[2023-06-05 02:54:19,191] [INFO] DFAST_QC pipeline started.
[2023-06-05 02:54:19,200] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 02:54:19,200] [INFO] DQC Reference Directory: /var/lib/cwl/stg6daa085c-9dd3-45c3-aadc-36c4fc8133be/dqc_reference
[2023-06-05 02:54:20,810] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 02:54:20,811] [INFO] Task started: Prodigal
[2023-06-05 02:54:20,813] [INFO] Running command: gunzip -c /var/lib/cwl/stg1d682d2e-93d6-4f10-b2b4-ab7beb9b2169/GCA_001604355.1_ASM160435v1_genomic.fna.gz | prodigal -d GCA_001604355.1_ASM160435v1_genomic.fna/cds.fna -a GCA_001604355.1_ASM160435v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 02:54:27,942] [INFO] Task succeeded: Prodigal
[2023-06-05 02:54:27,942] [INFO] Task started: HMMsearch
[2023-06-05 02:54:27,942] [INFO] Running command: hmmsearch --tblout GCA_001604355.1_ASM160435v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6daa085c-9dd3-45c3-aadc-36c4fc8133be/dqc_reference/reference_markers.hmm GCA_001604355.1_ASM160435v1_genomic.fna/protein.faa > /dev/null
[2023-06-05 02:54:28,186] [INFO] Task succeeded: HMMsearch
[2023-06-05 02:54:28,187] [INFO] Found 6/6 markers.
[2023-06-05 02:54:28,223] [INFO] Query marker FASTA was written to GCA_001604355.1_ASM160435v1_genomic.fna/markers.fasta
[2023-06-05 02:54:28,224] [INFO] Task started: Blastn
[2023-06-05 02:54:28,224] [INFO] Running command: blastn -query GCA_001604355.1_ASM160435v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6daa085c-9dd3-45c3-aadc-36c4fc8133be/dqc_reference/reference_markers.fasta -out GCA_001604355.1_ASM160435v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 02:54:28,813] [INFO] Task succeeded: Blastn
[2023-06-05 02:54:28,817] [INFO] Selected 17 target genomes.
[2023-06-05 02:54:28,818] [INFO] Target genome list was writen to GCA_001604355.1_ASM160435v1_genomic.fna/target_genomes.txt
[2023-06-05 02:54:28,861] [INFO] Task started: fastANI
[2023-06-05 02:54:28,862] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d682d2e-93d6-4f10-b2b4-ab7beb9b2169/GCA_001604355.1_ASM160435v1_genomic.fna.gz --refList GCA_001604355.1_ASM160435v1_genomic.fna/target_genomes.txt --output GCA_001604355.1_ASM160435v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 02:54:39,639] [INFO] Task succeeded: fastANI
[2023-06-05 02:54:39,639] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6daa085c-9dd3-45c3-aadc-36c4fc8133be/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 02:54:39,639] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6daa085c-9dd3-45c3-aadc-36c4fc8133be/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 02:54:39,644] [INFO] Found 2 fastANI hits (1 hits with ANI > threshold)
[2023-06-05 02:54:39,644] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-05 02:54:39,645] [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 brennaborense	strain=DSM 12168	GCA_000212415.1	81028	81028	type	True	99.2145	866	916	95	conclusive
Treponema maltophilum	strain=ATCC 51939	GCA_000413055.1	51160	51160	type	True	76.2898	89	916	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 02:54:39,647] [INFO] DFAST Taxonomy check result was written to GCA_001604355.1_ASM160435v1_genomic.fna/tc_result.tsv
[2023-06-05 02:54:39,647] [INFO] ===== Taxonomy check completed =====
[2023-06-05 02:54:39,648] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 02:54:39,648] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6daa085c-9dd3-45c3-aadc-36c4fc8133be/dqc_reference/checkm_data
[2023-06-05 02:54:39,649] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 02:54:39,690] [INFO] Task started: CheckM
[2023-06-05 02:54:39,691] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_001604355.1_ASM160435v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_001604355.1_ASM160435v1_genomic.fna/checkm_input GCA_001604355.1_ASM160435v1_genomic.fna/checkm_result
[2023-06-05 02:55:06,106] [INFO] Task succeeded: CheckM
[2023-06-05 02:55:06,107] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 02:55:06,131] [INFO] ===== Completeness check finished =====
[2023-06-05 02:55:06,132] [INFO] ===== Start GTDB Search =====
[2023-06-05 02:55:06,132] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_001604355.1_ASM160435v1_genomic.fna/markers.fasta)
[2023-06-05 02:55:06,132] [INFO] Task started: Blastn
[2023-06-05 02:55:06,133] [INFO] Running command: blastn -query GCA_001604355.1_ASM160435v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6daa085c-9dd3-45c3-aadc-36c4fc8133be/dqc_reference/reference_markers_gtdb.fasta -out GCA_001604355.1_ASM160435v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 02:55:06,973] [INFO] Task succeeded: Blastn
[2023-06-05 02:55:06,978] [INFO] Selected 31 target genomes.
[2023-06-05 02:55:06,978] [INFO] Target genome list was writen to GCA_001604355.1_ASM160435v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 02:55:07,414] [INFO] Task started: fastANI
[2023-06-05 02:55:07,414] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d682d2e-93d6-4f10-b2b4-ab7beb9b2169/GCA_001604355.1_ASM160435v1_genomic.fna.gz --refList GCA_001604355.1_ASM160435v1_genomic.fna/target_genomes_gtdb.txt --output GCA_001604355.1_ASM160435v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 02:55:19,757] [INFO] Task succeeded: fastANI
[2023-06-05 02:55:19,768] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 02:55:19,769] [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_000212415.1	s__Treponema_F brennaborense	99.2145	866	916	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_F	95.0	99.21	99.21	0.95	0.95	2	conclusive
GCA_019113455.1	s__DXHG01 sp019113455	76.3448	83	916	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__DXHG01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000413055.1	s__Treponema_C maltophilum	76.2898	89	916	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_C	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905372025.1	s__Treponema_C sp905372025	75.9992	83	916	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_C	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000413015.1	s__Treponema_D paredis	75.6482	64	916	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	95.58	95.58	0.90	0.90	2	-
GCF_014334325.1	s__Treponema_D sp014334325	75.6327	63	916	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	95.62	95.62	0.82	0.82	2	-
GCF_902983995.1	s__Treponema_D buccale	75.5544	74	916	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 02:55:19,770] [INFO] GTDB search result was written to GCA_001604355.1_ASM160435v1_genomic.fna/result_gtdb.tsv
[2023-06-05 02:55:19,771] [INFO] ===== GTDB Search completed =====
[2023-06-05 02:55:19,774] [INFO] DFAST_QC result json was written to GCA_001604355.1_ASM160435v1_genomic.fna/dqc_result.json
[2023-06-05 02:55:19,774] [INFO] DFAST_QC completed!
[2023-06-05 02:55:19,774] [INFO] Total running time: 0h1m1s