[2024-01-24 13:46:18,427] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:18,429] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:18,429] [INFO] DQC Reference Directory: /var/lib/cwl/stg9c892805-bb3d-4051-acbe-bd635d035272/dqc_reference
[2024-01-24 13:46:19,813] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:19,814] [INFO] Task started: Prodigal
[2024-01-24 13:46:19,814] [INFO] Running command: gunzip -c /var/lib/cwl/stgb91a7466-8996-45d6-88b3-fed302d6a893/GCF_013201725.1_ASM1320172v1_genomic.fna.gz | prodigal -d GCF_013201725.1_ASM1320172v1_genomic.fna/cds.fna -a GCF_013201725.1_ASM1320172v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:24,692] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:24,693] [INFO] Task started: HMMsearch
[2024-01-24 13:46:24,693] [INFO] Running command: hmmsearch --tblout GCF_013201725.1_ASM1320172v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9c892805-bb3d-4051-acbe-bd635d035272/dqc_reference/reference_markers.hmm GCF_013201725.1_ASM1320172v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:25,010] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:25,011] [INFO] Found 6/6 markers.
[2024-01-24 13:46:25,045] [INFO] Query marker FASTA was written to GCF_013201725.1_ASM1320172v1_genomic.fna/markers.fasta
[2024-01-24 13:46:25,045] [INFO] Task started: Blastn
[2024-01-24 13:46:25,046] [INFO] Running command: blastn -query GCF_013201725.1_ASM1320172v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9c892805-bb3d-4051-acbe-bd635d035272/dqc_reference/reference_markers.fasta -out GCF_013201725.1_ASM1320172v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:25,721] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:25,725] [INFO] Selected 9 target genomes.
[2024-01-24 13:46:25,725] [INFO] Target genome list was writen to GCF_013201725.1_ASM1320172v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:25,729] [INFO] Task started: fastANI
[2024-01-24 13:46:25,730] [INFO] Running command: fastANI --query /var/lib/cwl/stgb91a7466-8996-45d6-88b3-fed302d6a893/GCF_013201725.1_ASM1320172v1_genomic.fna.gz --refList GCF_013201725.1_ASM1320172v1_genomic.fna/target_genomes.txt --output GCF_013201725.1_ASM1320172v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:32,704] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:32,705] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9c892805-bb3d-4051-acbe-bd635d035272/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:32,705] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9c892805-bb3d-4051-acbe-bd635d035272/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:32,713] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:46:32,714] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:46:32,714] [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
Arcobacter defluvii	strain=LMG 25694	GCA_013201725.1	873191	873191	type	True	100.0	998	1007	95	conclusive
Arcobacter defluvii	strain=CECT 7697	GCA_004115775.1	873191	873191	type	True	99.9759	951	1007	95	conclusive
Arcobacter ellisii	strain=LMG 26155	GCA_003544915.1	913109	913109	type	True	88.4844	710	1007	95	below_threshold
Arcobacter ellisii	strain=CECT 7837	GCA_004115815.1	913109	913109	type	True	88.3459	701	1007	95	below_threshold
Arcobacter aquimarinus	strain=W63	GCA_013177635.1	1315211	1315211	type	True	85.5225	670	1007	95	below_threshold
Arcobacter aquimarinus	strain=CECT 8442	GCA_004115795.1	1315211	1315211	type	True	85.4867	639	1007	95	below_threshold
Arcobacter cloacae	strain=CECT 7834	GCA_004115805.1	1054034	1054034	type	True	84.9192	662	1007	95	below_threshold
Aliarcobacter butzleri	strain=RM4018	GCA_000014025.1	28197	28197	type	True	84.2143	565	1007	95	below_threshold
Arcobacter venerupis	strain=LMG 26156	GCA_013201665.1	1054033	1054033	type	True	83.6903	707	1007	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:32,715] [INFO] DFAST Taxonomy check result was written to GCF_013201725.1_ASM1320172v1_genomic.fna/tc_result.tsv
[2024-01-24 13:46:32,716] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:32,716] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:32,716] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9c892805-bb3d-4051-acbe-bd635d035272/dqc_reference/checkm_data
[2024-01-24 13:46:32,717] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:32,753] [INFO] Task started: CheckM
[2024-01-24 13:46:32,753] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013201725.1_ASM1320172v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013201725.1_ASM1320172v1_genomic.fna/checkm_input GCF_013201725.1_ASM1320172v1_genomic.fna/checkm_result
[2024-01-24 13:46:55,274] [INFO] Task succeeded: CheckM
[2024-01-24 13:46:55,275] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:46:55,321] [INFO] ===== Completeness check finished =====
[2024-01-24 13:46:55,321] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:46:55,322] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013201725.1_ASM1320172v1_genomic.fna/markers.fasta)
[2024-01-24 13:46:55,322] [INFO] Task started: Blastn
[2024-01-24 13:46:55,322] [INFO] Running command: blastn -query GCF_013201725.1_ASM1320172v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9c892805-bb3d-4051-acbe-bd635d035272/dqc_reference/reference_markers_gtdb.fasta -out GCF_013201725.1_ASM1320172v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:56,193] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:56,196] [INFO] Selected 11 target genomes.
[2024-01-24 13:46:56,196] [INFO] Target genome list was writen to GCF_013201725.1_ASM1320172v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:46:56,216] [INFO] Task started: fastANI
[2024-01-24 13:46:56,216] [INFO] Running command: fastANI --query /var/lib/cwl/stgb91a7466-8996-45d6-88b3-fed302d6a893/GCF_013201725.1_ASM1320172v1_genomic.fna.gz --refList GCF_013201725.1_ASM1320172v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013201725.1_ASM1320172v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:47:04,207] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:04,216] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:47:04,217] [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_013201725.1	s__Aliarcobacter defluvii	100.0	995	1007	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	98.85	98.15	0.93	0.88	4	conclusive
GCF_003544915.1	s__Aliarcobacter ellisii	88.4961	711	1007	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	98.73	97.46	0.92	0.84	3	-
GCF_013177635.1	s__Aliarcobacter aquimarinus	85.5228	671	1007	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013201935.1	s__Aliarcobacter cloacae	84.979	684	1007	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	97.96	95.91	0.93	0.87	3	-
GCF_003063295.1	s__Aliarcobacter lacus	84.4391	544	1007	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900187115.1	s__Aliarcobacter butzleri	84.1735	566	1007	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	97.53	96.98	0.89	0.81	50	-
GCF_003544815.1	s__Aliarcobacter suis	84.0039	644	1007	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013201665.1	s__Aliarcobacter venerupis	83.6177	705	1007	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	100.00	100.00	0.99	0.99	2	-
GCF_003063245.1	s__Aliarcobacter caeni	83.2823	580	1007	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018816105.1	s__Aliarcobacter sp018816105	82.8918	551	1007	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:47:04,225] [INFO] GTDB search result was written to GCF_013201725.1_ASM1320172v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:47:04,226] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:47:04,229] [INFO] DFAST_QC result json was written to GCF_013201725.1_ASM1320172v1_genomic.fna/dqc_result.json
[2024-01-24 13:47:04,230] [INFO] DFAST_QC completed!
[2024-01-24 13:47:04,230] [INFO] Total running time: 0h0m46s