[2024-01-24 13:01:07,835] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:07,836] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:07,837] [INFO] DQC Reference Directory: /var/lib/cwl/stg14573c6d-f7bb-4529-96ae-f9c3589be8ef/dqc_reference
[2024-01-24 13:01:09,025] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:09,025] [INFO] Task started: Prodigal
[2024-01-24 13:01:09,026] [INFO] Running command: gunzip -c /var/lib/cwl/stgcc16ffaa-bc4d-426f-b6c1-5c16140efb32/GCF_021300655.1_ASM2130065v1_genomic.fna.gz | prodigal -d GCF_021300655.1_ASM2130065v1_genomic.fna/cds.fna -a GCF_021300655.1_ASM2130065v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:01:12,607] [INFO] Task succeeded: Prodigal
[2024-01-24 13:01:12,608] [INFO] Task started: HMMsearch
[2024-01-24 13:01:12,608] [INFO] Running command: hmmsearch --tblout GCF_021300655.1_ASM2130065v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg14573c6d-f7bb-4529-96ae-f9c3589be8ef/dqc_reference/reference_markers.hmm GCF_021300655.1_ASM2130065v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:01:12,818] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:01:12,819] [INFO] Found 6/6 markers.
[2024-01-24 13:01:12,846] [INFO] Query marker FASTA was written to GCF_021300655.1_ASM2130065v1_genomic.fna/markers.fasta
[2024-01-24 13:01:12,846] [INFO] Task started: Blastn
[2024-01-24 13:01:12,847] [INFO] Running command: blastn -query GCF_021300655.1_ASM2130065v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg14573c6d-f7bb-4529-96ae-f9c3589be8ef/dqc_reference/reference_markers.fasta -out GCF_021300655.1_ASM2130065v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:01:13,532] [INFO] Task succeeded: Blastn
[2024-01-24 13:01:13,538] [INFO] Selected 12 target genomes.
[2024-01-24 13:01:13,539] [INFO] Target genome list was writen to GCF_021300655.1_ASM2130065v1_genomic.fna/target_genomes.txt
[2024-01-24 13:01:13,595] [INFO] Task started: fastANI
[2024-01-24 13:01:13,596] [INFO] Running command: fastANI --query /var/lib/cwl/stgcc16ffaa-bc4d-426f-b6c1-5c16140efb32/GCF_021300655.1_ASM2130065v1_genomic.fna.gz --refList GCF_021300655.1_ASM2130065v1_genomic.fna/target_genomes.txt --output GCF_021300655.1_ASM2130065v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:01:17,148] [INFO] Task succeeded: fastANI
[2024-01-24 13:01:17,149] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg14573c6d-f7bb-4529-96ae-f9c3589be8ef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:01:17,149] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg14573c6d-f7bb-4529-96ae-f9c3589be8ef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:01:17,154] [INFO] Found 4 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:01:17,154] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:01:17,155] [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 kayseriensis	strain=faydin-H23	GCA_021300655.1	2905877	2905877	type	True	100.0	460	461	95	conclusive
Helicobacter pametensis	strain=ATCC 51478	GCA_000518225.1	95149	95149	type	True	79.0914	236	461	95	below_threshold
Helicobacter cholecystus	strain=ATCC 700242	GCA_003364215.1	45498	45498	type	True	77.6818	103	461	95	below_threshold
Helicobacter brantae	strain=MIT 04-9366	GCA_003364205.1	375927	375927	type	True	77.6012	124	461	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:01:17,156] [INFO] DFAST Taxonomy check result was written to GCF_021300655.1_ASM2130065v1_genomic.fna/tc_result.tsv
[2024-01-24 13:01:17,157] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:01:17,157] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:01:17,157] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg14573c6d-f7bb-4529-96ae-f9c3589be8ef/dqc_reference/checkm_data
[2024-01-24 13:01:17,158] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:01:17,187] [INFO] Task started: CheckM
[2024-01-24 13:01:17,187] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021300655.1_ASM2130065v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021300655.1_ASM2130065v1_genomic.fna/checkm_input GCF_021300655.1_ASM2130065v1_genomic.fna/checkm_result
[2024-01-24 13:01:36,110] [INFO] Task succeeded: CheckM
[2024-01-24 13:01:36,111] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:01:36,134] [INFO] ===== Completeness check finished =====
[2024-01-24 13:01:36,134] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:01:36,135] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021300655.1_ASM2130065v1_genomic.fna/markers.fasta)
[2024-01-24 13:01:36,135] [INFO] Task started: Blastn
[2024-01-24 13:01:36,135] [INFO] Running command: blastn -query GCF_021300655.1_ASM2130065v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg14573c6d-f7bb-4529-96ae-f9c3589be8ef/dqc_reference/reference_markers_gtdb.fasta -out GCF_021300655.1_ASM2130065v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:01:37,011] [INFO] Task succeeded: Blastn
[2024-01-24 13:01:37,015] [INFO] Selected 16 target genomes.
[2024-01-24 13:01:37,015] [INFO] Target genome list was writen to GCF_021300655.1_ASM2130065v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:01:37,048] [INFO] Task started: fastANI
[2024-01-24 13:01:37,048] [INFO] Running command: fastANI --query /var/lib/cwl/stgcc16ffaa-bc4d-426f-b6c1-5c16140efb32/GCF_021300655.1_ASM2130065v1_genomic.fna.gz --refList GCF_021300655.1_ASM2130065v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021300655.1_ASM2130065v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:01:41,485] [INFO] Task succeeded: fastANI
[2024-01-24 13:01:41,491] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:01:41,491] [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_000518225.1	s__Helicobacter_G pametensis	79.1099	235	461	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_G	95.0	99.99	99.99	1.00	1.00	3	-
GCA_019115525.1	s__Helicobacter_G avistercoris	77.7777	97	461	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_G	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003364215.1	s__Helicobacter_G cholecystus	77.7124	102	461	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_G	95.0	99.98	99.98	0.99	0.98	3	-
GCF_003364205.1	s__Helicobacter_G brantae	77.6012	124	461	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_G	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:01:41,493] [INFO] GTDB search result was written to GCF_021300655.1_ASM2130065v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:01:41,494] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:01:41,497] [INFO] DFAST_QC result json was written to GCF_021300655.1_ASM2130065v1_genomic.fna/dqc_result.json
[2024-01-24 13:01:41,497] [INFO] DFAST_QC completed!
[2024-01-24 13:01:41,497] [INFO] Total running time: 0h0m34s