[2024-01-24 13:18:41,138] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:18:41,139] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:18:41,140] [INFO] DQC Reference Directory: /var/lib/cwl/stgcacb0ccf-952d-4eb6-b1fb-a7e123962421/dqc_reference
[2024-01-24 13:18:42,464] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:18:42,465] [INFO] Task started: Prodigal
[2024-01-24 13:18:42,465] [INFO] Running command: gunzip -c /var/lib/cwl/stg773aa973-4d7d-47db-9ffa-21c73aff3949/GCF_000200595.1_ASM20059v1_genomic.fna.gz | prodigal -d GCF_000200595.1_ASM20059v1_genomic.fna/cds.fna -a GCF_000200595.1_ASM20059v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:18:47,222] [INFO] Task succeeded: Prodigal
[2024-01-24 13:18:47,222] [INFO] Task started: HMMsearch
[2024-01-24 13:18:47,222] [INFO] Running command: hmmsearch --tblout GCF_000200595.1_ASM20059v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcacb0ccf-952d-4eb6-b1fb-a7e123962421/dqc_reference/reference_markers.hmm GCF_000200595.1_ASM20059v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:18:47,456] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:18:47,457] [INFO] Found 6/6 markers.
[2024-01-24 13:18:47,478] [INFO] Query marker FASTA was written to GCF_000200595.1_ASM20059v1_genomic.fna/markers.fasta
[2024-01-24 13:18:47,478] [INFO] Task started: Blastn
[2024-01-24 13:18:47,479] [INFO] Running command: blastn -query GCF_000200595.1_ASM20059v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcacb0ccf-952d-4eb6-b1fb-a7e123962421/dqc_reference/reference_markers.fasta -out GCF_000200595.1_ASM20059v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:48,082] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:48,086] [INFO] Selected 7 target genomes.
[2024-01-24 13:18:48,087] [INFO] Target genome list was writen to GCF_000200595.1_ASM20059v1_genomic.fna/target_genomes.txt
[2024-01-24 13:18:48,095] [INFO] Task started: fastANI
[2024-01-24 13:18:48,096] [INFO] Running command: fastANI --query /var/lib/cwl/stg773aa973-4d7d-47db-9ffa-21c73aff3949/GCF_000200595.1_ASM20059v1_genomic.fna.gz --refList GCF_000200595.1_ASM20059v1_genomic.fna/target_genomes.txt --output GCF_000200595.1_ASM20059v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:18:50,604] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:50,605] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcacb0ccf-952d-4eb6-b1fb-a7e123962421/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:18:50,605] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcacb0ccf-952d-4eb6-b1fb-a7e123962421/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:18:50,612] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:18:50,612] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:18:50,613] [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 felis	strain=ATCC 49179	GCA_000200595.1	214	214	type	True	100.0	557	557	95	conclusive
Helicobacter salomonis	strain=CIP 105607	GCA_017979425.1	56878	56878	type	True	81.5917	258	557	95	below_threshold
Helicobacter labacensis	strain=L9	GCA_003660285.1	2316079	2316079	type	True	80.4305	307	557	95	below_threshold
Helicobacter vulpis	strain=L2	GCA_003660395.1	2316076	2316076	type	True	80.407	289	557	95	below_threshold
Helicobacter bizzozeronii	strain=CIP 105233	GCA_017979515.1	56877	56877	type	True	79.4401	219	557	95	below_threshold
Helicobacter mehlei	strain=L15	GCA_003660265.1	2316080	2316080	type	True	79.333	224	557	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:18:50,614] [INFO] DFAST Taxonomy check result was written to GCF_000200595.1_ASM20059v1_genomic.fna/tc_result.tsv
[2024-01-24 13:18:50,615] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:18:50,615] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:18:50,615] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcacb0ccf-952d-4eb6-b1fb-a7e123962421/dqc_reference/checkm_data
[2024-01-24 13:18:50,616] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:18:50,639] [INFO] Task started: CheckM
[2024-01-24 13:18:50,639] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000200595.1_ASM20059v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000200595.1_ASM20059v1_genomic.fna/checkm_input GCF_000200595.1_ASM20059v1_genomic.fna/checkm_result
[2024-01-24 13:19:10,991] [INFO] Task succeeded: CheckM
[2024-01-24 13:19:10,992] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:19:11,033] [INFO] ===== Completeness check finished =====
[2024-01-24 13:19:11,034] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:19:11,034] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000200595.1_ASM20059v1_genomic.fna/markers.fasta)
[2024-01-24 13:19:11,035] [INFO] Task started: Blastn
[2024-01-24 13:19:11,035] [INFO] Running command: blastn -query GCF_000200595.1_ASM20059v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcacb0ccf-952d-4eb6-b1fb-a7e123962421/dqc_reference/reference_markers_gtdb.fasta -out GCF_000200595.1_ASM20059v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:11,867] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:11,871] [INFO] Selected 10 target genomes.
[2024-01-24 13:19:11,871] [INFO] Target genome list was writen to GCF_000200595.1_ASM20059v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:19:11,882] [INFO] Task started: fastANI
[2024-01-24 13:19:11,883] [INFO] Running command: fastANI --query /var/lib/cwl/stg773aa973-4d7d-47db-9ffa-21c73aff3949/GCF_000200595.1_ASM20059v1_genomic.fna.gz --refList GCF_000200595.1_ASM20059v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000200595.1_ASM20059v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:19:15,781] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:15,789] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:19:15,790] [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_000200595.1	s__Helicobacter_E felis	100.0	557	557	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_E	95.0	97.57	97.30	0.96	0.93	23	conclusive
GCF_900197855.1	s__Helicobacter_E cynogastricus	86.915	449	557	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_017979425.1	s__Helicobacter_E salomonis	81.5406	261	557	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_E	95.0	98.86	98.52	0.94	0.92	6	-
GCF_900197685.1	s__Helicobacter_E baculiformis	80.6782	256	557	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	80.4504	306	557	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_003660395.1	s__Helicobacter_E vulpis	80.407	289	557	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000263275.1	s__Helicobacter_E bizzozeronii	79.4919	235	557	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_003660265.1	s__Helicobacter_E mehlei	79.3329	224	557	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_E	95.0	99.56	99.56	0.97	0.96	3	-
GCF_902196135.1	s__Helicobacter_E suis_A	77.0454	135	557	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 13:19:15,792] [INFO] GTDB search result was written to GCF_000200595.1_ASM20059v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:19:15,792] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:19:15,801] [INFO] DFAST_QC result json was written to GCF_000200595.1_ASM20059v1_genomic.fna/dqc_result.json
[2024-01-24 13:19:15,802] [INFO] DFAST_QC completed!
[2024-01-24 13:19:15,802] [INFO] Total running time: 0h0m35s