[2024-01-24 13:18:58,385] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:18:58,387] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:18:58,387] [INFO] DQC Reference Directory: /var/lib/cwl/stgf4d1a40d-adf7-4f7e-89a7-571d1724bb5b/dqc_reference
[2024-01-24 13:18:59,686] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:18:59,687] [INFO] Task started: Prodigal
[2024-01-24 13:18:59,687] [INFO] Running command: gunzip -c /var/lib/cwl/stg367c3955-a38f-4287-88a6-5103d6fded6b/GCF_007995085.1_ASM799508v1_genomic.fna.gz | prodigal -d GCF_007995085.1_ASM799508v1_genomic.fna/cds.fna -a GCF_007995085.1_ASM799508v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:19:33,863] [INFO] Task succeeded: Prodigal
[2024-01-24 13:19:33,863] [INFO] Task started: HMMsearch
[2024-01-24 13:19:33,863] [INFO] Running command: hmmsearch --tblout GCF_007995085.1_ASM799508v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf4d1a40d-adf7-4f7e-89a7-571d1724bb5b/dqc_reference/reference_markers.hmm GCF_007995085.1_ASM799508v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:19:34,274] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:19:34,275] [INFO] Found 6/6 markers.
[2024-01-24 13:19:34,352] [INFO] Query marker FASTA was written to GCF_007995085.1_ASM799508v1_genomic.fna/markers.fasta
[2024-01-24 13:19:34,353] [INFO] Task started: Blastn
[2024-01-24 13:19:34,353] [INFO] Running command: blastn -query GCF_007995085.1_ASM799508v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf4d1a40d-adf7-4f7e-89a7-571d1724bb5b/dqc_reference/reference_markers.fasta -out GCF_007995085.1_ASM799508v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:35,425] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:35,429] [INFO] Selected 16 target genomes.
[2024-01-24 13:19:35,429] [INFO] Target genome list was writen to GCF_007995085.1_ASM799508v1_genomic.fna/target_genomes.txt
[2024-01-24 13:19:35,452] [INFO] Task started: fastANI
[2024-01-24 13:19:35,452] [INFO] Running command: fastANI --query /var/lib/cwl/stg367c3955-a38f-4287-88a6-5103d6fded6b/GCF_007995085.1_ASM799508v1_genomic.fna.gz --refList GCF_007995085.1_ASM799508v1_genomic.fna/target_genomes.txt --output GCF_007995085.1_ASM799508v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:20:16,455] [INFO] Task succeeded: fastANI
[2024-01-24 13:20:16,456] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf4d1a40d-adf7-4f7e-89a7-571d1724bb5b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:20:16,457] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf4d1a40d-adf7-4f7e-89a7-571d1724bb5b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:20:16,476] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:20:16,476] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:20:16,476] [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 azotifigens	strain=NF 2-5-3	GCA_007995085.1	2057004	2057004	type	True	100.0	3231	3232	95	conclusive
Paraburkholderia sabiae	strain=LMG 24235	GCA_904848645.1	273251	273251	type	True	91.7259	2398	3232	95	below_threshold
Paraburkholderia phymatum	strain=STM815	GCA_000020045.1	148447	148447	type	True	88.9992	2109	3232	95	below_threshold
Paraburkholderia phymatum	strain=LMG 21445	GCA_902833665.1	148447	148447	type	True	88.9759	2103	3232	95	below_threshold
Paraburkholderia hospita	strain=LMG 20598	GCA_902833685.1	169430	169430	type	True	88.0465	2295	3232	95	below_threshold
Paraburkholderia hospita	strain=LMG 20598	GCA_900108355.1	169430	169430	type	True	88.0259	2278	3232	95	below_threshold
Paraburkholderia hospita	strain=DSM 17164	GCA_002902965.1	169430	169430	type	True	88.0155	2389	3232	95	below_threshold
Paraburkholderia terrae	strain=NBRC 100964	GCA_000739835.1	311230	311230	type	True	87.9662	2179	3232	95	below_threshold
Paraburkholderia caribensis	strain=DSM 13236	GCA_002902945.1	75105	75105	type	True	87.8923	2188	3232	95	below_threshold
Paraburkholderia caribensis	strain=LMG 18531	GCA_902833515.1	75105	75105	type	True	87.8923	2157	3232	95	below_threshold
Paraburkholderia caribensis	strain=MWAP64	GCA_001449005.1	75105	75105	type	True	87.8868	2195	3232	95	below_threshold
Paraburkholderia piptadeniae	strain=STM 7183	GCA_900007165.2	1701573	1701573	type	True	86.8805	1854	3232	95	below_threshold
