[2024-01-24 14:42:02,939] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:42:02,941] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:42:02,942] [INFO] DQC Reference Directory: /var/lib/cwl/stga7cb6312-c59d-4c44-b35b-80b687e0a4db/dqc_reference
[2024-01-24 14:42:04,277] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:42:04,278] [INFO] Task started: Prodigal
[2024-01-24 14:42:04,278] [INFO] Running command: gunzip -c /var/lib/cwl/stg8af71863-f109-4c8e-b17f-223247df6cf7/GCF_001282945.1_gastric_feline_helicobacters_genomic.fna.gz | prodigal -d GCF_001282945.1_gastric_feline_helicobacters_genomic.fna/cds.fna -a GCF_001282945.1_gastric_feline_helicobacters_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:42:09,069] [INFO] Task succeeded: Prodigal
[2024-01-24 14:42:09,070] [INFO] Task started: HMMsearch
[2024-01-24 14:42:09,070] [INFO] Running command: hmmsearch --tblout GCF_001282945.1_gastric_feline_helicobacters_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga7cb6312-c59d-4c44-b35b-80b687e0a4db/dqc_reference/reference_markers.hmm GCF_001282945.1_gastric_feline_helicobacters_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:42:09,336] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:42:09,338] [INFO] Found 6/6 markers.
[2024-01-24 14:42:09,363] [INFO] Query marker FASTA was written to GCF_001282945.1_gastric_feline_helicobacters_genomic.fna/markers.fasta
[2024-01-24 14:42:09,363] [INFO] Task started: Blastn
[2024-01-24 14:42:09,364] [INFO] Running command: blastn -query GCF_001282945.1_gastric_feline_helicobacters_genomic.fna/markers.fasta -db /var/lib/cwl/stga7cb6312-c59d-4c44-b35b-80b687e0a4db/dqc_reference/reference_markers.fasta -out GCF_001282945.1_gastric_feline_helicobacters_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:42:09,964] [INFO] Task succeeded: Blastn
[2024-01-24 14:42:09,968] [INFO] Selected 8 target genomes.
[2024-01-24 14:42:09,968] [INFO] Target genome list was writen to GCF_001282945.1_gastric_feline_helicobacters_genomic.fna/target_genomes.txt
[2024-01-24 14:42:09,973] [INFO] Task started: fastANI
[2024-01-24 14:42:09,973] [INFO] Running command: fastANI --query /var/lib/cwl/stg8af71863-f109-4c8e-b17f-223247df6cf7/GCF_001282945.1_gastric_feline_helicobacters_genomic.fna.gz --refList GCF_001282945.1_gastric_feline_helicobacters_genomic.fna/target_genomes.txt --output GCF_001282945.1_gastric_feline_helicobacters_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:42:12,868] [INFO] Task succeeded: fastANI
[2024-01-24 14:42:12,869] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga7cb6312-c59d-4c44-b35b-80b687e0a4db/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:42:12,869] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga7cb6312-c59d-4c44-b35b-80b687e0a4db/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:42:12,877] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:42:12,877] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:42:12,877] [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 ailurogastricus		GCA_001282945.1	1578720	1578720	type	True	100.0	518	520	95	conclusive
Helicobacter heilmannii		GCA_001283065.1	35817	35817	type	True	83.7116	419	520	95	below_threshold
Helicobacter heilmannii	strain=LMG 26292	GCA_017979395.1	35817	35817	type	True	83.6834	389	520	95	below_threshold
Helicobacter mehlei	strain=L15	GCA_003660265.1	2316080	2316080	type	True	79.3551	205	520	95	below_threshold
Helicobacter bizzozeronii	strain=CIP 105233	GCA_017979515.1	56877	56877	type	True	79.1051	227	520	95	below_threshold
Helicobacter suis	strain=DSM 19735	GCA_017979375.1	104628	104628	type	True	77.5108	125	520	95	below_threshold
Helicobacter suis	strain=HS1	GCA_000187625.2	104628	104628	type	True	77.4776	128	520	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:42:12,879] [INFO] DFAST Taxonomy check result was written to GCF_001282945.1_gastric_feline_helicobacters_genomic.fna/tc_result.tsv
