[2023-06-29 22:30:17,885] [INFO] DFAST_QC pipeline started.
[2023-06-29 22:30:17,893] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 22:30:17,893] [INFO] DQC Reference Directory: /var/lib/cwl/stgbe8e2521-c710-4eb6-8461-7208413d21f6/dqc_reference
[2023-06-29 22:30:19,330] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 22:30:19,331] [INFO] Task started: Prodigal
[2023-06-29 22:30:19,331] [INFO] Running command: gunzip -c /var/lib/cwl/stge7eb1dd0-9245-40dc-8fb3-7b73da318f83/GCA_024684195.1_ASM2468419v1_genomic.fna.gz | prodigal -d GCA_024684195.1_ASM2468419v1_genomic.fna/cds.fna -a GCA_024684195.1_ASM2468419v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 22:30:22,934] [INFO] Task succeeded: Prodigal
[2023-06-29 22:30:22,934] [INFO] Task started: HMMsearch
[2023-06-29 22:30:22,934] [INFO] Running command: hmmsearch --tblout GCA_024684195.1_ASM2468419v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbe8e2521-c710-4eb6-8461-7208413d21f6/dqc_reference/reference_markers.hmm GCA_024684195.1_ASM2468419v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 22:30:23,203] [INFO] Task succeeded: HMMsearch
[2023-06-29 22:30:23,204] [INFO] Found 6/6 markers.
[2023-06-29 22:30:23,234] [INFO] Query marker FASTA was written to GCA_024684195.1_ASM2468419v1_genomic.fna/markers.fasta
[2023-06-29 22:30:23,234] [INFO] Task started: Blastn
[2023-06-29 22:30:23,234] [INFO] Running command: blastn -query GCA_024684195.1_ASM2468419v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbe8e2521-c710-4eb6-8461-7208413d21f6/dqc_reference/reference_markers.fasta -out GCA_024684195.1_ASM2468419v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 22:30:23,900] [INFO] Task succeeded: Blastn
[2023-06-29 22:30:23,905] [INFO] Selected 18 target genomes.
[2023-06-29 22:30:23,905] [INFO] Target genome list was writen to GCA_024684195.1_ASM2468419v1_genomic.fna/target_genomes.txt
[2023-06-29 22:30:23,908] [INFO] Task started: fastANI
[2023-06-29 22:30:23,908] [INFO] Running command: fastANI --query /var/lib/cwl/stge7eb1dd0-9245-40dc-8fb3-7b73da318f83/GCA_024684195.1_ASM2468419v1_genomic.fna.gz --refList GCA_024684195.1_ASM2468419v1_genomic.fna/target_genomes.txt --output GCA_024684195.1_ASM2468419v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 22:30:33,384] [INFO] Task succeeded: fastANI
[2023-06-29 22:30:33,384] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbe8e2521-c710-4eb6-8461-7208413d21f6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 22:30:33,385] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbe8e2521-c710-4eb6-8461-7208413d21f6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 22:30:33,393] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 22:30:33,393] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 22:30:33,394] [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 berlinense	strain=ATCC BAA-909	GCA_900167025.1	225004	225004	type	True	76.594	63	516	95	below_threshold
Treponema rectale	strain=DSM 103679	GCA_014202035.1	744512	744512	suspected-type	True	76.5879	54	516	95	below_threshold
Treponema porcinum	strain=ATCC BAA-908	GCA_900167145.1	261392	261392	type	True	76.4886	58	516	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 22:30:33,398] [INFO] DFAST Taxonomy check result was written to GCA_024684195.1_ASM2468419v1_genomic.fna/tc_result.tsv
[2023-06-29 22:30:33,399] [INFO] ===== Taxonomy check completed =====
[2023-06-29 22:30:33,399] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 22:30:33,399] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbe8e2521-c710-4eb6-8461-7208413d21f6/dqc_reference/checkm_data
[2023-06-29 22:30:33,400] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 22:30:33,428] [INFO] Task started: CheckM
[2023-06-29 22:30:33,429] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_024684195.1_ASM2468419v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_024684195.1_ASM2468419v1_genomic.fna/checkm_input GCA_024684195.1_ASM2468419v1_genomic.fna/checkm_result
[2023-06-29 22:30:52,884] [INFO] Task succeeded: CheckM
[2023-06-29 22:30:52,885] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 64.81%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 22:30:52,914] [INFO] ===== Completeness check finished =====
[2023-06-29 22:30:52,914] [INFO] ===== Start GTDB Search =====
[2023-06-29 22:30:52,915] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_024684195.1_ASM2468419v1_genomic.fna/markers.fasta)
[2023-06-29 22:30:52,915] [INFO] Task started: Blastn
[2023-06-29 22:30:52,916] [INFO] Running command: blastn -query GCA_024684195.1_ASM2468419v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbe8e2521-c710-4eb6-8461-7208413d21f6/dqc_reference/reference_markers_gtdb.fasta -out GCA_024684195.1_ASM2468419v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 22:30:53,912] [INFO] Task succeeded: Blastn
[2023-06-29 22:30:53,921] [INFO] Selected 22 target genomes.
