[2024-01-25 18:56:05,412] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:56:05,414] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:56:05,414] [INFO] DQC Reference Directory: /var/lib/cwl/stg639c58ce-c3a2-445d-bd83-853049a2f23c/dqc_reference
[2024-01-25 18:56:06,598] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:56:06,599] [INFO] Task started: Prodigal
[2024-01-25 18:56:06,599] [INFO] Running command: gunzip -c /var/lib/cwl/stgb8aff349-c9b2-4842-97bc-118e27183d7c/GCF_017979455.1_ASM1797945v1_genomic.fna.gz | prodigal -d GCF_017979455.1_ASM1797945v1_genomic.fna/cds.fna -a GCF_017979455.1_ASM1797945v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:56:10,377] [INFO] Task succeeded: Prodigal
[2024-01-25 18:56:10,377] [INFO] Task started: HMMsearch
[2024-01-25 18:56:10,377] [INFO] Running command: hmmsearch --tblout GCF_017979455.1_ASM1797945v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg639c58ce-c3a2-445d-bd83-853049a2f23c/dqc_reference/reference_markers.hmm GCF_017979455.1_ASM1797945v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:56:10,572] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:56:10,573] [INFO] Found 6/6 markers.
[2024-01-25 18:56:10,590] [INFO] Query marker FASTA was written to GCF_017979455.1_ASM1797945v1_genomic.fna/markers.fasta
[2024-01-25 18:56:10,591] [INFO] Task started: Blastn
[2024-01-25 18:56:10,591] [INFO] Running command: blastn -query GCF_017979455.1_ASM1797945v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg639c58ce-c3a2-445d-bd83-853049a2f23c/dqc_reference/reference_markers.fasta -out GCF_017979455.1_ASM1797945v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:56:11,111] [INFO] Task succeeded: Blastn
[2024-01-25 18:56:11,113] [INFO] Selected 12 target genomes.
[2024-01-25 18:56:11,114] [INFO] Target genome list was writen to GCF_017979455.1_ASM1797945v1_genomic.fna/target_genomes.txt
[2024-01-25 18:56:11,128] [INFO] Task started: fastANI
[2024-01-25 18:56:11,128] [INFO] Running command: fastANI --query /var/lib/cwl/stgb8aff349-c9b2-4842-97bc-118e27183d7c/GCF_017979455.1_ASM1797945v1_genomic.fna.gz --refList GCF_017979455.1_ASM1797945v1_genomic.fna/target_genomes.txt --output GCF_017979455.1_ASM1797945v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:56:15,772] [INFO] Task succeeded: fastANI
[2024-01-25 18:56:15,773] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg639c58ce-c3a2-445d-bd83-853049a2f23c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:56:15,773] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg639c58ce-c3a2-445d-bd83-853049a2f23c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:56:15,779] [INFO] Found 7 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:56:15,779] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:56:15,779] [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 canis	strain=CCUG 32756	GCA_017979455.1	29419	29419	type	True	100.0	581	585	95	conclusive
Helicobacter canis	strain=CCUG 32756T	GCA_008693005.1	29419	29419	type	True	99.9965	578	585	95	conclusive
Helicobacter cinaedi	strain=CCUG 18818	GCA_003215615.1	213	213	type	True	82.3748	100	585	95	below_threshold
Helicobacter cinaedi	strain=CCUG 18818	GCA_000155475.1	213	213	type	True	82.065	106	585	95	below_threshold
Helicobacter cinaedi	strain=DSM 5359	GCA_017979495.1	213	213	type	True	81.9757	110	585	95	below_threshold
Helicobacter fennelliae	strain=DSM 7491	GCA_017979365.1	215	215	suspected-type	True	77.6749	87	585	95	below_threshold
Helicobacter macacae	strain=MIT 99-5501	GCA_000507845.1	398626	398626	type	True	76.4927	122	585	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:56:15,781] [INFO] DFAST Taxonomy check result was written to GCF_017979455.1_ASM1797945v1_genomic.fna/tc_result.tsv
[2024-01-25 18:56:15,781] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:56:15,781] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:56:15,782] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg639c58ce-c3a2-445d-bd83-853049a2f23c/dqc_reference/checkm_data
[2024-01-25 18:56:15,782] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:56:15,805] [INFO] Task started: CheckM
[2024-01-25 18:56:15,805] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017979455.1_ASM1797945v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017979455.1_ASM1797945v1_genomic.fna/checkm_input GCF_017979455.1_ASM1797945v1_genomic.fna/checkm_result
[2024-01-25 18:56:32,611] [INFO] Task succeeded: CheckM
[2024-01-25 18:56:32,612] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:56:32,633] [INFO] ===== Completeness check finished =====
[2024-01-25 18:56:32,633] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:56:32,633] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017979455.1_ASM1797945v1_genomic.fna/markers.fasta)
[2024-01-25 18:56:32,633] [INFO] Task started: Blastn
[2024-01-25 18:56:32,633] [INFO] Running command: blastn -query GCF_017979455.1_ASM1797945v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg639c58ce-c3a2-445d-bd83-853049a2f23c/dqc_reference/reference_markers_gtdb.fasta -out GCF_017979455.1_ASM1797945v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:56:33,347] [INFO] Task succeeded: Blastn
[2024-01-25 18:56:33,349] [INFO] Selected 10 target genomes.
[2024-01-25 18:56:33,349] [INFO] Target genome list was writen to GCF_017979455.1_ASM1797945v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:56:33,360] [INFO] Task started: fastANI
[2024-01-25 18:56:33,360] [INFO] Running command: fastANI --query /var/lib/cwl/stgb8aff349-c9b2-4842-97bc-118e27183d7c/GCF_017979455.1_ASM1797945v1_genomic.fna.gz --refList GCF_017979455.1_ASM1797945v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017979455.1_ASM1797945v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:56:37,721] [INFO] Task succeeded: fastANI
[2024-01-25 18:56:37,726] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:56:37,727] [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_008693005.1	s__Helicobacter_B canis	99.9965	578	585	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_B	95.0	97.15	95.72	0.95	0.93	4	conclusive
GCA_017502485.1	s__Helicobacter_B sp017502485	88.7196	491	585	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900451095.1	s__Helicobacter_B canis_B	86.6626	512	585	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000155475.1	s__Helicobacter_C cinaedi	81.9939	107	585	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_C	95.0	99.33	98.84	0.97	0.91	38	-
GCF_017979365.1	s__Helicobacter_B fennelliae	77.6076	89	585	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_B	95.0	99.60	99.16	0.90	0.87	5	-
GCF_001854545.1	s__Helicobacter_B sp001854545	77.1258	147	585	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_B	95.0	99.98	99.96	0.99	0.98	4	-
--------------------------------------------------------------------------------
[2024-01-25 18:56:37,728] [INFO] GTDB search result was written to GCF_017979455.1_ASM1797945v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:56:37,728] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:56:37,731] [INFO] DFAST_QC result json was written to GCF_017979455.1_ASM1797945v1_genomic.fna/dqc_result.json
[2024-01-25 18:56:37,731] [INFO] DFAST_QC completed!
[2024-01-25 18:56:37,731] [INFO] Total running time: 0h0m32s