[2023-06-28 16:24:16,241] [INFO] DFAST_QC pipeline started.
[2023-06-28 16:24:16,243] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 16:24:16,244] [INFO] DQC Reference Directory: /var/lib/cwl/stgf454038a-c352-4b99-ad4c-30bae0898809/dqc_reference
[2023-06-28 16:24:17,482] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 16:24:17,483] [INFO] Task started: Prodigal
[2023-06-28 16:24:17,483] [INFO] Running command: gunzip -c /var/lib/cwl/stg757dc915-7c00-45a8-9458-d293b3fe84b3/GCA_017448735.1_ASM1744873v1_genomic.fna.gz | prodigal -d GCA_017448735.1_ASM1744873v1_genomic.fna/cds.fna -a GCA_017448735.1_ASM1744873v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 16:24:24,678] [INFO] Task succeeded: Prodigal
[2023-06-28 16:24:24,679] [INFO] Task started: HMMsearch
[2023-06-28 16:24:24,679] [INFO] Running command: hmmsearch --tblout GCA_017448735.1_ASM1744873v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf454038a-c352-4b99-ad4c-30bae0898809/dqc_reference/reference_markers.hmm GCA_017448735.1_ASM1744873v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 16:24:24,949] [INFO] Task succeeded: HMMsearch
[2023-06-28 16:24:24,951] [INFO] Found 6/6 markers.
[2023-06-28 16:24:24,995] [INFO] Query marker FASTA was written to GCA_017448735.1_ASM1744873v1_genomic.fna/markers.fasta
[2023-06-28 16:24:24,995] [INFO] Task started: Blastn
[2023-06-28 16:24:24,995] [INFO] Running command: blastn -query GCA_017448735.1_ASM1744873v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf454038a-c352-4b99-ad4c-30bae0898809/dqc_reference/reference_markers.fasta -out GCA_017448735.1_ASM1744873v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 16:24:25,572] [INFO] Task succeeded: Blastn
[2023-06-28 16:24:25,579] [INFO] Selected 12 target genomes.
[2023-06-28 16:24:25,580] [INFO] Target genome list was writen to GCA_017448735.1_ASM1744873v1_genomic.fna/target_genomes.txt
[2023-06-28 16:24:25,583] [INFO] Task started: fastANI
[2023-06-28 16:24:25,584] [INFO] Running command: fastANI --query /var/lib/cwl/stg757dc915-7c00-45a8-9458-d293b3fe84b3/GCA_017448735.1_ASM1744873v1_genomic.fna.gz --refList GCA_017448735.1_ASM1744873v1_genomic.fna/target_genomes.txt --output GCA_017448735.1_ASM1744873v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 16:24:32,855] [INFO] Task succeeded: fastANI
[2023-06-28 16:24:32,856] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf454038a-c352-4b99-ad4c-30bae0898809/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 16:24:32,857] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf454038a-c352-4b99-ad4c-30bae0898809/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 16:24:32,863] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 16:24:32,863] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 16:24:32,864] [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
Treponema ruminis	strain=DSM 103462	GCA_014201975.1	744515	744515	type	True	83.0216	317	646	95	below_threshold
Treponema berlinense	strain=ATCC BAA-909	GCA_900167025.1	225004	225004	type	True	78.0945	74	646	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 16:24:32,866] [INFO] DFAST Taxonomy check result was written to GCA_017448735.1_ASM1744873v1_genomic.fna/tc_result.tsv
[2023-06-28 16:24:32,867] [INFO] ===== Taxonomy check completed =====
[2023-06-28 16:24:32,867] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 16:24:32,867] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf454038a-c352-4b99-ad4c-30bae0898809/dqc_reference/checkm_data
[2023-06-28 16:24:32,868] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 16:24:32,905] [INFO] Task started: CheckM
[2023-06-28 16:24:32,905] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017448735.1_ASM1744873v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017448735.1_ASM1744873v1_genomic.fna/checkm_input GCA_017448735.1_ASM1744873v1_genomic.fna/checkm_result
[2023-06-28 16:25:01,880] [INFO] Task succeeded: CheckM
[2023-06-28 16:25:01,882] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.79%
Contamintation: 1.85%
Strain heterogeneity: 25.00%
--------------------------------------------------------------------------------
[2023-06-28 16:25:01,910] [INFO] ===== Completeness check finished =====
[2023-06-28 16:25:01,911] [INFO] ===== Start GTDB Search =====
[2023-06-28 16:25:01,911] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017448735.1_ASM1744873v1_genomic.fna/markers.fasta)
[2023-06-28 16:25:01,912] [INFO] Task started: Blastn
[2023-06-28 16:25:01,912] [INFO] Running command: blastn -query GCA_017448735.1_ASM1744873v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf454038a-c352-4b99-ad4c-30bae0898809/dqc_reference/reference_markers_gtdb.fasta -out GCA_017448735.1_ASM1744873v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 16:25:02,699] [INFO] Task succeeded: Blastn
[2023-06-28 16:25:02,704] [INFO] Selected 11 target genomes.
[2023-06-28 16:25:02,704] [INFO] Target genome list was writen to GCA_017448735.1_ASM1744873v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 16:25:02,729] [INFO] Task started: fastANI
[2023-06-28 16:25:02,730] [INFO] Running command: fastANI --query /var/lib/cwl/stg757dc915-7c00-45a8-9458-d293b3fe84b3/GCA_017448735.1_ASM1744873v1_genomic.fna.gz --refList GCA_017448735.1_ASM1744873v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017448735.1_ASM1744873v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 16:25:09,509] [INFO] Task succeeded: fastANI
[2023-06-28 16:25:09,519] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 16:25:09,519] [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_017430385.1	s__Treponema_D sp017430385	96.5634	421	646	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902785455.1	s__Treponema_D sp902785455	85.6849	312	646	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017161305.1	s__Treponema_D ruminis	82.9382	240	646	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	99.98	99.98	0.92	0.92	2	-
GCA_017449265.1	s__Treponema_D sp017449265	82.1053	103	646	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	97.79	97.79	0.82	0.82	2	-
GCA_017469785.1	s__Treponema_D sp017469785	81.7953	252	646	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	97.36	97.36	0.82	0.82	2	-
GCA_017395545.1	s__Treponema_D sp017395545	81.2576	188	646	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002368605.1	s__Treponema_D sp002368605	81.2397	201	646	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	96.93	96.81	0.81	0.77	3	-
GCA_002393835.1	s__Treponema_D sp002393835	79.9762	206	646	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	96.83	96.83	0.78	0.78	2	-
GCA_017468745.1	s__Treponema_D sp017468745	79.4889	124	646	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017484285.1	s__Treponema_D sp017484285	79.3791	194	646	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 16:25:09,521] [INFO] GTDB search result was written to GCA_017448735.1_ASM1744873v1_genomic.fna/result_gtdb.tsv
[2023-06-28 16:25:09,521] [INFO] ===== GTDB Search completed =====
[2023-06-28 16:25:09,524] [INFO] DFAST_QC result json was written to GCA_017448735.1_ASM1744873v1_genomic.fna/dqc_result.json
[2023-06-28 16:25:09,524] [INFO] DFAST_QC completed!
[2023-06-28 16:25:09,524] [INFO] Total running time: 0h0m53s