[2024-01-24 11:52:04,733] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:52:04,735] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:52:04,735] [INFO] DQC Reference Directory: /var/lib/cwl/stg2a3e0933-2ceb-490f-80c5-50624b2d8b1e/dqc_reference
[2024-01-24 11:52:05,953] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:52:05,954] [INFO] Task started: Prodigal
[2024-01-24 11:52:05,954] [INFO] Running command: gunzip -c /var/lib/cwl/stgafedc08e-0ef1-43e9-9849-8772286681a0/GCF_016117655.1_ASM1611765v1_genomic.fna.gz | prodigal -d GCF_016117655.1_ASM1611765v1_genomic.fna/cds.fna -a GCF_016117655.1_ASM1611765v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:52:12,323] [INFO] Task succeeded: Prodigal
[2024-01-24 11:52:12,323] [INFO] Task started: HMMsearch
[2024-01-24 11:52:12,323] [INFO] Running command: hmmsearch --tblout GCF_016117655.1_ASM1611765v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2a3e0933-2ceb-490f-80c5-50624b2d8b1e/dqc_reference/reference_markers.hmm GCF_016117655.1_ASM1611765v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:52:12,559] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:52:12,560] [INFO] Found 6/6 markers.
[2024-01-24 11:52:12,587] [INFO] Query marker FASTA was written to GCF_016117655.1_ASM1611765v1_genomic.fna/markers.fasta
[2024-01-24 11:52:12,588] [INFO] Task started: Blastn
[2024-01-24 11:52:12,588] [INFO] Running command: blastn -query GCF_016117655.1_ASM1611765v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2a3e0933-2ceb-490f-80c5-50624b2d8b1e/dqc_reference/reference_markers.fasta -out GCF_016117655.1_ASM1611765v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:13,140] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:13,144] [INFO] Selected 14 target genomes.
[2024-01-24 11:52:13,144] [INFO] Target genome list was writen to GCF_016117655.1_ASM1611765v1_genomic.fna/target_genomes.txt
[2024-01-24 11:52:13,191] [INFO] Task started: fastANI
[2024-01-24 11:52:13,191] [INFO] Running command: fastANI --query /var/lib/cwl/stgafedc08e-0ef1-43e9-9849-8772286681a0/GCF_016117655.1_ASM1611765v1_genomic.fna.gz --refList GCF_016117655.1_ASM1611765v1_genomic.fna/target_genomes.txt --output GCF_016117655.1_ASM1611765v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:52:21,158] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:21,159] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2a3e0933-2ceb-490f-80c5-50624b2d8b1e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:52:21,160] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2a3e0933-2ceb-490f-80c5-50624b2d8b1e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:52:21,171] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:52:21,171] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:52:21,171] [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	100.0	911	912	95	conclusive
Treponema succinifaciens	strain=DSM 2489	GCA_000195275.1	167	167	type	True	79.1069	181	912	95	below_threshold
Treponema berlinense	strain=ATCC BAA-909	GCA_900167025.1	225004	225004	type	True	78.1063	91	912	95	below_threshold
Treponema rectale	strain=DSM 103679	GCA_014202035.1	744512	744512	suspected-type	True	77.4172	142	912	95	below_threshold
Treponema porcinum	strain=ATCC BAA-908	GCA_900167145.1	261392	261392	type	True	77.3307	83	912	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:52:21,174] [INFO] DFAST Taxonomy check result was written to GCF_016117655.1_ASM1611765v1_genomic.fna/tc_result.tsv
[2024-01-24 11:52:21,174] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:52:21,175] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:52:21,175] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2a3e0933-2ceb-490f-80c5-50624b2d8b1e/dqc_reference/checkm_data
[2024-01-24 11:52:21,176] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:52:21,206] [INFO] Task started: CheckM
[2024-01-24 11:52:21,206] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016117655.1_ASM1611765v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016117655.1_ASM1611765v1_genomic.fna/checkm_input GCF_016117655.1_ASM1611765v1_genomic.fna/checkm_result
[2024-01-24 11:52:46,165] [INFO] Task succeeded: CheckM
[2024-01-24 11:52:46,167] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:52:46,190] [INFO] ===== Completeness check finished =====
[2024-01-24 11:52:46,191] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:52:46,191] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016117655.1_ASM1611765v1_genomic.fna/markers.fasta)
[2024-01-24 11:52:46,191] [INFO] Task started: Blastn
[2024-01-24 11:52:46,191] [INFO] Running command: blastn -query GCF_016117655.1_ASM1611765v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2a3e0933-2ceb-490f-80c5-50624b2d8b1e/dqc_reference/reference_markers_gtdb.fasta -out GCF_016117655.1_ASM1611765v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:47,014] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:47,019] [INFO] Selected 25 target genomes.
[2024-01-24 11:52:47,019] [INFO] Target genome list was writen to GCF_016117655.1_ASM1611765v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:52:47,079] [INFO] Task started: fastANI
[2024-01-24 11:52:47,080] [INFO] Running command: fastANI --query /var/lib/cwl/stgafedc08e-0ef1-43e9-9849-8772286681a0/GCF_016117655.1_ASM1611765v1_genomic.fna.gz --refList GCF_016117655.1_ASM1611765v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016117655.1_ASM1611765v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:52:59,320] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:59,333] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:52:59,334] [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_016117655.1	s__Treponema_D sp900541995	100.0	911	912	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	98.86	98.78	0.96	0.96	3	conclusive
GCF_000195275.1	s__Treponema_D succinifaciens	79.1854	181	912	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	98.40	98.24	0.92	0.91	3	-
GCA_002449305.1	s__Treponema_D sp002449305	77.6531	159	912	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	98.77	97.10	0.90	0.86	10	-
GCA_016294035.1	s__Treponema_D sp016294035	77.4753	101	912	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_014202035.1	s__Treponema_D rectale	77.4172	142	912	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	97.45	97.19	0.93	0.91	3	-
GCA_002309305.1	s__Treponema_D sp002309305	77.0561	94	912	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	97.47	97.07	0.88	0.84	3	-
GCA_016282455.1	s__Treponema_D sp016282455	76.8918	94	912	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_017961705.1	s__Treponema_D sp017961705	76.8805	103	912	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	97.01	97.01	0.82	0.82	2	-
GCA_017935745.1	s__Treponema_D sp017935745	76.6503	103	912	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_902766125.1	s__Treponema_D sp902766125	76.5841	125	912	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	99.55	99.55	0.96	0.96	2	-
GCA_018064785.1	s__Treponema_D sp018064785	76.5518	60	912	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	76.3241	58	912	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	75.9427	70	912	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_018064525.1	s__Treponema_D sp018064525	75.8492	59	912	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_017617145.1	s__Treponema_D sp017617145	75.7178	59	912	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:52:59,335] [INFO] GTDB search result was written to GCF_016117655.1_ASM1611765v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:52:59,336] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:52:59,340] [INFO] DFAST_QC result json was written to GCF_016117655.1_ASM1611765v1_genomic.fna/dqc_result.json
[2024-01-24 11:52:59,340] [INFO] DFAST_QC completed!
[2024-01-24 11:52:59,340] [INFO] Total running time: 0h0m55s