[2024-01-25 19:34:50,836] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:34:50,837] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:34:50,837] [INFO] DQC Reference Directory: /var/lib/cwl/stga90b0951-c1dd-4e6c-a681-a955e7fe7369/dqc_reference
[2024-01-25 19:34:51,924] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:34:51,925] [INFO] Task started: Prodigal
[2024-01-25 19:34:51,925] [INFO] Running command: gunzip -c /var/lib/cwl/stg821eec48-2feb-45f7-a512-5eeb10aac0de/GCF_900108945.1_IMG-taxon_2654588103_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900108945.1_IMG-taxon_2654588103_annotated_assembly_genomic.fna/cds.fna -a GCF_900108945.1_IMG-taxon_2654588103_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:35:15,262] [INFO] Task succeeded: Prodigal
[2024-01-25 19:35:15,263] [INFO] Task started: HMMsearch
[2024-01-25 19:35:15,263] [INFO] Running command: hmmsearch --tblout GCF_900108945.1_IMG-taxon_2654588103_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga90b0951-c1dd-4e6c-a681-a955e7fe7369/dqc_reference/reference_markers.hmm GCF_900108945.1_IMG-taxon_2654588103_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:35:15,612] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:35:15,612] [INFO] Found 6/6 markers.
[2024-01-25 19:35:15,677] [INFO] Query marker FASTA was written to GCF_900108945.1_IMG-taxon_2654588103_annotated_assembly_genomic.fna/markers.fasta
[2024-01-25 19:35:15,678] [INFO] Task started: Blastn
[2024-01-25 19:35:15,678] [INFO] Running command: blastn -query GCF_900108945.1_IMG-taxon_2654588103_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stga90b0951-c1dd-4e6c-a681-a955e7fe7369/dqc_reference/reference_markers.fasta -out GCF_900108945.1_IMG-taxon_2654588103_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:35:16,623] [INFO] Task succeeded: Blastn
[2024-01-25 19:35:16,625] [INFO] Selected 13 target genomes.
[2024-01-25 19:35:16,626] [INFO] Target genome list was writen to GCF_900108945.1_IMG-taxon_2654588103_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-25 19:35:16,629] [INFO] Task started: fastANI
[2024-01-25 19:35:16,630] [INFO] Running command: fastANI --query /var/lib/cwl/stg821eec48-2feb-45f7-a512-5eeb10aac0de/GCF_900108945.1_IMG-taxon_2654588103_annotated_assembly_genomic.fna.gz --refList GCF_900108945.1_IMG-taxon_2654588103_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900108945.1_IMG-taxon_2654588103_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:35:43,361] [INFO] Task succeeded: fastANI
[2024-01-25 19:35:43,361] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga90b0951-c1dd-4e6c-a681-a955e7fe7369/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:35:43,361] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga90b0951-c1dd-4e6c-a681-a955e7fe7369/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:35:43,370] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:35:43,370] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:35:43,370] [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
Paraburkholderia diazotrophica	strain=LMG 26031	GCA_900108945.1	667676	667676	type	True	100.0	2833	2840	95	conclusive
Paraburkholderia franconis	strain=CNPSo 3157	GCA_009362735.1	2654983	2654983	type	True	93.8776	2291	2840	95	below_threshold
Paraburkholderia piptadeniae	strain=STM 7183	GCA_900007165.2	1701573	1701573	type	True	93.3197	2116	2840	95	below_threshold
Paraburkholderia sabiae	strain=LMG 24235	GCA_904848645.1	273251	273251	type	True	87.0531	1959	2840	95	below_threshold
Paraburkholderia terrae	strain=NBRC 100964	GCA_000739835.1	311230	311230	type	True	86.8392	1793	2840	95	below_threshold
Paraburkholderia terrae	strain=DSM 17804	GCA_002902925.1	311230	311230	type	True	86.7935	1853	2840	95	below_threshold
Paraburkholderia azotifigens	strain=NF 2-5-3	GCA_007995085.1	2057004	2057004	type	True	86.7926	1924	2840	95	below_threshold
Paraburkholderia phymatum	strain=LMG 21445	GCA_902833665.1	148447	148447	type	True	86.4514	1826	2840	95	below_threshold
Paraburkholderia phymatum	strain=STM815	GCA_000020045.1	148447	148447	type	True	86.435	1835	2840	95	below_threshold
Paraburkholderia flava	strain=LD6	GCA_004359985.1	2547393	2547393	type	True	82.9301	1267	2840	95	below_threshold
Paraburkholderia podalyriae	strain=WC7.3b	GCA_014397785.1	1938811	1938811	type	True	82.6919	1408	2840	95	below_threshold