[2023-06-29 22:30:53,921] [INFO] Target genome list was writen to GCA_024684195.1_ASM2468419v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 22:30:53,926] [INFO] Task started: fastANI
[2023-06-29 22:30:53,926] [INFO] Running command: fastANI --query /var/lib/cwl/stge7eb1dd0-9245-40dc-8fb3-7b73da318f83/GCA_024684195.1_ASM2468419v1_genomic.fna.gz --refList GCA_024684195.1_ASM2468419v1_genomic.fna/target_genomes_gtdb.txt --output GCA_024684195.1_ASM2468419v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 22:31:03,078] [INFO] Task succeeded: fastANI
[2023-06-29 22:31:03,096] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 22:31:03,096] [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_016287815.1	s__Treponema_D sp016287815	97.6545	463	516	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_016296655.1	s__Treponema_D sp016296655	77.9885	191	516	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_017381365.1	s__Treponema_D sp017381365	77.4384	50	516	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	97.14	97.14	0.75	0.75	2	-
GCA_900769985.1	s__Treponema_D sp900769985	77.1592	64	516	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	98.33	98.33	0.87	0.87	2	-
GCA_017940255.1	s__Treponema_D sp017940255	77.1067	62	516	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_016297415.1	s__Treponema_D sp016297415	76.8544	50	516	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_018385395.1	s__Treponema_D sp018385395	76.8417	51	516	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_017553635.1	s__Treponema_D sp017553635	76.7642	81	516	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	98.74	98.74	0.94	0.94	2	-
GCA_017963165.1	s__Treponema_D sp017963165	76.6813	51	516	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_902802305.1	s__Treponema_D sp902802305	76.6016	69	516	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_902789325.1	s__Treponema_D sp902789325	76.4308	63	516	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_017392945.1	s__Treponema_D sp017392945	76.4072	52	516	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_016283615.1	s__Treponema_D sp016283615	76.3612	56	516	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_900317625.1	s__Treponema_D sp900317625	76.3601	60	516	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	99.21	99.03	0.90	0.87	4	-
GCA_902797305.1	s__Treponema_D sp902797305	76.3447	57	516	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_902772975.1	s__Treponema_D sp902772975	76.28	57	516	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_002477955.1	s__Treponema_D sp002477955	76.1652	59	516	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	99.57	99.37	0.91	0.86	7	-
--------------------------------------------------------------------------------
[2023-06-29 22:31:03,098] [INFO] GTDB search result was written to GCA_024684195.1_ASM2468419v1_genomic.fna/result_gtdb.tsv
[2023-06-29 22:31:03,099] [INFO] ===== GTDB Search completed =====
[2023-06-29 22:31:03,103] [INFO] DFAST_QC result json was written to GCA_024684195.1_ASM2468419v1_genomic.fna/dqc_result.json
[2023-06-29 22:31:03,103] [INFO] DFAST_QC completed!
[2023-06-29 22:31:03,103] [INFO] Total running time: 0h0m45s