[2024-01-24 11:20:03,022] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:20:03,024] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:20:03,024] [INFO] DQC Reference Directory: /var/lib/cwl/stg728858dc-6cde-4f76-ab6a-ea3dd675f8e6/dqc_reference
[2024-01-24 11:20:04,184] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:20:04,184] [INFO] Task started: Prodigal
[2024-01-24 11:20:04,185] [INFO] Running command: gunzip -c /var/lib/cwl/stg69f916da-4b68-4387-9902-dbd1724481b9/GCF_017161325.1_ASM1716132v1_genomic.fna.gz | prodigal -d GCF_017161325.1_ASM1716132v1_genomic.fna/cds.fna -a GCF_017161325.1_ASM1716132v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:20:09,596] [INFO] Task succeeded: Prodigal
[2024-01-24 11:20:09,596] [INFO] Task started: HMMsearch
[2024-01-24 11:20:09,596] [INFO] Running command: hmmsearch --tblout GCF_017161325.1_ASM1716132v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg728858dc-6cde-4f76-ab6a-ea3dd675f8e6/dqc_reference/reference_markers.hmm GCF_017161325.1_ASM1716132v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:20:09,774] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:20:09,775] [INFO] Found 6/6 markers.
[2024-01-24 11:20:09,798] [INFO] Query marker FASTA was written to GCF_017161325.1_ASM1716132v1_genomic.fna/markers.fasta
[2024-01-24 11:20:09,798] [INFO] Task started: Blastn
[2024-01-24 11:20:09,798] [INFO] Running command: blastn -query GCF_017161325.1_ASM1716132v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg728858dc-6cde-4f76-ab6a-ea3dd675f8e6/dqc_reference/reference_markers.fasta -out GCF_017161325.1_ASM1716132v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:20:10,328] [INFO] Task succeeded: Blastn
[2024-01-24 11:20:10,331] [INFO] Selected 9 target genomes.
[2024-01-24 11:20:10,331] [INFO] Target genome list was writen to GCF_017161325.1_ASM1716132v1_genomic.fna/target_genomes.txt
[2024-01-24 11:20:10,370] [INFO] Task started: fastANI
[2024-01-24 11:20:10,371] [INFO] Running command: fastANI --query /var/lib/cwl/stg69f916da-4b68-4387-9902-dbd1724481b9/GCF_017161325.1_ASM1716132v1_genomic.fna.gz --refList GCF_017161325.1_ASM1716132v1_genomic.fna/target_genomes.txt --output GCF_017161325.1_ASM1716132v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:20:15,364] [INFO] Task succeeded: fastANI
[2024-01-24 11:20:15,365] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg728858dc-6cde-4f76-ab6a-ea3dd675f8e6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:20:15,365] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg728858dc-6cde-4f76-ab6a-ea3dd675f8e6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:20:15,371] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:20:15,371] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:20:15,371] [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 pedis	strain=T3552B	GCA_017161325.1	409322	409322	type	True	100.0	963	963	95	conclusive
Treponema denticola	strain=ATCC 35405	GCA_000008185.1	158	158	type	True	78.3352	220	963	95	below_threshold
Treponema putidum	strain=OMZ 758	GCA_000755145.1	221027	221027	type	True	78.0007	237	963	95	below_threshold
Treponema putidum	strain=ATCC 700334	GCA_007830595.1	221027	221027	type	True	77.7098	235	963	95	below_threshold
Treponema phagedenis	strain=B43.1	GCA_008153345.1	162	162	type	True	76.7351	69	963	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:20:15,372] [INFO] DFAST Taxonomy check result was written to GCF_017161325.1_ASM1716132v1_genomic.fna/tc_result.tsv
[2024-01-24 11:20:15,373] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:20:15,373] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:20:15,373] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg728858dc-6cde-4f76-ab6a-ea3dd675f8e6/dqc_reference/checkm_data
[2024-01-24 11:20:15,374] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:20:15,402] [INFO] Task started: CheckM
[2024-01-24 11:20:15,402] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017161325.1_ASM1716132v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017161325.1_ASM1716132v1_genomic.fna/checkm_input GCF_017161325.1_ASM1716132v1_genomic.fna/checkm_result
[2024-01-24 11:20:36,416] [INFO] Task succeeded: CheckM
[2024-01-24 11:20:36,417] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:20:36,433] [INFO] ===== Completeness check finished =====
[2024-01-24 11:20:36,433] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:20:36,433] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017161325.1_ASM1716132v1_genomic.fna/markers.fasta)
[2024-01-24 11:20:36,434] [INFO] Task started: Blastn
[2024-01-24 11:20:36,434] [INFO] Running command: blastn -query GCF_017161325.1_ASM1716132v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg728858dc-6cde-4f76-ab6a-ea3dd675f8e6/dqc_reference/reference_markers_gtdb.fasta -out GCF_017161325.1_ASM1716132v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:20:37,291] [INFO] Task succeeded: Blastn
[2024-01-24 11:20:37,295] [INFO] Selected 14 target genomes.
[2024-01-24 11:20:37,295] [INFO] Target genome list was writen to GCF_017161325.1_ASM1716132v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:20:37,330] [INFO] Task started: fastANI
[2024-01-24 11:20:37,330] [INFO] Running command: fastANI --query /var/lib/cwl/stg69f916da-4b68-4387-9902-dbd1724481b9/GCF_017161325.1_ASM1716132v1_genomic.fna.gz --refList GCF_017161325.1_ASM1716132v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017161325.1_ASM1716132v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:20:43,789] [INFO] Task succeeded: fastANI
[2024-01-24 11:20:43,795] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:20:43,795] [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_017161325.1	s__Treponema_B pedis	100.0	963	963	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_B	95.0	98.52	98.29	0.95	0.86	7	conclusive
GCF_000008185.1	s__Treponema_B denticola	78.3352	220	963	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_B	95.0	97.58	96.70	0.92	0.88	17	-
GCF_000755145.1	s__Treponema_B putidum	77.9697	237	963	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_B	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000413095.1	s__Treponema_B denticola_A	77.9591	235	963	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_B	95.0	99.93	99.93	0.99	0.99	2	-
GCA_905372345.1	s__Treponema_B sp905372345	77.4778	143	963	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008153345.1	s__Treponema phagedenis	76.7347	69	963	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema	95.0	99.50	99.07	0.94	0.88	14	-
--------------------------------------------------------------------------------
[2024-01-24 11:20:43,797] [INFO] GTDB search result was written to GCF_017161325.1_ASM1716132v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:20:43,797] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:20:43,800] [INFO] DFAST_QC result json was written to GCF_017161325.1_ASM1716132v1_genomic.fna/dqc_result.json
[2024-01-24 11:20:43,800] [INFO] DFAST_QC completed!
[2024-01-24 11:20:43,800] [INFO] Total running time: 0h0m41s