[2024-01-25 19:47:35,955] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:47:35,957] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:47:35,957] [INFO] DQC Reference Directory: /var/lib/cwl/stg8c665f3e-0d0c-43bd-8e10-40ba28bb43d0/dqc_reference
[2024-01-25 19:47:37,100] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:47:37,101] [INFO] Task started: Prodigal
[2024-01-25 19:47:37,101] [INFO] Running command: gunzip -c /var/lib/cwl/stg49e21e40-5c85-4a4d-8091-28378fb8b611/GCF_900461455.1_57530_D01_genomic.fna.gz | prodigal -d GCF_900461455.1_57530_D01_genomic.fna/cds.fna -a GCF_900461455.1_57530_D01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:47:40,292] [INFO] Task succeeded: Prodigal
[2024-01-25 19:47:40,292] [INFO] Task started: HMMsearch
[2024-01-25 19:47:40,292] [INFO] Running command: hmmsearch --tblout GCF_900461455.1_57530_D01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8c665f3e-0d0c-43bd-8e10-40ba28bb43d0/dqc_reference/reference_markers.hmm GCF_900461455.1_57530_D01_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:47:40,455] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:47:40,457] [INFO] Found 6/6 markers.
[2024-01-25 19:47:40,474] [INFO] Query marker FASTA was written to GCF_900461455.1_57530_D01_genomic.fna/markers.fasta
[2024-01-25 19:47:40,474] [INFO] Task started: Blastn
[2024-01-25 19:47:40,474] [INFO] Running command: blastn -query GCF_900461455.1_57530_D01_genomic.fna/markers.fasta -db /var/lib/cwl/stg8c665f3e-0d0c-43bd-8e10-40ba28bb43d0/dqc_reference/reference_markers.fasta -out GCF_900461455.1_57530_D01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:47:41,001] [INFO] Task succeeded: Blastn
[2024-01-25 19:47:41,005] [INFO] Selected 6 target genomes.
[2024-01-25 19:47:41,005] [INFO] Target genome list was writen to GCF_900461455.1_57530_D01_genomic.fna/target_genomes.txt
[2024-01-25 19:47:41,014] [INFO] Task started: fastANI
[2024-01-25 19:47:41,014] [INFO] Running command: fastANI --query /var/lib/cwl/stg49e21e40-5c85-4a4d-8091-28378fb8b611/GCF_900461455.1_57530_D01_genomic.fna.gz --refList GCF_900461455.1_57530_D01_genomic.fna/target_genomes.txt --output GCF_900461455.1_57530_D01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:47:43,574] [INFO] Task succeeded: fastANI
[2024-01-25 19:47:43,574] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8c665f3e-0d0c-43bd-8e10-40ba28bb43d0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:47:43,574] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8c665f3e-0d0c-43bd-8e10-40ba28bb43d0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:47:43,580] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:47:43,580] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:47:43,580] [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
Helicobacter acinonychis	strain=NCTC12686	GCA_900461455.1	212	212	type	True	100.0	521	525	95	conclusive
Helicobacter pylori	strain=CCUG 17874	GCA_000258845.1	210	210	type	True	89.8018	384	525	95	below_threshold
Helicobacter pylori	strain=FDAARGOS_298	GCA_003050665.1	210	210	type	True	89.7233	453	525	95	below_threshold
Helicobacter pylori	strain=ATCC 43504	GCA_004295525.1	210	210	type	True	89.6916	459	525	95	below_threshold
Helicobacter pylori	strain=NCTC 11637	GCA_900478295.1	210	210	type	True	89.6581	458	525	95	below_threshold
Helicobacter pylori	strain=JCM 12093	GCA_014654435.1	210	210	type	True	89.5185	417	525	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:47:43,581] [INFO] DFAST Taxonomy check result was written to GCF_900461455.1_57530_D01_genomic.fna/tc_result.tsv
[2024-01-25 19:47:43,584] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:47:43,584] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:47:43,584] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8c665f3e-0d0c-43bd-8e10-40ba28bb43d0/dqc_reference/checkm_data
