[2023-06-17 18:33:44,344] [INFO] DFAST_QC pipeline started.
[2023-06-17 18:33:44,349] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 18:33:44,350] [INFO] DQC Reference Directory: /var/lib/cwl/stgb2a50b4c-725a-439b-a6b9-09dd87cae9cb/dqc_reference
[2023-06-17 18:33:45,902] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 18:33:45,903] [INFO] Task started: Prodigal
[2023-06-17 18:33:45,903] [INFO] Running command: gunzip -c /var/lib/cwl/stg2254ce6f-2441-4a64-841b-0031131a06b2/GCA_009839425.1_ASM983942v1_genomic.fna.gz | prodigal -d GCA_009839425.1_ASM983942v1_genomic.fna/cds.fna -a GCA_009839425.1_ASM983942v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 18:33:56,816] [INFO] Task succeeded: Prodigal
[2023-06-17 18:33:56,816] [INFO] Task started: HMMsearch
[2023-06-17 18:33:56,816] [INFO] Running command: hmmsearch --tblout GCA_009839425.1_ASM983942v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb2a50b4c-725a-439b-a6b9-09dd87cae9cb/dqc_reference/reference_markers.hmm GCA_009839425.1_ASM983942v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 18:33:57,102] [INFO] Task succeeded: HMMsearch
[2023-06-17 18:33:57,104] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg2254ce6f-2441-4a64-841b-0031131a06b2/GCA_009839425.1_ASM983942v1_genomic.fna.gz]
[2023-06-17 18:33:57,151] [INFO] Query marker FASTA was written to GCA_009839425.1_ASM983942v1_genomic.fna/markers.fasta
[2023-06-17 18:33:57,151] [INFO] Task started: Blastn
[2023-06-17 18:33:57,151] [INFO] Running command: blastn -query GCA_009839425.1_ASM983942v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb2a50b4c-725a-439b-a6b9-09dd87cae9cb/dqc_reference/reference_markers.fasta -out GCA_009839425.1_ASM983942v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 18:33:58,068] [INFO] Task succeeded: Blastn
[2023-06-17 18:33:58,072] [INFO] Selected 15 target genomes.
[2023-06-17 18:33:58,073] [INFO] Target genome list was writen to GCA_009839425.1_ASM983942v1_genomic.fna/target_genomes.txt
[2023-06-17 18:33:58,074] [INFO] Task started: fastANI
[2023-06-17 18:33:58,075] [INFO] Running command: fastANI --query /var/lib/cwl/stg2254ce6f-2441-4a64-841b-0031131a06b2/GCA_009839425.1_ASM983942v1_genomic.fna.gz --refList GCA_009839425.1_ASM983942v1_genomic.fna/target_genomes.txt --output GCA_009839425.1_ASM983942v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 18:34:10,971] [INFO] Task succeeded: fastANI
[2023-06-17 18:34:10,971] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb2a50b4c-725a-439b-a6b9-09dd87cae9cb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 18:34:10,972] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb2a50b4c-725a-439b-a6b9-09dd87cae9cb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 18:34:10,976] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 18:34:10,977] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-17 18:34:10,977] [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
Fulvimonas soli	strain=LMG 19981	GCA_006352285.1	155197	155197	type	True	74.8678	50	1150	95	below_threshold
Nonomuraea fuscirosea	strain=CGMCC 4.7104	GCA_003001935.1	1291556	1291556	type	True	74.7099	92	1150	95	below_threshold
Streptomyces atratus	strain=JCM 3386	GCA_014648655.1	1893	1893	suspected-type	True	74.5707	53	1150	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 18:34:10,979] [INFO] DFAST Taxonomy check result was written to GCA_009839425.1_ASM983942v1_genomic.fna/tc_result.tsv
[2023-06-17 18:34:10,979] [INFO] ===== Taxonomy check completed =====
[2023-06-17 18:34:10,980] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 18:34:10,980] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb2a50b4c-725a-439b-a6b9-09dd87cae9cb/dqc_reference/checkm_data
[2023-06-17 18:34:10,981] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 18:34:11,021] [INFO] Task started: CheckM
[2023-06-17 18:34:11,022] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_009839425.1_ASM983942v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_009839425.1_ASM983942v1_genomic.fna/checkm_input GCA_009839425.1_ASM983942v1_genomic.fna/checkm_result
[2023-06-17 18:34:45,271] [INFO] Task succeeded: CheckM
[2023-06-17 18:34:45,273] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 88.74%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 18:34:45,297] [INFO] ===== Completeness check finished =====
[2023-06-17 18:34:45,297] [INFO] ===== Start GTDB Search =====
[2023-06-17 18:34:45,297] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_009839425.1_ASM983942v1_genomic.fna/markers.fasta)
[2023-06-17 18:34:45,298] [INFO] Task started: Blastn
[2023-06-17 18:34:45,298] [INFO] Running command: blastn -query GCA_009839425.1_ASM983942v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb2a50b4c-725a-439b-a6b9-09dd87cae9cb/dqc_reference/reference_markers_gtdb.fasta -out GCA_009839425.1_ASM983942v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 18:34:46,328] [INFO] Task succeeded: Blastn
[2023-06-17 18:34:46,333] [INFO] Selected 16 target genomes.
[2023-06-17 18:34:46,333] [INFO] Target genome list was writen to GCA_009839425.1_ASM983942v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 18:34:46,345] [INFO] Task started: fastANI
[2023-06-17 18:34:46,346] [INFO] Running command: fastANI --query /var/lib/cwl/stg2254ce6f-2441-4a64-841b-0031131a06b2/GCA_009839425.1_ASM983942v1_genomic.fna.gz --refList GCA_009839425.1_ASM983942v1_genomic.fna/target_genomes_gtdb.txt --output GCA_009839425.1_ASM983942v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 18:34:55,830] [INFO] Task succeeded: fastANI
[2023-06-17 18:34:55,839] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 18:34:55,839] [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_009839425.1	s__UBA11872 sp009839425	100.0	1141	1150	d__Bacteria;p__Chloroflexota;c__UBA11872;o__UBA11872;f__UBA11872;g__UBA11872	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_011523785.1	s__UBA11872 sp011523785	87.6551	685	1150	d__Bacteria;p__Chloroflexota;c__UBA11872;o__UBA11872;f__UBA11872;g__UBA11872	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001898385.1	s__Paludisphaera sp001898385	74.8163	75	1150	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Isosphaerales;f__Isosphaeraceae;g__Paludisphaera	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 18:34:55,841] [INFO] GTDB search result was written to GCA_009839425.1_ASM983942v1_genomic.fna/result_gtdb.tsv
[2023-06-17 18:34:55,842] [INFO] ===== GTDB Search completed =====
[2023-06-17 18:34:55,844] [INFO] DFAST_QC result json was written to GCA_009839425.1_ASM983942v1_genomic.fna/dqc_result.json
[2023-06-17 18:34:55,845] [INFO] DFAST_QC completed!
[2023-06-17 18:34:55,845] [INFO] Total running time: 0h1m12s