[2024-01-24 14:42:12,880] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:42:12,880] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:42:12,880] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga7cb6312-c59d-4c44-b35b-80b687e0a4db/dqc_reference/checkm_data
[2024-01-24 14:42:12,882] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:42:12,901] [INFO] Task started: CheckM
[2024-01-24 14:42:12,901] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001282945.1_gastric_feline_helicobacters_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001282945.1_gastric_feline_helicobacters_genomic.fna/checkm_input GCF_001282945.1_gastric_feline_helicobacters_genomic.fna/checkm_result
[2024-01-24 14:42:33,954] [INFO] Task succeeded: CheckM
[2024-01-24 14:42:33,955] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:42:33,973] [INFO] ===== Completeness check finished =====
[2024-01-24 14:42:33,973] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:42:33,974] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001282945.1_gastric_feline_helicobacters_genomic.fna/markers.fasta)
[2024-01-24 14:42:33,974] [INFO] Task started: Blastn
[2024-01-24 14:42:33,974] [INFO] Running command: blastn -query GCF_001282945.1_gastric_feline_helicobacters_genomic.fna/markers.fasta -db /var/lib/cwl/stga7cb6312-c59d-4c44-b35b-80b687e0a4db/dqc_reference/reference_markers_gtdb.fasta -out GCF_001282945.1_gastric_feline_helicobacters_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:42:34,767] [INFO] Task succeeded: Blastn
[2024-01-24 14:42:34,773] [INFO] Selected 13 target genomes.
[2024-01-24 14:42:34,773] [INFO] Target genome list was writen to GCF_001282945.1_gastric_feline_helicobacters_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:42:34,783] [INFO] Task started: fastANI
[2024-01-24 14:42:34,783] [INFO] Running command: fastANI --query /var/lib/cwl/stg8af71863-f109-4c8e-b17f-223247df6cf7/GCF_001282945.1_gastric_feline_helicobacters_genomic.fna.gz --refList GCF_001282945.1_gastric_feline_helicobacters_genomic.fna/target_genomes_gtdb.txt --output GCF_001282945.1_gastric_feline_helicobacters_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:42:39,656] [INFO] Task succeeded: fastANI
[2024-01-24 14:42:39,667] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:42:39,667] [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_001282945.1	s__Helicobacter_E ailurogastricus	100.0	518	520	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_E	95.0	98.41	98.32	0.95	0.92	6	conclusive
GCF_001283065.1	s__Helicobacter_E heilmannii	83.728	418	520	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_E	95.0	98.65	98.18	0.97	0.95	9	-
GCF_003660265.1	s__Helicobacter_E mehlei	79.3551	205	520	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_E	95.0	99.56	99.56	0.97	0.96	3	-
GCA_000263275.1	s__Helicobacter_E bizzozeronii	79.032	242	520	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_E	95.0	96.96	95.19	0.90	0.83	11	-
GCF_000200595.1	s__Helicobacter_E felis	78.9147	184	520	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_E	95.0	97.57	97.30	0.96	0.93	23	-
GCF_900197855.1	s__Helicobacter_E cynogastricus	78.8316	154	520	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003660285.1	s__Helicobacter_E labacensis	78.4095	198	520	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_E	95.0	98.30	98.30	0.89	0.89	2	-
GCF_000187625.1	s__Helicobacter_E suis	77.4984	127	520	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_E	95.0	99.74	99.56	0.96	0.89	27	-
GCF_902196135.1	s__Helicobacter_E suis_A	77.139	134	520	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_E	95.0	97.68	97.34	0.95	0.91	4	-
--------------------------------------------------------------------------------
[2024-01-24 14:42:39,669] [INFO] GTDB search result was written to GCF_001282945.1_gastric_feline_helicobacters_genomic.fna/result_gtdb.tsv
[2024-01-24 14:42:39,670] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:42:39,675] [INFO] DFAST_QC result json was written to GCF_001282945.1_gastric_feline_helicobacters_genomic.fna/dqc_result.json
[2024-01-24 14:42:39,675] [INFO] DFAST_QC completed!
[2024-01-24 14:42:39,675] [INFO] Total running time: 0h0m37s