succeeded: fastANI
[2023-06-29 15:00:16,061] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 15:00:16,062] [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_011389075.1	s__DTNP01 sp011389075	78.1051	394	1067	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__DTNP01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003967555.1	s__Dictyobacter kobayashii	76.4034	57	1067	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__Dictyobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004208415.1	s__Ktedonosporobacter rubrisoli	76.0505	57	1067	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__Ktedonosporobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005881495.1	s__UBA11361 sp005881495	75.9105	54	1067	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__UBA11361	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 15:00:16,064] [INFO] GTDB search result was written to GCA_021828635.1_ASM2182863v1_genomic.fna/result_gtdb.tsv
[2023-06-29 15:00:16,065] [INFO] ===== GTDB Search completed =====
[2023-06-29 15:00:16,068] [INFO] DFAST_QC result json was written to GCA_021828635.1_ASM2182863v1_genomic.fna/dqc_result.json
[2023-06-29 15:00:16,069] [INFO] DFAST_QC completed!
[2023-06-29 15:00:16,069] [INFO] Total running time: 0h1m12s