[2024-01-24 13:25:31,250] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:25:31,255] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:25:31,256] [INFO] DQC Reference Directory: /var/lib/cwl/stg855ac41f-a29d-4b32-95dd-b7c0ebaa1c00/dqc_reference
[2024-01-24 13:25:32,560] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:25:32,560] [INFO] Task started: Prodigal
[2024-01-24 13:25:32,561] [INFO] Running command: gunzip -c /var/lib/cwl/stg2ae78987-4781-4534-a306-cd813d6620d6/GCF_000014025.1_ASM1402v1_genomic.fna.gz | prodigal -d GCF_000014025.1_ASM1402v1_genomic.fna/cds.fna -a GCF_000014025.1_ASM1402v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:25:36,446] [INFO] Task succeeded: Prodigal
[2024-01-24 13:25:36,447] [INFO] Task started: HMMsearch
[2024-01-24 13:25:36,447] [INFO] Running command: hmmsearch --tblout GCF_000014025.1_ASM1402v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg855ac41f-a29d-4b32-95dd-b7c0ebaa1c00/dqc_reference/reference_markers.hmm GCF_000014025.1_ASM1402v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:25:36,696] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:25:36,697] [INFO] Found 6/6 markers.
[2024-01-24 13:25:36,718] [INFO] Query marker FASTA was written to GCF_000014025.1_ASM1402v1_genomic.fna/markers.fasta
[2024-01-24 13:25:36,719] [INFO] Task started: Blastn
[2024-01-24 13:25:36,719] [INFO] Running command: blastn -query GCF_000014025.1_ASM1402v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg855ac41f-a29d-4b32-95dd-b7c0ebaa1c00/dqc_reference/reference_markers.fasta -out GCF_000014025.1_ASM1402v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:25:37,356] [INFO] Task succeeded: Blastn
[2024-01-24 13:25:37,361] [INFO] Selected 12 target genomes.
[2024-01-24 13:25:37,361] [INFO] Target genome list was writen to GCF_000014025.1_ASM1402v1_genomic.fna/target_genomes.txt
[2024-01-24 13:25:37,373] [INFO] Task started: fastANI
[2024-01-24 13:25:37,373] [INFO] Running command: fastANI --query /var/lib/cwl/stg2ae78987-4781-4534-a306-cd813d6620d6/GCF_000014025.1_ASM1402v1_genomic.fna.gz --refList GCF_000014025.1_ASM1402v1_genomic.fna/target_genomes.txt --output GCF_000014025.1_ASM1402v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:25:44,670] [INFO] Task succeeded: fastANI
[2024-01-24 13:25:44,671] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg855ac41f-a29d-4b32-95dd-b7c0ebaa1c00/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:25:44,671] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg855ac41f-a29d-4b32-95dd-b7c0ebaa1c00/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:25:44,682] [INFO] Found 12 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:25:44,682] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:25:44,682] [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
Aliarcobacter butzleri	strain=RM4018	GCA_000014025.1	28197	28197	type	True	100.0	777	780	95	conclusive
Aliarcobacter butzleri	strain=NCTC 12481	GCA_900187115.1	28197	28197	type	True	99.9976	777	780	95	conclusive
Aliarcobacter butzleri	strain=LMG 10828	GCA_024584145.1	28197	28197	type	True	99.9748	752	780	95	conclusive
Arcobacter ellisii	strain=LMG 26155	GCA_003544915.1	913109	913109	type	True	84.5914	555	780	95	below_threshold
Arcobacter ellisii	strain=CECT 7837	GCA_004115815.1	913109	913109	type	True	84.4827	538	780	95	below_threshold
Arcobacter defluvii	strain=LMG 25694	GCA_013201725.1	873191	873191	type	True	84.3279	557	780	95	below_threshold
Arcobacter defluvii	strain=CECT 7697	GCA_004115775.1	873191	873191	type	True	84.1314	539	780	95	below_threshold
Arcobacter aquimarinus	strain=W63	GCA_013177635.1	1315211	1315211	type	True	83.6982	548	780	95	below_threshold
Arcobacter aquimarinus	strain=CECT 8442	GCA_004115795.1	1315211	1315211	type	True	83.4332	527	780	95	below_threshold
Arcobacter cloacae	strain=CECT 7834	GCA_004115805.1	1054034	1054034	type	True	83.1986	522	780	95	below_threshold
Aliarcobacter vitoriensis	strain=LMG 30050	GCA_024583985.1	2011099	2011099	type	True	82.7899	525	780	95	below_threshold
