[2024-01-24 13:46:26,042] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:26,078] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:26,078] [INFO] DQC Reference Directory: /var/lib/cwl/stgc60e7d94-5924-4e72-a3e4-401e35bf5c62/dqc_reference
[2024-01-24 13:46:27,735] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:27,736] [INFO] Task started: Prodigal
[2024-01-24 13:46:27,736] [INFO] Running command: gunzip -c /var/lib/cwl/stg543abf6e-b382-4a70-b50a-5139f4db0663/GCF_000685075.1_ASM68507v1_genomic.fna.gz | prodigal -d GCF_000685075.1_ASM68507v1_genomic.fna/cds.fna -a GCF_000685075.1_ASM68507v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:56,262] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:56,262] [INFO] Task started: HMMsearch
[2024-01-24 13:46:56,262] [INFO] Running command: hmmsearch --tblout GCF_000685075.1_ASM68507v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc60e7d94-5924-4e72-a3e4-401e35bf5c62/dqc_reference/reference_markers.hmm GCF_000685075.1_ASM68507v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:56,762] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:56,763] [INFO] Found 6/6 markers.
[2024-01-24 13:46:56,847] [INFO] Query marker FASTA was written to GCF_000685075.1_ASM68507v1_genomic.fna/markers.fasta
[2024-01-24 13:46:56,847] [INFO] Task started: Blastn
[2024-01-24 13:46:56,847] [INFO] Running command: blastn -query GCF_000685075.1_ASM68507v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc60e7d94-5924-4e72-a3e4-401e35bf5c62/dqc_reference/reference_markers.fasta -out GCF_000685075.1_ASM68507v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:57,881] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:57,884] [INFO] Selected 11 target genomes.
[2024-01-24 13:46:57,884] [INFO] Target genome list was writen to GCF_000685075.1_ASM68507v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:57,891] [INFO] Task started: fastANI
[2024-01-24 13:46:57,891] [INFO] Running command: fastANI --query /var/lib/cwl/stg543abf6e-b382-4a70-b50a-5139f4db0663/GCF_000685075.1_ASM68507v1_genomic.fna.gz --refList GCF_000685075.1_ASM68507v1_genomic.fna/target_genomes.txt --output GCF_000685075.1_ASM68507v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:47:21,901] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:21,902] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc60e7d94-5924-4e72-a3e4-401e35bf5c62/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:47:21,902] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc60e7d94-5924-4e72-a3e4-401e35bf5c62/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:47:21,910] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:47:21,910] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:47:21,910] [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 oxyphila	strain=NBRC 105797	GCA_000685075.1	614212	614212	type	True	100.0	3383	3398	95	inconclusive
Paraburkholderia pallida	strain=7MH5	GCA_004524855.1	2547399	2547399	type	True	95.3189	2523	3398	95	inconclusive
Paraburkholderia silviterrae	strain=4M-K11	GCA_004353915.1	2528715	2528715	type	True	93.5919	2200	3398	95	below_threshold
Paraburkholderia sacchari	strain=LMG 19450	GCA_000785435.2	159450	159450	type	True	88.5841	1711	3398	95	below_threshold
Paraburkholderia sacchari	strain=LMG 19450	GCA_902833715.1	159450	159450	type	True	88.5306	1705	3398	95	below_threshold
Paraburkholderia heleia	strain=NBRC 101817	GCA_000739775.1	634127	634127	type	True	85.4249	1543	3398	95	below_threshold
Paraburkholderia acidiphila	strain=7Q-K02	GCA_009789655.1	2571747	2571747	type	True	85.2821	1629	3398	95	below_threshold
Paraburkholderia guartelaensis	strain=CNPSo 3008	GCA_004353905.1	2546446	2546446	type	True	85.2574	1719	3398	95	below_threshold
Paraburkholderia podalyriae	strain=WC7.3b	GCA_014397785.1	1938811	1938811	type	True	81.2533	1234	3398	95	below_threshold
Burkholderia ubonensis		GCA_902499185.1	101571	101571	type	True	81.1278	1195	3398	95	below_threshold
Burkholderia perseverans	strain=INN12	GCA_022870505.1	2615214	2615214	type	True	81.1189	1141	3398	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:47:21,911] [INFO] DFAST Taxonomy check result was written to GCF_000685075.1_ASM68507v1_genomic.fna/tc_result.tsv
