[2024-01-25 20:16:05,642] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:16:05,644] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:16:05,644] [INFO] DQC Reference Directory: /var/lib/cwl/stgf62c5366-a494-4137-a71b-f91aeb7a6002/dqc_reference
[2024-01-25 20:16:06,817] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:16:06,818] [INFO] Task started: Prodigal
[2024-01-25 20:16:06,818] [INFO] Running command: gunzip -c /var/lib/cwl/stgf6e846cc-8eac-4e78-b98f-3793924de37d/GCF_000212415.1_ASM21241v1_genomic.fna.gz | prodigal -d GCF_000212415.1_ASM21241v1_genomic.fna/cds.fna -a GCF_000212415.1_ASM21241v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:16:13,833] [INFO] Task succeeded: Prodigal
[2024-01-25 20:16:13,834] [INFO] Task started: HMMsearch
[2024-01-25 20:16:13,834] [INFO] Running command: hmmsearch --tblout GCF_000212415.1_ASM21241v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf62c5366-a494-4137-a71b-f91aeb7a6002/dqc_reference/reference_markers.hmm GCF_000212415.1_ASM21241v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:16:14,029] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:16:14,031] [INFO] Found 6/6 markers.
[2024-01-25 20:16:14,056] [INFO] Query marker FASTA was written to GCF_000212415.1_ASM21241v1_genomic.fna/markers.fasta
[2024-01-25 20:16:14,056] [INFO] Task started: Blastn
[2024-01-25 20:16:14,056] [INFO] Running command: blastn -query GCF_000212415.1_ASM21241v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf62c5366-a494-4137-a71b-f91aeb7a6002/dqc_reference/reference_markers.fasta -out GCF_000212415.1_ASM21241v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:16:14,597] [INFO] Task succeeded: Blastn
[2024-01-25 20:16:14,600] [INFO] Selected 17 target genomes.
[2024-01-25 20:16:14,600] [INFO] Target genome list was writen to GCF_000212415.1_ASM21241v1_genomic.fna/target_genomes.txt
[2024-01-25 20:16:14,605] [INFO] Task started: fastANI
[2024-01-25 20:16:14,605] [INFO] Running command: fastANI --query /var/lib/cwl/stgf6e846cc-8eac-4e78-b98f-3793924de37d/GCF_000212415.1_ASM21241v1_genomic.fna.gz --refList GCF_000212415.1_ASM21241v1_genomic.fna/target_genomes.txt --output GCF_000212415.1_ASM21241v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:16:25,454] [INFO] Task succeeded: fastANI
[2024-01-25 20:16:25,455] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf62c5366-a494-4137-a71b-f91aeb7a6002/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:16:25,455] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf62c5366-a494-4137-a71b-f91aeb7a6002/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:16:25,460] [INFO] Found 2 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:16:25,460] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:16:25,460] [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	100.0	1018	1018	95	conclusive
Treponema maltophilum	strain=ATCC 51939	GCA_000413055.1	51160	51160	type	True	77.1281	80	1018	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:16:25,461] [INFO] DFAST Taxonomy check result was written to GCF_000212415.1_ASM21241v1_genomic.fna/tc_result.tsv
[2024-01-25 20:16:25,462] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:16:25,462] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:16:25,462] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf62c5366-a494-4137-a71b-f91aeb7a6002/dqc_reference/checkm_data
[2024-01-25 20:16:25,463] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:16:25,496] [INFO] Task started: CheckM
[2024-01-25 20:16:25,496] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000212415.1_ASM21241v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000212415.1_ASM21241v1_genomic.fna/checkm_input GCF_000212415.1_ASM21241v1_genomic.fna/checkm_result
[2024-01-25 20:16:49,714] [INFO] Task succeeded: CheckM
[2024-01-25 20:16:49,715] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:16:49,743] [INFO] ===== Completeness check finished =====
[2024-01-25 20:16:49,743] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:16:49,744] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000212415.1_ASM21241v1_genomic.fna/markers.fasta)
[2024-01-25 20:16:49,744] [INFO] Task started: Blastn
[2024-01-25 20:16:49,744] [INFO] Running command: blastn -query GCF_000212415.1_ASM21241v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf62c5366-a494-4137-a71b-f91aeb7a6002/dqc_reference/reference_markers_gtdb.fasta -out GCF_000212415.1_ASM21241v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:16:50,512] [INFO] Task succeeded: Blastn
[2024-01-25 20:16:50,516] [INFO] Selected 30 target genomes.
[2024-01-25 20:16:50,516] [INFO] Target genome list was writen to GCF_000212415.1_ASM21241v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:16:50,539] [INFO] Task started: fastANI
[2024-01-25 20:16:50,539] [INFO] Running command: fastANI --query /var/lib/cwl/stgf6e846cc-8eac-4e78-b98f-3793924de37d/GCF_000212415.1_ASM21241v1_genomic.fna.gz --refList GCF_000212415.1_ASM21241v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000212415.1_ASM21241v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:17:03,802] [INFO] Task succeeded: fastANI
[2024-01-25 20:17:03,808] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:17:03,808] [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	100.0	1018	1018	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
GCF_000413055.1	s__Treponema_C maltophilum	77.1279	80	1018	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902983995.1	s__Treponema_D buccale	76.5299	64	1018	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_019113455.1	s__DXHG01 sp019113455	76.4028	78	1018	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__DXHG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000413015.1	s__Treponema_D paredis	76.2403	68	1018	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	95.58	95.58	0.90	0.90	2	-
GCA_905372025.1	s__Treponema_C sp905372025	76.0071	74	1018	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014334325.1	s__Treponema_D sp014334325	75.8331	67	1018	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	95.62	95.62	0.82	0.82	2	-
--------------------------------------------------------------------------------
[2024-01-25 20:17:03,810] [INFO] GTDB search result was written to GCF_000212415.1_ASM21241v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:17:03,810] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:17:03,812] [INFO] DFAST_QC result json was written to GCF_000212415.1_ASM21241v1_genomic.fna/dqc_result.json
[2024-01-25 20:17:03,812] [INFO] DFAST_QC completed!
[2024-01-25 20:17:03,812] [INFO] Total running time: 0h0m58s