Aliarcobacter vitoriensis	strain=CECT 9230	GCA_003316695.1	2011099	2011099	type	True	82.7246	527	780	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:25:44,683] [INFO] DFAST Taxonomy check result was written to GCF_000014025.1_ASM1402v1_genomic.fna/tc_result.tsv
[2024-01-24 13:25:44,684] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:25:44,684] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:25:44,684] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg855ac41f-a29d-4b32-95dd-b7c0ebaa1c00/dqc_reference/checkm_data
[2024-01-24 13:25:44,685] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:25:44,712] [INFO] Task started: CheckM
[2024-01-24 13:25:44,712] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000014025.1_ASM1402v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000014025.1_ASM1402v1_genomic.fna/checkm_input GCF_000014025.1_ASM1402v1_genomic.fna/checkm_result
[2024-01-24 13:26:04,215] [INFO] Task succeeded: CheckM
[2024-01-24 13:26:04,217] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:26:04,238] [INFO] ===== Completeness check finished =====
[2024-01-24 13:26:04,238] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:26:04,239] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000014025.1_ASM1402v1_genomic.fna/markers.fasta)
[2024-01-24 13:26:04,239] [INFO] Task started: Blastn
[2024-01-24 13:26:04,239] [INFO] Running command: blastn -query GCF_000014025.1_ASM1402v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg855ac41f-a29d-4b32-95dd-b7c0ebaa1c00/dqc_reference/reference_markers_gtdb.fasta -out GCF_000014025.1_ASM1402v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:26:05,087] [INFO] Task succeeded: Blastn
[2024-01-24 13:26:05,092] [INFO] Selected 10 target genomes.
[2024-01-24 13:26:05,092] [INFO] Target genome list was writen to GCF_000014025.1_ASM1402v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:26:05,098] [INFO] Task started: fastANI
[2024-01-24 13:26:05,099] [INFO] Running command: fastANI --query /var/lib/cwl/stg2ae78987-4781-4534-a306-cd813d6620d6/GCF_000014025.1_ASM1402v1_genomic.fna.gz --refList GCF_000014025.1_ASM1402v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000014025.1_ASM1402v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:26:11,139] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:11,149] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:26:11,149] [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_900187115.1	s__Aliarcobacter butzleri	99.9976	776	780	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	97.53	96.98	0.89	0.81	50	conclusive
GCF_003063295.1	s__Aliarcobacter lacus	94.5574	614	780	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003544915.1	s__Aliarcobacter ellisii	84.5261	554	780	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	98.73	97.46	0.92	0.84	3	-
GCF_013201725.1	s__Aliarcobacter defluvii	84.306	555	780	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	98.85	98.15	0.93	0.88	4	-
GCF_013177635.1	s__Aliarcobacter aquimarinus	83.6674	550	780	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	83.193	547	780	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	97.96	95.91	0.93	0.87	3	-
GCA_003316695.1	s__Aliarcobacter sp003316695	82.751	525	780	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	97.67	97.67	0.88	0.88	2	-
GCF_013201705.1	s__Aliarcobacter faecis	82.1088	489	780	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	99.88	99.77	0.97	0.95	3	-
GCF_004214815.1	s__Aliarcobacter thereius	81.0385	396	780	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	99.14	98.62	0.93	0.89	8	-
GCF_004299785.2	s__Aliarcobacter porcinus	80.977	402	780	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	98.76	98.06	0.91	0.88	6	-
--------------------------------------------------------------------------------
[2024-01-24 13:26:11,151] [INFO] GTDB search result was written to GCF_000014025.1_ASM1402v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:26:11,152] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:26:11,156] [INFO] DFAST_QC result json was written to GCF_000014025.1_ASM1402v1_genomic.fna/dqc_result.json
[2024-01-24 13:26:11,156] [INFO] DFAST_QC completed!
[2024-01-24 13:26:11,156] [INFO] Total running time: 0h0m40s