[2024-01-24 13:47:21,912] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:47:21,912] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:47:21,912] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc60e7d94-5924-4e72-a3e4-401e35bf5c62/dqc_reference/checkm_data
[2024-01-24 13:47:21,913] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:47:22,011] [INFO] Task started: CheckM
[2024-01-24 13:47:22,011] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000685075.1_ASM68507v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000685075.1_ASM68507v1_genomic.fna/checkm_input GCF_000685075.1_ASM68507v1_genomic.fna/checkm_result
[2024-01-24 13:48:43,704] [INFO] Task succeeded: CheckM
[2024-01-24 13:48:43,705] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:48:43,725] [INFO] ===== Completeness check finished =====
[2024-01-24 13:48:43,725] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:48:43,725] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000685075.1_ASM68507v1_genomic.fna/markers.fasta)
[2024-01-24 13:48:43,726] [INFO] Task started: Blastn
[2024-01-24 13:48:43,726] [INFO] Running command: blastn -query GCF_000685075.1_ASM68507v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc60e7d94-5924-4e72-a3e4-401e35bf5c62/dqc_reference/reference_markers_gtdb.fasta -out GCF_000685075.1_ASM68507v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:48:45,735] [INFO] Task succeeded: Blastn
[2024-01-24 13:48:45,737] [INFO] Selected 11 target genomes.
[2024-01-24 13:48:45,738] [INFO] Target genome list was writen to GCF_000685075.1_ASM68507v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:48:45,747] [INFO] Task started: fastANI
[2024-01-24 13:48:45,747] [INFO] Running command: fastANI --query /var/lib/cwl/stg543abf6e-b382-4a70-b50a-5139f4db0663/GCF_000685075.1_ASM68507v1_genomic.fna.gz --refList GCF_000685075.1_ASM68507v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000685075.1_ASM68507v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:49:08,330] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:08,338] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:49:08,338] [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_000685075.1	s__Paraburkholderia oxyphila	100.0	3383	3398	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	95.32	95.32	0.74	0.74	2	conclusive
GCF_004353915.1	s__Paraburkholderia sp004353915	93.5839	2201	3398	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000785435.2	s__Paraburkholderia sacchari	88.5613	1714	3398	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	98.05	96.11	0.93	0.86	3	-
GCF_902859945.1	s__Paraburkholderia caffeinitolerans	88.5159	1851	3398	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	99.86	99.86	0.95	0.95	2	-
GCF_002917095.1	s__Paraburkholderia eburnea	86.0297	1543	3398	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	99.11	98.22	0.96	0.92	3	-
GCF_000739775.1	s__Paraburkholderia heleia	85.4125	1545	3398	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.5542	N/A	N/A	N/A	N/A	1	-
GCF_003096715.1	s__Paraburkholderia silvatlantica	85.3849	1527	3398	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.5542	99.65	99.23	0.96	0.92	5	-
GCF_017104965.1	s__Paraburkholderia sp017104965	85.3085	1563	3398	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009789655.1	s__Paraburkholderia acidiphila	85.2902	1628	3398	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004353905.1	s__Paraburkholderia guartelaensis	85.2536	1719	3398	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009789675.1	s__Paraburkholderia acidisoli	84.6463	1517	3398	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 13:49:08,339] [INFO] GTDB search result was written to GCF_000685075.1_ASM68507v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:49:08,340] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:49:08,342] [INFO] DFAST_QC result json was written to GCF_000685075.1_ASM68507v1_genomic.fna/dqc_result.json
[2024-01-24 13:49:08,342] [INFO] DFAST_QC completed!
[2024-01-24 13:49:08,342] [INFO] Total running time: 0h2m42s