[2024-01-25 18:48:20,452] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:48:20,454] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:48:20,454] [INFO] DQC Reference Directory: /var/lib/cwl/stgcfc02c3c-4d37-48f2-94e8-520f1a822791/dqc_reference
[2024-01-25 18:48:21,641] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:48:21,642] [INFO] Task started: Prodigal
[2024-01-25 18:48:21,642] [INFO] Running command: gunzip -c /var/lib/cwl/stgd1c124e6-a277-4ced-8a23-871d75cc9bd1/GCF_017979425.1_ASM1797942v1_genomic.fna.gz | prodigal -d GCF_017979425.1_ASM1797942v1_genomic.fna/cds.fna -a GCF_017979425.1_ASM1797942v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:48:24,955] [INFO] Task succeeded: Prodigal
[2024-01-25 18:48:24,955] [INFO] Task started: HMMsearch
[2024-01-25 18:48:24,956] [INFO] Running command: hmmsearch --tblout GCF_017979425.1_ASM1797942v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcfc02c3c-4d37-48f2-94e8-520f1a822791/dqc_reference/reference_markers.hmm GCF_017979425.1_ASM1797942v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:48:25,114] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:48:25,115] [INFO] Found 6/6 markers.
[2024-01-25 18:48:25,133] [INFO] Query marker FASTA was written to GCF_017979425.1_ASM1797942v1_genomic.fna/markers.fasta
[2024-01-25 18:48:25,133] [INFO] Task started: Blastn
[2024-01-25 18:48:25,133] [INFO] Running command: blastn -query GCF_017979425.1_ASM1797942v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcfc02c3c-4d37-48f2-94e8-520f1a822791/dqc_reference/reference_markers.fasta -out GCF_017979425.1_ASM1797942v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:48:25,650] [INFO] Task succeeded: Blastn
[2024-01-25 18:48:25,652] [INFO] Selected 11 target genomes.
[2024-01-25 18:48:25,652] [INFO] Target genome list was writen to GCF_017979425.1_ASM1797942v1_genomic.fna/target_genomes.txt
[2024-01-25 18:48:25,669] [INFO] Task started: fastANI
[2024-01-25 18:48:25,669] [INFO] Running command: fastANI --query /var/lib/cwl/stgd1c124e6-a277-4ced-8a23-871d75cc9bd1/GCF_017979425.1_ASM1797942v1_genomic.fna.gz --refList GCF_017979425.1_ASM1797942v1_genomic.fna/target_genomes.txt --output GCF_017979425.1_ASM1797942v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:48:29,116] [INFO] Task succeeded: fastANI
[2024-01-25 18:48:29,117] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcfc02c3c-4d37-48f2-94e8-520f1a822791/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:48:29,117] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcfc02c3c-4d37-48f2-94e8-520f1a822791/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:48:29,125] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:48:29,125] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:48:29,125] [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 salomonis	strain=CIP 105607	GCA_017979425.1	56878	56878	type	True	100.0	452	455	95	conclusive
Helicobacter felis	strain=ATCC 49179	GCA_000200595.1	214	214	type	True	81.5321	258	455	95	below_threshold
Helicobacter labacensis	strain=L9	GCA_003660285.1	2316079	2316079	type	True	81.1617	277	455	95	below_threshold
Helicobacter vulpis	strain=L2	GCA_003660395.1	2316076	2316076	type	True	81.0362	262	455	95	below_threshold
Helicobacter bizzozeronii	strain=CIP 105233	GCA_017979515.1	56877	56877	type	True	80.0063	169	455	95	below_threshold
Helicobacter mehlei	strain=L15	GCA_003660265.1	2316080	2316080	type	True	79.3255	168	455	95	below_threshold
Helicobacter heilmannii	strain=LMG 26292	GCA_017979395.1	35817	35817	type	True	77.2977	106	455	95	below_threshold
Helicobacter heilmannii		GCA_001283065.1	35817	35817	type	True	77.2494	108	455	95	below_threshold
Helicobacter suis	strain=HS1	GCA_000187625.2	104628	104628	type	True	77.0862	91	455	95	below_threshold
Helicobacter suis	strain=DSM 19735	GCA_017979375.1	104628	104628	type	True	77.0733	93	455	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:48:29,127] [INFO] DFAST Taxonomy check result was written to GCF_017979425.1_ASM1797942v1_genomic.fna/tc_result.tsv