[2024-01-25 19:47:43,585] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:47:43,602] [INFO] Task started: CheckM
[2024-01-25 19:47:43,603] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900461455.1_57530_D01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900461455.1_57530_D01_genomic.fna/checkm_input GCF_900461455.1_57530_D01_genomic.fna/checkm_result
[2024-01-25 19:47:59,954] [INFO] Task succeeded: CheckM
[2024-01-25 19:47:59,955] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 11.11%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-25 19:47:59,973] [INFO] ===== Completeness check finished =====
[2024-01-25 19:47:59,973] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:47:59,973] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900461455.1_57530_D01_genomic.fna/markers.fasta)
[2024-01-25 19:47:59,973] [INFO] Task started: Blastn
[2024-01-25 19:47:59,974] [INFO] Running command: blastn -query GCF_900461455.1_57530_D01_genomic.fna/markers.fasta -db /var/lib/cwl/stg8c665f3e-0d0c-43bd-8e10-40ba28bb43d0/dqc_reference/reference_markers_gtdb.fasta -out GCF_900461455.1_57530_D01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:48:00,730] [INFO] Task succeeded: Blastn
[2024-01-25 19:48:00,733] [INFO] Selected 10 target genomes.
[2024-01-25 19:48:00,733] [INFO] Target genome list was writen to GCF_900461455.1_57530_D01_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:48:00,742] [INFO] Task started: fastANI
[2024-01-25 19:48:00,742] [INFO] Running command: fastANI --query /var/lib/cwl/stg49e21e40-5c85-4a4d-8091-28378fb8b611/GCF_900461455.1_57530_D01_genomic.fna.gz --refList GCF_900461455.1_57530_D01_genomic.fna/target_genomes_gtdb.txt --output GCF_900461455.1_57530_D01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:48:05,136] [INFO] Task succeeded: fastANI
[2024-01-25 19:48:05,143] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:48:05,144] [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_900461455.1	s__Helicobacter acinonychis	100.0	521	525	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter	95.0	99.53	97.65	0.99	0.97	8	conclusive
GCF_001653455.1	s__Helicobacter pylori_A	92.0581	462	525	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter	95.0	96.27	95.96	0.96	0.93	36	-
GCF_000476275.1	s__Helicobacter pylori_CL	90.2463	442	525	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter	95.0096	99.99	99.99	0.99	0.99	2	-
GCF_003637665.1	s__Helicobacter pylori_CK	90.0051	452	525	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter	95.0255	95.54	95.27	0.95	0.93	16	-
GCF_003636935.1	s__Helicobacter pylori_CH	89.8858	447	525	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003637685.1	s__Helicobacter pylori_CJ	89.7607	448	525	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter	95.1579	95.67	95.36	0.94	0.91	66	-
GCF_001653475.1	s__Helicobacter pylori_CM	89.7532	442	525	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter	95.1561	95.99	95.99	0.96	0.96	2	-
GCF_000277405.1	s__Helicobacter pylori_C	89.7359	450	525	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter	95.2184	96.43	95.23	0.96	0.89	435	-
GCF_900478295.1	s__Helicobacter pylori	89.6732	457	525	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter	95.1033	95.74	95.20	0.96	0.89	759	-
GCF_900120335.1	s__Helicobacter pylori_BU	89.5259	456	525	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter	95.0	96.42	95.28	0.96	0.91	376	-
--------------------------------------------------------------------------------
[2024-01-25 19:48:05,145] [INFO] GTDB search result was written to GCF_900461455.1_57530_D01_genomic.fna/result_gtdb.tsv
[2024-01-25 19:48:05,145] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:48:05,157] [INFO] DFAST_QC result json was written to GCF_900461455.1_57530_D01_genomic.fna/dqc_result.json
[2024-01-25 19:48:05,157] [INFO] DFAST_QC completed!
[2024-01-25 19:48:05,157] [INFO] Total running time: 0h0m29s