[2024-01-25 20:03:50,729] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:03:50,730] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:03:50,730] [INFO] DQC Reference Directory: /var/lib/cwl/stgcec4da5e-ed55-4ba1-a944-3437d370b93c/dqc_reference
[2024-01-25 20:03:51,835] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:03:51,836] [INFO] Task started: Prodigal
[2024-01-25 20:03:51,836] [INFO] Running command: gunzip -c /var/lib/cwl/stg74995d76-f28c-406f-98d5-281760cf4a24/GCF_014201975.1_ASM1420197v1_genomic.fna.gz | prodigal -d GCF_014201975.1_ASM1420197v1_genomic.fna/cds.fna -a GCF_014201975.1_ASM1420197v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:03:59,016] [INFO] Task succeeded: Prodigal
[2024-01-25 20:03:59,016] [INFO] Task started: HMMsearch
[2024-01-25 20:03:59,016] [INFO] Running command: hmmsearch --tblout GCF_014201975.1_ASM1420197v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcec4da5e-ed55-4ba1-a944-3437d370b93c/dqc_reference/reference_markers.hmm GCF_014201975.1_ASM1420197v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:03:59,294] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:03:59,295] [INFO] Found 6/6 markers.
[2024-01-25 20:03:59,320] [INFO] Query marker FASTA was written to GCF_014201975.1_ASM1420197v1_genomic.fna/markers.fasta
[2024-01-25 20:03:59,320] [INFO] Task started: Blastn
[2024-01-25 20:03:59,320] [INFO] Running command: blastn -query GCF_014201975.1_ASM1420197v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcec4da5e-ed55-4ba1-a944-3437d370b93c/dqc_reference/reference_markers.fasta -out GCF_014201975.1_ASM1420197v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:03:59,838] [INFO] Task succeeded: Blastn
[2024-01-25 20:03:59,842] [INFO] Selected 14 target genomes.
[2024-01-25 20:03:59,842] [INFO] Target genome list was writen to GCF_014201975.1_ASM1420197v1_genomic.fna/target_genomes.txt
[2024-01-25 20:03:59,851] [INFO] Task started: fastANI
[2024-01-25 20:03:59,852] [INFO] Running command: fastANI --query /var/lib/cwl/stg74995d76-f28c-406f-98d5-281760cf4a24/GCF_014201975.1_ASM1420197v1_genomic.fna.gz --refList GCF_014201975.1_ASM1420197v1_genomic.fna/target_genomes.txt --output GCF_014201975.1_ASM1420197v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:04:06,279] [INFO] Task succeeded: fastANI
[2024-01-25 20:04:06,279] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcec4da5e-ed55-4ba1-a944-3437d370b93c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:04:06,280] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcec4da5e-ed55-4ba1-a944-3437d370b93c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:04:06,283] [INFO] Found 2 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:04:06,283] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:04:06,284] [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	100.0	1101	1101	95	conclusive
Treponema berlinense	strain=ATCC BAA-909	GCA_900167025.1	225004	225004	type	True	77.515	127	1101	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:04:06,285] [INFO] DFAST Taxonomy check result was written to GCF_014201975.1_ASM1420197v1_genomic.fna/tc_result.tsv
[2024-01-25 20:04:06,285] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:04:06,285] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:04:06,286] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcec4da5e-ed55-4ba1-a944-3437d370b93c/dqc_reference/checkm_data
[2024-01-25 20:04:06,286] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:04:06,329] [INFO] Task started: CheckM
[2024-01-25 20:04:06,329] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014201975.1_ASM1420197v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014201975.1_ASM1420197v1_genomic.fna/checkm_input GCF_014201975.1_ASM1420197v1_genomic.fna/checkm_result
[2024-01-25 20:04:32,831] [INFO] Task succeeded: CheckM
[2024-01-25 20:04:32,832] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:04:32,847] [INFO] ===== Completeness check finished =====
[2024-01-25 20:04:32,847] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:04:32,848] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014201975.1_ASM1420197v1_genomic.fna/markers.fasta)
[2024-01-25 20:04:32,848] [INFO] Task started: Blastn
[2024-01-25 20:04:32,848] [INFO] Running command: blastn -query GCF_014201975.1_ASM1420197v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcec4da5e-ed55-4ba1-a944-3437d370b93c/dqc_reference/reference_markers_gtdb.fasta -out GCF_014201975.1_ASM1420197v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:04:33,658] [INFO] Task succeeded: Blastn
[2024-01-25 20:04:33,662] [INFO] Selected 12 target genomes.
[2024-01-25 20:04:33,662] [INFO] Target genome list was writen to GCF_014201975.1_ASM1420197v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:04:33,673] [INFO] Task started: fastANI
[2024-01-25 20:04:33,673] [INFO] Running command: fastANI --query /var/lib/cwl/stg74995d76-f28c-406f-98d5-281760cf4a24/GCF_014201975.1_ASM1420197v1_genomic.fna.gz --refList GCF_014201975.1_ASM1420197v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014201975.1_ASM1420197v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:04:41,224] [INFO] Task succeeded: fastANI
[2024-01-25 20:04:41,232] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:04:41,232] [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_017161305.1	s__Treponema_D ruminis	99.9778	890	1101	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	99.98	99.98	0.92	0.92	2	conclusive
GCA_902785455.1	s__Treponema_D sp902785455	87.0574	698	1101	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_017430385.1	s__Treponema_D sp017430385	83.0324	595	1101	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_017469785.1	s__Treponema_D sp017469785	80.4078	445	1101	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	80.1865	334	1101	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	80.0528	422	1101	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	79.6314	345	1101	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_017484285.1	s__Treponema_D sp017484285	79.2181	369	1101	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_017464425.1	s__Treponema_D sp017464425	78.9489	338	1101	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_017449265.1	s__Treponema_D sp017449265	78.9339	172	1101	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_902803735.1	s__Treponema_D sp902803735	78.2443	106	1101	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_017449285.1	s__Treponema_D sp017449285	77.6576	119	1101	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:04:41,234] [INFO] GTDB search result was written to GCF_014201975.1_ASM1420197v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:04:41,234] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:04:41,237] [INFO] DFAST_QC result json was written to GCF_014201975.1_ASM1420197v1_genomic.fna/dqc_result.json
[2024-01-25 20:04:41,237] [INFO] DFAST_QC completed!
[2024-01-25 20:04:41,237] [INFO] Total running time: 0h0m51s