[2023-06-19 04:14:51,371] [INFO] DFAST_QC pipeline started.
[2023-06-19 04:14:51,374] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 04:14:51,374] [INFO] DQC Reference Directory: /var/lib/cwl/stgafa3b0df-678e-4748-a82e-a06d69fa230b/dqc_reference
[2023-06-19 04:14:52,916] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 04:14:52,917] [INFO] Task started: Prodigal
[2023-06-19 04:14:52,917] [INFO] Running command: gunzip -c /var/lib/cwl/stgccb4e01a-ca91-435e-b1b9-1da11ac60de5/GCA_018064785.1_ASM1806478v1_genomic.fna.gz | prodigal -d GCA_018064785.1_ASM1806478v1_genomic.fna/cds.fna -a GCA_018064785.1_ASM1806478v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 04:14:57,056] [INFO] Task succeeded: Prodigal
[2023-06-19 04:14:57,056] [INFO] Task started: HMMsearch
[2023-06-19 04:14:57,057] [INFO] Running command: hmmsearch --tblout GCA_018064785.1_ASM1806478v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgafa3b0df-678e-4748-a82e-a06d69fa230b/dqc_reference/reference_markers.hmm GCA_018064785.1_ASM1806478v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 04:14:57,268] [INFO] Task succeeded: HMMsearch
[2023-06-19 04:14:57,269] [INFO] Found 6/6 markers.
[2023-06-19 04:14:57,289] [INFO] Query marker FASTA was written to GCA_018064785.1_ASM1806478v1_genomic.fna/markers.fasta
[2023-06-19 04:14:57,289] [INFO] Task started: Blastn
[2023-06-19 04:14:57,289] [INFO] Running command: blastn -query GCA_018064785.1_ASM1806478v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgafa3b0df-678e-4748-a82e-a06d69fa230b/dqc_reference/reference_markers.fasta -out GCA_018064785.1_ASM1806478v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 04:14:57,891] [INFO] Task succeeded: Blastn
[2023-06-19 04:14:57,895] [INFO] Selected 12 target genomes.
[2023-06-19 04:14:57,895] [INFO] Target genome list was writen to GCA_018064785.1_ASM1806478v1_genomic.fna/target_genomes.txt
[2023-06-19 04:14:57,899] [INFO] Task started: fastANI
[2023-06-19 04:14:57,899] [INFO] Running command: fastANI --query /var/lib/cwl/stgccb4e01a-ca91-435e-b1b9-1da11ac60de5/GCA_018064785.1_ASM1806478v1_genomic.fna.gz --refList GCA_018064785.1_ASM1806478v1_genomic.fna/target_genomes.txt --output GCA_018064785.1_ASM1806478v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 04:15:03,291] [INFO] Task succeeded: fastANI
[2023-06-19 04:15:03,292] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgafa3b0df-678e-4748-a82e-a06d69fa230b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 04:15:03,293] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgafa3b0df-678e-4748-a82e-a06d69fa230b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 04:15:03,301] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 04:15:03,302] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 04:15:03,302] [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 peruense	strain=RCC2812	GCA_016117655.1	2787628	2787628	type	True	76.6974	51	509	95	below_threshold
Treponema succinifaciens	strain=DSM 2489	GCA_000195275.1	167	167	type	True	76.6204	62	509	95	below_threshold
Treponema rectale	strain=DSM 103679	GCA_014202035.1	744512	744512	suspected-type	True	76.4831	54	509	95	below_threshold
Treponema ruminis	strain=DSM 103462	GCA_014201975.1	744515	744515	type	True	75.7655	50	509	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 04:15:03,304] [INFO] DFAST Taxonomy check result was written to GCA_018064785.1_ASM1806478v1_genomic.fna/tc_result.tsv
[2023-06-19 04:15:03,304] [INFO] ===== Taxonomy check completed =====
[2023-06-19 04:15:03,304] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 04:15:03,305] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgafa3b0df-678e-4748-a82e-a06d69fa230b/dqc_reference/checkm_data
[2023-06-19 04:15:03,306] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 04:15:03,327] [INFO] Task started: CheckM
[2023-06-19 04:15:03,327] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018064785.1_ASM1806478v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018064785.1_ASM1806478v1_genomic.fna/checkm_input GCA_018064785.1_ASM1806478v1_genomic.fna/checkm_result
[2023-06-19 04:15:23,069] [INFO] Task succeeded: CheckM
[2023-06-19 04:15:23,070] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 63.65%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 04:15:23,100] [INFO] ===== Completeness check finished =====
[2023-06-19 04:15:23,100] [INFO] ===== Start GTDB Search =====
[2023-06-19 04:15:23,101] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018064785.1_ASM1806478v1_genomic.fna/markers.fasta)
[2023-06-19 04:15:23,101] [INFO] Task started: Blastn
[2023-06-19 04:15:23,101] [INFO] Running command: blastn -query GCA_018064785.1_ASM1806478v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgafa3b0df-678e-4748-a82e-a06d69fa230b/dqc_reference/reference_markers_gtdb.fasta -out GCA_018064785.1_ASM1806478v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 04:15:23,977] [INFO] Task succeeded: Blastn
[2023-06-19 04:15:23,982] [INFO] Selected 15 target genomes.
[2023-06-19 04:15:23,982] [INFO] Target genome list was writen to GCA_018064785.1_ASM1806478v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 04:15:24,062] [INFO] Task started: fastANI
[2023-06-19 04:15:24,063] [INFO] Running command: fastANI --query /var/lib/cwl/stgccb4e01a-ca91-435e-b1b9-1da11ac60de5/GCA_018064785.1_ASM1806478v1_genomic.fna.gz --refList GCA_018064785.1_ASM1806478v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018064785.1_ASM1806478v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 04:15:29,958] [INFO] Task succeeded: fastANI
[2023-06-19 04:15:29,969] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 04:15:29,969] [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_018064785.1	s__Treponema_D sp018064785	100.0	496	509	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_016293645.1	s__Treponema_D sp016293645	81.9129	308	509	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_018384055.1	s__Treponema_D sp018384055	81.8782	307	509	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	98.95	98.78	0.89	0.86	3	-
GCA_016294035.1	s__Treponema_D sp016294035	78.4069	117	509	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	98.69	98.66	0.93	0.91	3	-
GCF_016117655.1	s__Treponema_D sp900541995	76.6974	51	509	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	98.86	98.78	0.96	0.96	3	-
GCA_002394685.1	s__Treponema_D sp002394685	76.6963	55	509	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	98.10	97.94	0.89	0.88	4	-
GCA_002449305.1	s__Treponema_D sp002449305	76.5407	61	509	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	98.77	97.10	0.90	0.86	10	-
--------------------------------------------------------------------------------
[2023-06-19 04:15:29,971] [INFO] GTDB search result was written to GCA_018064785.1_ASM1806478v1_genomic.fna/result_gtdb.tsv
[2023-06-19 04:15:29,972] [INFO] ===== GTDB Search completed =====
[2023-06-19 04:15:29,975] [INFO] DFAST_QC result json was written to GCA_018064785.1_ASM1806478v1_genomic.fna/dqc_result.json
[2023-06-19 04:15:29,975] [INFO] DFAST_QC completed!
[2023-06-19 04:15:29,975] [INFO] Total running time: 0h0m39s