[2024-01-25 18:48:29,128] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:48:29,128] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:48:29,128] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcfc02c3c-4d37-48f2-94e8-520f1a822791/dqc_reference/checkm_data
[2024-01-25 18:48:29,129] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:48:29,145] [INFO] Task started: CheckM
[2024-01-25 18:48:29,145] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017979425.1_ASM1797942v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017979425.1_ASM1797942v1_genomic.fna/checkm_input GCF_017979425.1_ASM1797942v1_genomic.fna/checkm_result
[2024-01-25 18:48:44,750] [INFO] Task succeeded: CheckM
[2024-01-25 18:48:44,751] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:48:44,766] [INFO] ===== Completeness check finished =====
[2024-01-25 18:48:44,766] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:48:44,766] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017979425.1_ASM1797942v1_genomic.fna/markers.fasta)
[2024-01-25 18:48:44,767] [INFO] Task started: Blastn
[2024-01-25 18:48:44,767] [INFO] Running command: blastn -query GCF_017979425.1_ASM1797942v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcfc02c3c-4d37-48f2-94e8-520f1a822791/dqc_reference/reference_markers_gtdb.fasta -out GCF_017979425.1_ASM1797942v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:48:45,473] [INFO] Task succeeded: Blastn
[2024-01-25 18:48:45,477] [INFO] Selected 10 target genomes.
[2024-01-25 18:48:45,477] [INFO] Target genome list was writen to GCF_017979425.1_ASM1797942v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:48:45,487] [INFO] Task started: fastANI
[2024-01-25 18:48:45,487] [INFO] Running command: fastANI --query /var/lib/cwl/stgd1c124e6-a277-4ced-8a23-871d75cc9bd1/GCF_017979425.1_ASM1797942v1_genomic.fna.gz --refList GCF_017979425.1_ASM1797942v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017979425.1_ASM1797942v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:48:48,916] [INFO] Task succeeded: fastANI
[2024-01-25 18:48:48,923] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:48:48,923] [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_017979425.1	s__Helicobacter_E salomonis	100.0	452	455	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_E	95.0	98.86	98.52	0.94	0.92	6	conclusive
GCF_000200595.1	s__Helicobacter_E felis	81.5321	258	455	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_003660285.1	s__Helicobacter_E labacensis	81.1617	277	455	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_900197855.1	s__Helicobacter_E cynogastricus	81.1305	224	455	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	80.9619	265	455	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_900197685.1	s__Helicobacter_E baculiformis	80.1764	253	455	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_001283065.1	s__Helicobacter_E heilmannii	77.2246	109	455	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_000187625.1	s__Helicobacter_E suis	77.0585	92	455	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_E	95.0	99.74	99.56	0.96	0.89	27	-
GCF_902196135.1	s__Helicobacter_E suis_A	76.999	90	455	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_E	95.0	97.68	97.34	0.95	0.91	4	-
GCF_902196125.1	s__Helicobacter_E suis_B	76.9597	84	455	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_E	95.0	96.42	96.42	0.94	0.90	3	-
--------------------------------------------------------------------------------
[2024-01-25 18:48:48,925] [INFO] GTDB search result was written to GCF_017979425.1_ASM1797942v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:48:48,925] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:48:48,928] [INFO] DFAST_QC result json was written to GCF_017979425.1_ASM1797942v1_genomic.fna/dqc_result.json
[2024-01-25 18:48:48,928] [INFO] DFAST_QC completed!
[2024-01-25 18:48:48,928] [INFO] Total running time: 0h0m28s