[2024-01-24 12:47:12,368] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:47:12,370] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:47:12,370] [INFO] DQC Reference Directory: /var/lib/cwl/stga8e0ebc9-cb12-482c-b6f9-aaa5f76b9bf9/dqc_reference
[2024-01-24 12:47:13,774] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:47:13,775] [INFO] Task started: Prodigal
[2024-01-24 12:47:13,775] [INFO] Running command: gunzip -c /var/lib/cwl/stg509635d2-1836-4c7e-b86c-945d4571e273/GCF_021300615.1_ASM2130061v1_genomic.fna.gz | prodigal -d GCF_021300615.1_ASM2130061v1_genomic.fna/cds.fna -a GCF_021300615.1_ASM2130061v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:47:16,942] [INFO] Task succeeded: Prodigal
[2024-01-24 12:47:16,942] [INFO] Task started: HMMsearch
[2024-01-24 12:47:16,942] [INFO] Running command: hmmsearch --tblout GCF_021300615.1_ASM2130061v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga8e0ebc9-cb12-482c-b6f9-aaa5f76b9bf9/dqc_reference/reference_markers.hmm GCF_021300615.1_ASM2130061v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:47:17,158] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:47:17,160] [INFO] Found 6/6 markers.
[2024-01-24 12:47:17,195] [INFO] Query marker FASTA was written to GCF_021300615.1_ASM2130061v1_genomic.fna/markers.fasta
[2024-01-24 12:47:17,196] [INFO] Task started: Blastn
[2024-01-24 12:47:17,196] [INFO] Running command: blastn -query GCF_021300615.1_ASM2130061v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga8e0ebc9-cb12-482c-b6f9-aaa5f76b9bf9/dqc_reference/reference_markers.fasta -out GCF_021300615.1_ASM2130061v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:17,803] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:17,806] [INFO] Selected 20 target genomes.
[2024-01-24 12:47:17,807] [INFO] Target genome list was writen to GCF_021300615.1_ASM2130061v1_genomic.fna/target_genomes.txt
[2024-01-24 12:47:17,819] [INFO] Task started: fastANI
[2024-01-24 12:47:17,819] [INFO] Running command: fastANI --query /var/lib/cwl/stg509635d2-1836-4c7e-b86c-945d4571e273/GCF_021300615.1_ASM2130061v1_genomic.fna.gz --refList GCF_021300615.1_ASM2130061v1_genomic.fna/target_genomes.txt --output GCF_021300615.1_ASM2130061v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:47:23,499] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:23,500] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga8e0ebc9-cb12-482c-b6f9-aaa5f76b9bf9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:47:23,500] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga8e0ebc9-cb12-482c-b6f9-aaa5f76b9bf9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:47:23,507] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:47:23,507] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:47:23,507] [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 anatolicus	strain=faydin-H8	GCA_021300615.1	2905874	2905874	type	True	100.0	497	497	95	conclusive
Helicobacter anseris	strain=MIT 04-9362	GCA_003364335.1	375926	375926	type	True	78.0234	164	497	95	below_threshold
Helicobacter mustelae	strain=NCTC12198	GCA_900476215.1	217	217	type	True	77.492	84	497	95	below_threshold
Helicobacter burdigaliensis	strain=CNRCH 2005/566H	GCA_003670295.1	2315334	2315334	type	True	77.132	61	497	95	below_threshold
Helicobacter japonicus	strain=MIT 01-6451	GCA_000762845.2	425400	425400	type	True	77.0301	54	497	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:47:23,509] [INFO] DFAST Taxonomy check result was written to GCF_021300615.1_ASM2130061v1_genomic.fna/tc_result.tsv
[2024-01-24 12:47:23,509] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:47:23,510] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:47:23,510] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga8e0ebc9-cb12-482c-b6f9-aaa5f76b9bf9/dqc_reference/checkm_data
[2024-01-24 12:47:23,511] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:47:23,533] [INFO] Task started: CheckM
[2024-01-24 12:47:23,533] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021300615.1_ASM2130061v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021300615.1_ASM2130061v1_genomic.fna/checkm_input GCF_021300615.1_ASM2130061v1_genomic.fna/checkm_result
[2024-01-24 12:47:41,592] [INFO] Task succeeded: CheckM
[2024-01-24 12:47:41,593] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:47:41,618] [INFO] ===== Completeness check finished =====
[2024-01-24 12:47:41,618] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:47:41,619] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021300615.1_ASM2130061v1_genomic.fna/markers.fasta)
[2024-01-24 12:47:41,619] [INFO] Task started: Blastn
[2024-01-24 12:47:41,620] [INFO] Running command: blastn -query GCF_021300615.1_ASM2130061v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga8e0ebc9-cb12-482c-b6f9-aaa5f76b9bf9/dqc_reference/reference_markers_gtdb.fasta -out GCF_021300615.1_ASM2130061v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:42,527] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:42,530] [INFO] Selected 23 target genomes.
[2024-01-24 12:47:42,531] [INFO] Target genome list was writen to GCF_021300615.1_ASM2130061v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:47:42,582] [INFO] Task started: fastANI
[2024-01-24 12:47:42,582] [INFO] Running command: fastANI --query /var/lib/cwl/stg509635d2-1836-4c7e-b86c-945d4571e273/GCF_021300615.1_ASM2130061v1_genomic.fna.gz --refList GCF_021300615.1_ASM2130061v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021300615.1_ASM2130061v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:47:49,434] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:49,451] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:47:49,451] [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_003364335.1	s__Helicobacter_H anseris	78.0234	164	497	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_H	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900199585.1	s__Helicobacter_H sp900199585	77.8659	156	497	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_H	95.0	99.99	99.99	1.00	1.00	2	-
GCF_004368235.1	s__Helicobacter_H anseris_A	77.5028	106	497	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_H	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900476215.1	s__Helicobacter_H mustelae	77.492	84	497	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_H	95.0	99.73	99.46	1.00	0.99	3	-
GCF_002272895.1	s__Helicobacter_J sp002272895	77.2292	70	497	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_J	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000762845.2	s__Helicobacter_C japonicus	77.0301	54	497	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_C	95.0	99.98	99.98	0.99	0.99	2	-
GCF_900198655.1	s__Helicobacter_F equorum_A	76.8753	57	497	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_F	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002272785.1	s__Helicobacter_J sp002272785	76.8733	70	497	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_J	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002272795.1	s__Helicobacter_J sp002272795	76.8349	73	497	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_J	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002272835.1	s__Helicobacter_J sp002272835	76.7917	80	497	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_J	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000007905.1	s__Helicobacter_C hepaticus	76.2327	57	497	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_C	95.0	98.74	98.74	0.96	0.95	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:47:49,455] [INFO] GTDB search result was written to GCF_021300615.1_ASM2130061v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:47:49,459] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:47:49,465] [INFO] DFAST_QC result json was written to GCF_021300615.1_ASM2130061v1_genomic.fna/dqc_result.json
[2024-01-24 12:47:49,466] [INFO] DFAST_QC completed!
[2024-01-24 12:47:49,466] [INFO] Total running time: 0h0m37s