[2024-01-25 19:00:05,755] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:00:05,757] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:00:05,757] [INFO] DQC Reference Directory: /var/lib/cwl/stg2e8bc1b8-7cc4-4e31-a049-0bd0de240dbb/dqc_reference
[2024-01-25 19:00:07,001] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:00:07,001] [INFO] Task started: Prodigal
[2024-01-25 19:00:07,002] [INFO] Running command: gunzip -c /var/lib/cwl/stg65bcaa3f-35a9-4cf1-bb41-d85a59509906/GCF_017979515.1_ASM1797951v1_genomic.fna.gz | prodigal -d GCF_017979515.1_ASM1797951v1_genomic.fna/cds.fna -a GCF_017979515.1_ASM1797951v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:00:10,948] [INFO] Task succeeded: Prodigal
[2024-01-25 19:00:10,948] [INFO] Task started: HMMsearch
[2024-01-25 19:00:10,948] [INFO] Running command: hmmsearch --tblout GCF_017979515.1_ASM1797951v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2e8bc1b8-7cc4-4e31-a049-0bd0de240dbb/dqc_reference/reference_markers.hmm GCF_017979515.1_ASM1797951v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:00:11,154] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:00:11,155] [INFO] Found 6/6 markers.
[2024-01-25 19:00:11,174] [INFO] Query marker FASTA was written to GCF_017979515.1_ASM1797951v1_genomic.fna/markers.fasta
[2024-01-25 19:00:11,175] [INFO] Task started: Blastn
[2024-01-25 19:00:11,175] [INFO] Running command: blastn -query GCF_017979515.1_ASM1797951v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2e8bc1b8-7cc4-4e31-a049-0bd0de240dbb/dqc_reference/reference_markers.fasta -out GCF_017979515.1_ASM1797951v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:00:11,707] [INFO] Task succeeded: Blastn
[2024-01-25 19:00:11,711] [INFO] Selected 9 target genomes.
[2024-01-25 19:00:11,711] [INFO] Target genome list was writen to GCF_017979515.1_ASM1797951v1_genomic.fna/target_genomes.txt
[2024-01-25 19:00:11,718] [INFO] Task started: fastANI
[2024-01-25 19:00:11,719] [INFO] Running command: fastANI --query /var/lib/cwl/stg65bcaa3f-35a9-4cf1-bb41-d85a59509906/GCF_017979515.1_ASM1797951v1_genomic.fna.gz --refList GCF_017979515.1_ASM1797951v1_genomic.fna/target_genomes.txt --output GCF_017979515.1_ASM1797951v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:00:15,187] [INFO] Task succeeded: fastANI
[2024-01-25 19:00:15,188] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2e8bc1b8-7cc4-4e31-a049-0bd0de240dbb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:00:15,188] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2e8bc1b8-7cc4-4e31-a049-0bd0de240dbb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:00:15,194] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:00:15,194] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:00:15,195] [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 bizzozeronii	strain=CIP 105233	GCA_017979515.1	56877	56877	type	True	100.0	481	484	95	conclusive
Helicobacter mehlei	strain=L15	GCA_003660265.1	2316080	2316080	type	True	90.6965	404	484	95	below_threshold
Helicobacter salomonis	strain=CIP 105607	GCA_017979425.1	56878	56878	type	True	79.9066	159	484	95	below_threshold
Helicobacter vulpis	strain=L2	GCA_003660395.1	2316076	2316076	type	True	79.3717	208	484	95	below_threshold
Helicobacter felis	strain=ATCC 49179	GCA_000200595.1	214	214	type	True	79.3223	212	484	95	below_threshold
Helicobacter ailurogastricus		GCA_001282945.1	1578720	1578720	type	True	78.9323	219	484	95	below_threshold
Helicobacter heilmannii	strain=LMG 26292	GCA_017979395.1	35817	35817	type	True	78.514	179	484	95	below_threshold
Helicobacter heilmannii		GCA_001283065.1	35817	35817	type	True	78.4801	187	484	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:00:15,196] [INFO] DFAST Taxonomy check result was written to GCF_017979515.1_ASM1797951v1_genomic.fna/tc_result.tsv
[2024-01-25 19:00:15,196] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:00:15,197] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:00:15,197] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2e8bc1b8-7cc4-4e31-a049-0bd0de240dbb/dqc_reference/checkm_data
[2024-01-25 19:00:15,197] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:00:15,219] [INFO] Task started: CheckM
[2024-01-25 19:00:15,219] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017979515.1_ASM1797951v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017979515.1_ASM1797951v1_genomic.fna/checkm_input GCF_017979515.1_ASM1797951v1_genomic.fna/checkm_result
[2024-01-25 19:00:32,151] [INFO] Task succeeded: CheckM
[2024-01-25 19:00:32,152] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:00:32,169] [INFO] ===== Completeness check finished =====
[2024-01-25 19:00:32,169] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:00:32,169] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017979515.1_ASM1797951v1_genomic.fna/markers.fasta)
[2024-01-25 19:00:32,169] [INFO] Task started: Blastn
[2024-01-25 19:00:32,169] [INFO] Running command: blastn -query GCF_017979515.1_ASM1797951v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2e8bc1b8-7cc4-4e31-a049-0bd0de240dbb/dqc_reference/reference_markers_gtdb.fasta -out GCF_017979515.1_ASM1797951v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:00:32,858] [INFO] Task succeeded: Blastn
[2024-01-25 19:00:32,860] [INFO] Selected 9 target genomes.
[2024-01-25 19:00:32,861] [INFO] Target genome list was writen to GCF_017979515.1_ASM1797951v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:00:32,869] [INFO] Task started: fastANI
[2024-01-25 19:00:32,869] [INFO] Running command: fastANI --query /var/lib/cwl/stg65bcaa3f-35a9-4cf1-bb41-d85a59509906/GCF_017979515.1_ASM1797951v1_genomic.fna.gz --refList GCF_017979515.1_ASM1797951v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017979515.1_ASM1797951v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:00:35,824] [INFO] Task succeeded: fastANI
[2024-01-25 19:00:35,831] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:00:35,831] [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
GCA_000263275.1	s__Helicobacter_E bizzozeronii	98.2038	462	484	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_E	95.0	96.96	95.19	0.90	0.83	11	conclusive
GCF_003660265.1	s__Helicobacter_E mehlei	90.6965	404	484	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_017979425.1	s__Helicobacter_E salomonis	79.8306	159	484	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_900197855.1	s__Helicobacter_E cynogastricus	79.6524	189	484	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_003660395.1	s__Helicobacter_E vulpis	79.3498	209	484	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_000200595.1	s__Helicobacter_E felis	79.2773	214	484	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_001282945.1	s__Helicobacter_E ailurogastricus	78.9323	219	484	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_E	95.0	98.41	98.32	0.95	0.92	6	-
GCF_001283065.1	s__Helicobacter_E heilmannii	78.4496	189	484	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_902196135.1	s__Helicobacter_E suis_A	77.3559	158	484	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_E	95.0	97.68	97.34	0.95	0.91	4	-
--------------------------------------------------------------------------------
[2024-01-25 19:00:35,833] [INFO] GTDB search result was written to GCF_017979515.1_ASM1797951v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:00:35,833] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:00:35,835] [INFO] DFAST_QC result json was written to GCF_017979515.1_ASM1797951v1_genomic.fna/dqc_result.json
[2024-01-25 19:00:35,836] [INFO] DFAST_QC completed!
[2024-01-25 19:00:35,836] [INFO] Total running time: 0h0m30s