[2024-01-24 12:21:36,225] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:21:36,227] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:21:36,228] [INFO] DQC Reference Directory: /var/lib/cwl/stg32265dba-f32b-460f-aeb4-09ce286c51d4/dqc_reference
[2024-01-24 12:21:37,448] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:21:37,449] [INFO] Task started: Prodigal
[2024-01-24 12:21:37,449] [INFO] Running command: gunzip -c /var/lib/cwl/stg4be93265-1c13-4319-8584-a911e6a2ea8a/GCF_003660265.1_ASM366026v1_genomic.fna.gz | prodigal -d GCF_003660265.1_ASM366026v1_genomic.fna/cds.fna -a GCF_003660265.1_ASM366026v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:21:41,860] [INFO] Task succeeded: Prodigal
[2024-01-24 12:21:41,861] [INFO] Task started: HMMsearch
[2024-01-24 12:21:41,861] [INFO] Running command: hmmsearch --tblout GCF_003660265.1_ASM366026v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg32265dba-f32b-460f-aeb4-09ce286c51d4/dqc_reference/reference_markers.hmm GCF_003660265.1_ASM366026v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:21:42,076] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:21:42,078] [INFO] Found 6/6 markers.
[2024-01-24 12:21:42,100] [INFO] Query marker FASTA was written to GCF_003660265.1_ASM366026v1_genomic.fna/markers.fasta
[2024-01-24 12:21:42,101] [INFO] Task started: Blastn
[2024-01-24 12:21:42,101] [INFO] Running command: blastn -query GCF_003660265.1_ASM366026v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg32265dba-f32b-460f-aeb4-09ce286c51d4/dqc_reference/reference_markers.fasta -out GCF_003660265.1_ASM366026v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:21:42,692] [INFO] Task succeeded: Blastn
[2024-01-24 12:21:42,696] [INFO] Selected 9 target genomes.
[2024-01-24 12:21:42,696] [INFO] Target genome list was writen to GCF_003660265.1_ASM366026v1_genomic.fna/target_genomes.txt
[2024-01-24 12:21:42,781] [INFO] Task started: fastANI
[2024-01-24 12:21:42,782] [INFO] Running command: fastANI --query /var/lib/cwl/stg4be93265-1c13-4319-8584-a911e6a2ea8a/GCF_003660265.1_ASM366026v1_genomic.fna.gz --refList GCF_003660265.1_ASM366026v1_genomic.fna/target_genomes.txt --output GCF_003660265.1_ASM366026v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:21:45,878] [INFO] Task succeeded: fastANI
[2024-01-24 12:21:45,879] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg32265dba-f32b-460f-aeb4-09ce286c51d4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:21:45,879] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg32265dba-f32b-460f-aeb4-09ce286c51d4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:21:45,888] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:21:45,889] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:21:45,889] [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 mehlei	strain=L15	GCA_003660265.1	2316080	2316080	type	True	100.0	510	510	95	conclusive
Helicobacter bizzozeronii	strain=CIP 105233	GCA_017979515.1	56877	56877	type	True	90.7249	406	510	95	below_threshold
Helicobacter vulpis	strain=L2	GCA_003660395.1	2316076	2316076	type	True	81.2381	252	510	95	below_threshold
Helicobacter labacensis	strain=L9	GCA_003660285.1	2316079	2316079	type	True	79.5193	242	510	95	below_threshold
Helicobacter felis	strain=ATCC 49179	GCA_000200595.1	214	214	type	True	79.3251	220	510	95	below_threshold
Helicobacter ailurogastricus		GCA_001282945.1	1578720	1578720	type	True	79.3153	205	510	95	below_threshold
Helicobacter salomonis	strain=CIP 105607	GCA_017979425.1	56878	56878	type	True	79.0013	176	510	95	below_threshold
Helicobacter heilmannii		GCA_001283065.1	35817	35817	type	True	78.6384	197	510	95	below_threshold
Helicobacter heilmannii	strain=LMG 26292	GCA_017979395.1	35817	35817	type	True	78.5882	186	510	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:21:45,891] [INFO] DFAST Taxonomy check result was written to GCF_003660265.1_ASM366026v1_genomic.fna/tc_result.tsv
[2024-01-24 12:21:45,892] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:21:45,892] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:21:45,892] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg32265dba-f32b-460f-aeb4-09ce286c51d4/dqc_reference/checkm_data
[2024-01-24 12:21:45,893] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:21:45,915] [INFO] Task started: CheckM
[2024-01-24 12:21:45,916] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003660265.1_ASM366026v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003660265.1_ASM366026v1_genomic.fna/checkm_input GCF_003660265.1_ASM366026v1_genomic.fna/checkm_result
[2024-01-24 12:22:05,620] [INFO] Task succeeded: CheckM
[2024-01-24 12:22:05,621] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:22:05,642] [INFO] ===== Completeness check finished =====
[2024-01-24 12:22:05,643] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:22:05,643] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003660265.1_ASM366026v1_genomic.fna/markers.fasta)
[2024-01-24 12:22:05,644] [INFO] Task started: Blastn
[2024-01-24 12:22:05,644] [INFO] Running command: blastn -query GCF_003660265.1_ASM366026v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg32265dba-f32b-460f-aeb4-09ce286c51d4/dqc_reference/reference_markers_gtdb.fasta -out GCF_003660265.1_ASM366026v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:06,372] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:06,377] [INFO] Selected 11 target genomes.
[2024-01-24 12:22:06,377] [INFO] Target genome list was writen to GCF_003660265.1_ASM366026v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:22:06,396] [INFO] Task started: fastANI
[2024-01-24 12:22:06,397] [INFO] Running command: fastANI --query /var/lib/cwl/stg4be93265-1c13-4319-8584-a911e6a2ea8a/GCF_003660265.1_ASM366026v1_genomic.fna.gz --refList GCF_003660265.1_ASM366026v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003660265.1_ASM366026v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:22:10,129] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:10,141] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:22:10,141] [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_003660265.1	s__Helicobacter_E mehlei	100.0	510	510	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_E	95.0	99.56	99.56	0.97	0.96	3	conclusive
GCA_000263275.1	s__Helicobacter_E bizzozeronii	90.7937	428	510	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_003660395.1	s__Helicobacter_E vulpis	81.2392	252	510	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	79.438	246	510	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	79.3877	192	510	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	79.3109	222	510	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	79.2916	206	510	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	78.6813	195	510	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	77.308	159	510	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 12:22:10,143] [INFO] GTDB search result was written to GCF_003660265.1_ASM366026v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:22:10,143] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:22:10,147] [INFO] DFAST_QC result json was written to GCF_003660265.1_ASM366026v1_genomic.fna/dqc_result.json
[2024-01-24 12:22:10,147] [INFO] DFAST_QC completed!
[2024-01-24 12:22:10,147] [INFO] Total running time: 0h0m34s