[2024-01-24 11:12:58,107] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:58,109] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:58,109] [INFO] DQC Reference Directory: /var/lib/cwl/stgdb2048fb-5710-41aa-a6b7-1c1f9fa39707/dqc_reference
[2024-01-24 11:12:59,559] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:59,560] [INFO] Task started: Prodigal
[2024-01-24 11:12:59,560] [INFO] Running command: gunzip -c /var/lib/cwl/stg9dc8f0ab-d239-4af1-95eb-fd9d8f1e7f49/GCF_017979365.1_ASM1797936v1_genomic.fna.gz | prodigal -d GCF_017979365.1_ASM1797936v1_genomic.fna/cds.fna -a GCF_017979365.1_ASM1797936v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:13:03,635] [INFO] Task succeeded: Prodigal
[2024-01-24 11:13:03,635] [INFO] Task started: HMMsearch
[2024-01-24 11:13:03,635] [INFO] Running command: hmmsearch --tblout GCF_017979365.1_ASM1797936v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdb2048fb-5710-41aa-a6b7-1c1f9fa39707/dqc_reference/reference_markers.hmm GCF_017979365.1_ASM1797936v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:13:03,873] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:13:03,874] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg9dc8f0ab-d239-4af1-95eb-fd9d8f1e7f49/GCF_017979365.1_ASM1797936v1_genomic.fna.gz]
[2024-01-24 11:13:03,894] [INFO] Query marker FASTA was written to GCF_017979365.1_ASM1797936v1_genomic.fna/markers.fasta
[2024-01-24 11:13:03,894] [INFO] Task started: Blastn
[2024-01-24 11:13:03,894] [INFO] Running command: blastn -query GCF_017979365.1_ASM1797936v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdb2048fb-5710-41aa-a6b7-1c1f9fa39707/dqc_reference/reference_markers.fasta -out GCF_017979365.1_ASM1797936v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:04,450] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:04,453] [INFO] Selected 9 target genomes.
[2024-01-24 11:13:04,453] [INFO] Target genome list was writen to GCF_017979365.1_ASM1797936v1_genomic.fna/target_genomes.txt
[2024-01-24 11:13:04,483] [INFO] Task started: fastANI
[2024-01-24 11:13:04,484] [INFO] Running command: fastANI --query /var/lib/cwl/stg9dc8f0ab-d239-4af1-95eb-fd9d8f1e7f49/GCF_017979365.1_ASM1797936v1_genomic.fna.gz --refList GCF_017979365.1_ASM1797936v1_genomic.fna/target_genomes.txt --output GCF_017979365.1_ASM1797936v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:13:08,519] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:08,520] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdb2048fb-5710-41aa-a6b7-1c1f9fa39707/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:13:08,520] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdb2048fb-5710-41aa-a6b7-1c1f9fa39707/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:13:08,527] [INFO] Found 4 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:13:08,527] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:13:08,527] [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 fennelliae	strain=DSM 7491	GCA_017979365.1	215	215	suspected-type	True	100.0	518	542	95	conclusive
Helicobacter labetoulli	strain=48519	GCA_003670275.1	2315333	2315333	type	True	78.381	68	542	95	below_threshold
Helicobacter canis	strain=CCUG 32756T	GCA_008693005.1	29419	29419	type	True	77.6028	91	542	95	below_threshold
Helicobacter canis	strain=CCUG 32756	GCA_017979455.1	29419	29419	type	True	77.5168	88	542	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:13:08,529] [INFO] DFAST Taxonomy check result was written to GCF_017979365.1_ASM1797936v1_genomic.fna/tc_result.tsv
[2024-01-24 11:13:08,529] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:13:08,530] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:13:08,530] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdb2048fb-5710-41aa-a6b7-1c1f9fa39707/dqc_reference/checkm_data
[2024-01-24 11:13:08,531] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:13:08,550] [INFO] Task started: CheckM
[2024-01-24 11:13:08,551] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017979365.1_ASM1797936v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017979365.1_ASM1797936v1_genomic.fna/checkm_input GCF_017979365.1_ASM1797936v1_genomic.fna/checkm_result
[2024-01-24 11:13:30,514] [INFO] Task succeeded: CheckM
[2024-01-24 11:13:30,515] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 20.83%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 11:13:30,541] [INFO] ===== Completeness check finished =====
[2024-01-24 11:13:30,541] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:13:30,542] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017979365.1_ASM1797936v1_genomic.fna/markers.fasta)
[2024-01-24 11:13:30,542] [INFO] Task started: Blastn
[2024-01-24 11:13:30,542] [INFO] Running command: blastn -query GCF_017979365.1_ASM1797936v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdb2048fb-5710-41aa-a6b7-1c1f9fa39707/dqc_reference/reference_markers_gtdb.fasta -out GCF_017979365.1_ASM1797936v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:31,170] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:31,173] [INFO] Selected 9 target genomes.
[2024-01-24 11:13:31,174] [INFO] Target genome list was writen to GCF_017979365.1_ASM1797936v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:13:31,187] [INFO] Task started: fastANI
[2024-01-24 11:13:31,188] [INFO] Running command: fastANI --query /var/lib/cwl/stg9dc8f0ab-d239-4af1-95eb-fd9d8f1e7f49/GCF_017979365.1_ASM1797936v1_genomic.fna.gz --refList GCF_017979365.1_ASM1797936v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017979365.1_ASM1797936v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:13:35,337] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:35,343] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:13:35,344] [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_017979365.1	s__Helicobacter_B fennelliae	100.0	519	542	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_B	95.0	99.60	99.16	0.90	0.87	5	conclusive
GCF_003670275.1	s__Helicobacter_C labetoulli	78.381	68	542	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008693005.1	s__Helicobacter_B canis	77.6359	90	542	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_B	95.0	97.15	95.72	0.95	0.93	4	-
GCF_900451095.1	s__Helicobacter_B canis_B	77.5778	82	542	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_001854545.1	s__Helicobacter_B sp001854545	77.3013	110	542	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_B	95.0	99.98	99.96	0.99	0.98	4	-
GCA_017502485.1	s__Helicobacter_B sp017502485	76.8552	77	542	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:13:35,345] [INFO] GTDB search result was written to GCF_017979365.1_ASM1797936v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:13:35,349] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:13:35,352] [INFO] DFAST_QC result json was written to GCF_017979365.1_ASM1797936v1_genomic.fna/dqc_result.json
[2024-01-24 11:13:35,352] [INFO] DFAST_QC completed!
[2024-01-24 11:13:35,353] [INFO] Total running time: 0h0m37s