[2023-06-30 13:46:56,940] [INFO] DFAST_QC pipeline started.
[2023-06-30 13:46:56,943] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 13:46:56,943] [INFO] DQC Reference Directory: /var/lib/cwl/stg59a334b0-37c2-431d-ad07-5b40771102c7/dqc_reference
[2023-06-30 13:46:58,175] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 13:46:58,176] [INFO] Task started: Prodigal
[2023-06-30 13:46:58,176] [INFO] Running command: gunzip -c /var/lib/cwl/stgdc34de44-58c7-45f6-a379-eb9c1ace0d19/GCA_015478575.1_ASM1547857v1_genomic.fna.gz | prodigal -d GCA_015478575.1_ASM1547857v1_genomic.fna/cds.fna -a GCA_015478575.1_ASM1547857v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 13:47:08,160] [INFO] Task succeeded: Prodigal
[2023-06-30 13:47:08,161] [INFO] Task started: HMMsearch
[2023-06-30 13:47:08,161] [INFO] Running command: hmmsearch --tblout GCA_015478575.1_ASM1547857v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg59a334b0-37c2-431d-ad07-5b40771102c7/dqc_reference/reference_markers.hmm GCA_015478575.1_ASM1547857v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 13:47:08,398] [INFO] Task succeeded: HMMsearch
[2023-06-30 13:47:08,399] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgdc34de44-58c7-45f6-a379-eb9c1ace0d19/GCA_015478575.1_ASM1547857v1_genomic.fna.gz]
[2023-06-30 13:47:08,434] [INFO] Query marker FASTA was written to GCA_015478575.1_ASM1547857v1_genomic.fna/markers.fasta
[2023-06-30 13:47:08,434] [INFO] Task started: Blastn
[2023-06-30 13:47:08,434] [INFO] Running command: blastn -query GCA_015478575.1_ASM1547857v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg59a334b0-37c2-431d-ad07-5b40771102c7/dqc_reference/reference_markers.fasta -out GCA_015478575.1_ASM1547857v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 13:47:09,127] [INFO] Task succeeded: Blastn
[2023-06-30 13:47:09,132] [INFO] Selected 23 target genomes.
[2023-06-30 13:47:09,133] [INFO] Target genome list was writen to GCA_015478575.1_ASM1547857v1_genomic.fna/target_genomes.txt
[2023-06-30 13:47:09,138] [INFO] Task started: fastANI
[2023-06-30 13:47:09,138] [INFO] Running command: fastANI --query /var/lib/cwl/stgdc34de44-58c7-45f6-a379-eb9c1ace0d19/GCA_015478575.1_ASM1547857v1_genomic.fna.gz --refList GCA_015478575.1_ASM1547857v1_genomic.fna/target_genomes.txt --output GCA_015478575.1_ASM1547857v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 13:47:29,763] [INFO] Task succeeded: fastANI
[2023-06-30 13:47:29,764] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg59a334b0-37c2-431d-ad07-5b40771102c7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 13:47:29,765] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg59a334b0-37c2-431d-ad07-5b40771102c7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 13:47:29,772] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 13:47:29,773] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 13:47:29,773] [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
Actinomadura montaniterrae	strain=CYP1-1B	GCA_008923365.1	1803903	1803903	type	True	74.6031	63	780	95	below_threshold
Dactylosporangium vinaceum	strain=NRRL B-16297	GCA_019904175.1	53362	53362	type	True	74.5836	57	780	95	below_threshold
Streptomyces gossypiisoli	strain=TRM 44567	GCA_013433285.1	2748864	2748864	type	True	74.5759	52	780	95	below_threshold
Conexibacter arvalis	strain=DSM 23288	GCA_014199525.1	912552	912552	type	True	74.5754	63	780	95	below_threshold
Dactylosporangium matsuzakiense	strain=NRRL B-16293	GCA_025264725.1	53360	53360	type	True	74.5735	58	780	95	below_threshold
Conexibacter woesei	strain=DSM 14684	GCA_000025265.1	191495	191495	type	True	74.5399	59	780	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 13:47:29,775] [INFO] DFAST Taxonomy check result was written to GCA_015478575.1_ASM1547857v1_genomic.fna/tc_result.tsv
[2023-06-30 13:47:29,776] [INFO] ===== Taxonomy check completed =====
[2023-06-30 13:47:29,776] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 13:47:29,776] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg59a334b0-37c2-431d-ad07-5b40771102c7/dqc_reference/checkm_data
[2023-06-30 13:47:29,777] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 13:47:29,824] [INFO] Task started: CheckM
[2023-06-30 13:47:29,824] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_015478575.1_ASM1547857v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_015478575.1_ASM1547857v1_genomic.fna/checkm_input GCA_015478575.1_ASM1547857v1_genomic.fna/checkm_result
[2023-06-30 13:48:03,097] [INFO] Task succeeded: CheckM
[2023-06-30 13:48:03,098] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.74%
Contamintation: 4.63%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-06-30 13:48:03,126] [INFO] ===== Completeness check finished =====
[2023-06-30 13:48:03,126] [INFO] ===== Start GTDB Search =====
[2023-06-30 13:48:03,127] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_015478575.1_ASM1547857v1_genomic.fna/markers.fasta)
[2023-06-30 13:48:03,127] [INFO] Task started: Blastn
[2023-06-30 13:48:03,127] [INFO] Running command: blastn -query GCA_015478575.1_ASM1547857v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg59a334b0-37c2-431d-ad07-5b40771102c7/dqc_reference/reference_markers_gtdb.fasta -out GCA_015478575.1_ASM1547857v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 13:48:04,049] [INFO] Task succeeded: Blastn
[2023-06-30 13:48:04,055] [INFO] Selected 30 target genomes.
[2023-06-30 13:48:04,055] [INFO] Target genome list was writen to GCA_015478575.1_ASM1547857v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 13:48:04,098] [INFO] Task started: fastANI
[2023-06-30 13:48:04,098] [INFO] Running command: fastANI --query /var/lib/cwl/stgdc34de44-58c7-45f6-a379-eb9c1ace0d19/GCA_015478575.1_ASM1547857v1_genomic.fna.gz --refList GCA_015478575.1_ASM1547857v1_genomic.fna/target_genomes_gtdb.txt --output GCA_015478575.1_ASM1547857v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 13:48:22,385] [INFO] Task succeeded: fastANI
[2023-06-30 13:48:22,391] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 13:48:22,392] [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_014651135.1	s__Streptomyces echinoruber	74.5163	50	780	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 13:48:22,394] [INFO] GTDB search result was written to GCA_015478575.1_ASM1547857v1_genomic.fna/result_gtdb.tsv
[2023-06-30 13:48:22,395] [INFO] ===== GTDB Search completed =====
[2023-06-30 13:48:22,399] [INFO] DFAST_QC result json was written to GCA_015478575.1_ASM1547857v1_genomic.fna/dqc_result.json
[2023-06-30 13:48:22,399] [INFO] DFAST_QC completed!
[2023-06-30 13:48:22,399] [INFO] Total running time: 0h1m25s