Paraburkholderia gardini	strain=LMG 32171	GCA_907164575.1	2823469	2823469	type	True	82.6626	1180	2840	95	below_threshold
Paraburkholderia saeva	strain=LMG 31841	GCA_907164555.1	2777537	2777537	type	True	82.3423	1191	2840	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:35:43,371] [INFO] DFAST Taxonomy check result was written to GCF_900108945.1_IMG-taxon_2654588103_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-25 19:35:43,372] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:35:43,372] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:35:43,372] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga90b0951-c1dd-4e6c-a681-a955e7fe7369/dqc_reference/checkm_data
[2024-01-25 19:35:43,373] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:35:43,451] [INFO] Task started: CheckM
[2024-01-25 19:35:43,451] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900108945.1_IMG-taxon_2654588103_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900108945.1_IMG-taxon_2654588103_annotated_assembly_genomic.fna/checkm_input GCF_900108945.1_IMG-taxon_2654588103_annotated_assembly_genomic.fna/checkm_result
[2024-01-25 19:36:52,436] [INFO] Task succeeded: CheckM
[2024-01-25 19:36:52,437] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:36:52,452] [INFO] ===== Completeness check finished =====
[2024-01-25 19:36:52,452] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:36:52,453] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900108945.1_IMG-taxon_2654588103_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-25 19:36:52,453] [INFO] Task started: Blastn
[2024-01-25 19:36:52,453] [INFO] Running command: blastn -query GCF_900108945.1_IMG-taxon_2654588103_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stga90b0951-c1dd-4e6c-a681-a955e7fe7369/dqc_reference/reference_markers_gtdb.fasta -out GCF_900108945.1_IMG-taxon_2654588103_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:36:54,368] [INFO] Task succeeded: Blastn
[2024-01-25 19:36:54,371] [INFO] Selected 10 target genomes.
[2024-01-25 19:36:54,371] [INFO] Target genome list was writen to GCF_900108945.1_IMG-taxon_2654588103_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:36:54,377] [INFO] Task started: fastANI
[2024-01-25 19:36:54,377] [INFO] Running command: fastANI --query /var/lib/cwl/stg821eec48-2feb-45f7-a512-5eeb10aac0de/GCF_900108945.1_IMG-taxon_2654588103_annotated_assembly_genomic.fna.gz --refList GCF_900108945.1_IMG-taxon_2654588103_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900108945.1_IMG-taxon_2654588103_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:37:17,693] [INFO] Task succeeded: fastANI
[2024-01-25 19:37:17,702] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:37:17,702] [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_900108945.1	s__Paraburkholderia diazotrophica	100.0	2833	2840	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009362735.1	s__Paraburkholderia franconis	93.8927	2289	2840	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900007165.1	s__Paraburkholderia piptadeniae	93.3261	2115	2840	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017814945.1	s__Paraburkholderia sp017814945	87.4943	1817	2840	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_904848645.1	s__Paraburkholderia sabiae	87.0466	1960	2840	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013426895.1	s__Paraburkholderia sp013426895	86.82	1775	2840	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007995085.1	s__Paraburkholderia azotifigens	86.7774	1928	2840	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	98.91	98.91	0.86	0.86	2	-
GCF_017104565.1	s__Paraburkholderia sp017104565	86.7277	1839	2840	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001319865.1	s__Paraburkholderia sp001319865	86.4577	1570	2840	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000020045.1	s__Paraburkholderia phymatum	86.4293	1835	2840	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:37:17,703] [INFO] GTDB search result was written to GCF_900108945.1_IMG-taxon_2654588103_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-25 19:37:17,704] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:37:17,706] [INFO] DFAST_QC result json was written to GCF_900108945.1_IMG-taxon_2654588103_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-25 19:37:17,707] [INFO] DFAST_QC completed!
[2024-01-25 19:37:17,707] [INFO] Total running time: 0h2m27s