Paraburkholderia gardini	strain=LMG 32171	GCA_907164575.1	2823469	2823469	type	True	82.488	1237	3232	95	below_threshold
Paraburkholderia podalyriae	strain=WC7.3b	GCA_014397785.1	1938811	1938811	type	True	82.3651	1403	3232	95	below_threshold
Paraburkholderia saeva	strain=LMG 31841	GCA_907164555.1	2777537	2777537	type	True	82.237	1241	3232	95	below_threshold
Paraburkholderia kirstenboschensis	strain=KB15	GCA_001636975.1	1245436	1245436	type	True	81.5613	1146	3232	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:20:16,478] [INFO] DFAST Taxonomy check result was written to GCF_007995085.1_ASM799508v1_genomic.fna/tc_result.tsv
[2024-01-24 13:20:16,479] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:20:16,479] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:20:16,479] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf4d1a40d-adf7-4f7e-89a7-571d1724bb5b/dqc_reference/checkm_data
[2024-01-24 13:20:16,480] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:20:16,569] [INFO] Task started: CheckM
[2024-01-24 13:20:16,569] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007995085.1_ASM799508v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007995085.1_ASM799508v1_genomic.fna/checkm_input GCF_007995085.1_ASM799508v1_genomic.fna/checkm_result
[2024-01-24 13:21:51,488] [INFO] Task succeeded: CheckM
[2024-01-24 13:21:51,490] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:21:51,518] [INFO] ===== Completeness check finished =====
[2024-01-24 13:21:51,518] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:21:51,519] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007995085.1_ASM799508v1_genomic.fna/markers.fasta)
[2024-01-24 13:21:51,519] [INFO] Task started: Blastn
[2024-01-24 13:21:51,519] [INFO] Running command: blastn -query GCF_007995085.1_ASM799508v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf4d1a40d-adf7-4f7e-89a7-571d1724bb5b/dqc_reference/reference_markers_gtdb.fasta -out GCF_007995085.1_ASM799508v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:21:53,339] [INFO] Task succeeded: Blastn
[2024-01-24 13:21:53,343] [INFO] Selected 10 target genomes.
[2024-01-24 13:21:53,343] [INFO] Target genome list was writen to GCF_007995085.1_ASM799508v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:21:53,367] [INFO] Task started: fastANI
[2024-01-24 13:21:53,367] [INFO] Running command: fastANI --query /var/lib/cwl/stg367c3955-a38f-4287-88a6-5103d6fded6b/GCF_007995085.1_ASM799508v1_genomic.fna.gz --refList GCF_007995085.1_ASM799508v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007995085.1_ASM799508v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:22:22,064] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:22,074] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:22:22,074] [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_007995085.1	s__Paraburkholderia azotifigens	100.0	3230	3232	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	98.91	98.91	0.86	0.86	2	conclusive
GCF_904848645.1	s__Paraburkholderia sabiae	91.724	2399	3232	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017104565.1	s__Paraburkholderia sp017104565	90.4302	2262	3232	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	89.0117	2105	3232	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002902965.1	s__Paraburkholderia hospita	87.9959	2393	3232	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.2599	98.45	97.70	0.87	0.82	14	-
GCF_017104715.1	s__Paraburkholderia sp017104715	87.475	2193	3232	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003121405.1	s__Paraburkholderia sp003121405	87.0657	1933	3232	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	87.0556	1813	3232	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	86.8527	1861	3232	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	86.8255	1946	3232	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:22:22,076] [INFO] GTDB search result was written to GCF_007995085.1_ASM799508v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:22:22,076] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:22:22,086] [INFO] DFAST_QC result json was written to GCF_007995085.1_ASM799508v1_genomic.fna/dqc_result.json
[2024-01-24 13:22:22,086] [INFO] DFAST_QC completed!
[2024-01-24 13:22:22,086] [INFO] Total running time: 0h3m24s