[2024-01-24 12:31:03,520] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:03,522] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:03,522] [INFO] DQC Reference Directory: /var/lib/cwl/stged6feb69-7b22-4c14-a1a1-6d00593da9e9/dqc_reference
[2024-01-24 12:31:04,842] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:31:04,843] [INFO] Task started: Prodigal
[2024-01-24 12:31:04,843] [INFO] Running command: gunzip -c /var/lib/cwl/stg7334c9bc-24e7-433a-8ff0-2be5ebda796d/GCF_000739775.1_ASM73977v1_genomic.fna.gz | prodigal -d GCF_000739775.1_ASM73977v1_genomic.fna/cds.fna -a GCF_000739775.1_ASM73977v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:31:29,524] [INFO] Task succeeded: Prodigal
[2024-01-24 12:31:29,525] [INFO] Task started: HMMsearch
[2024-01-24 12:31:29,525] [INFO] Running command: hmmsearch --tblout GCF_000739775.1_ASM73977v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stged6feb69-7b22-4c14-a1a1-6d00593da9e9/dqc_reference/reference_markers.hmm GCF_000739775.1_ASM73977v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:31:29,900] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:31:29,902] [INFO] Found 6/6 markers.
[2024-01-24 12:31:29,968] [INFO] Query marker FASTA was written to GCF_000739775.1_ASM73977v1_genomic.fna/markers.fasta
[2024-01-24 12:31:29,969] [INFO] Task started: Blastn
[2024-01-24 12:31:29,969] [INFO] Running command: blastn -query GCF_000739775.1_ASM73977v1_genomic.fna/markers.fasta -db /var/lib/cwl/stged6feb69-7b22-4c14-a1a1-6d00593da9e9/dqc_reference/reference_markers.fasta -out GCF_000739775.1_ASM73977v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:30,899] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:30,902] [INFO] Selected 15 target genomes.
[2024-01-24 12:31:30,903] [INFO] Target genome list was writen to GCF_000739775.1_ASM73977v1_genomic.fna/target_genomes.txt
[2024-01-24 12:31:30,910] [INFO] Task started: fastANI
[2024-01-24 12:31:30,911] [INFO] Running command: fastANI --query /var/lib/cwl/stg7334c9bc-24e7-433a-8ff0-2be5ebda796d/GCF_000739775.1_ASM73977v1_genomic.fna.gz --refList GCF_000739775.1_ASM73977v1_genomic.fna/target_genomes.txt --output GCF_000739775.1_ASM73977v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:31:57,861] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:57,862] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stged6feb69-7b22-4c14-a1a1-6d00593da9e9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:31:57,862] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stged6feb69-7b22-4c14-a1a1-6d00593da9e9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:31:57,882] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:31:57,882] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:31:57,882] [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 heleia	strain=NBRC 101817	GCA_000739775.1	634127	634127	type	True	100.0	2612	2615	95	conclusive
Paraburkholderia nodosa	strain=DSM 21604	GCA_000519185.1	392320	392320	type	True	93.0869	1988	2615	95	below_threshold
Paraburkholderia guartelaensis	strain=CNPSo 3008	GCA_004353905.1	2546446	2546446	type	True	92.6608	1935	2615	95	below_threshold
Paraburkholderia hiiakae	strain=LMG 27952	GCA_904848665.1	1081782	1081782	type	True	91.3016	1812	2615	95	below_threshold
Paraburkholderia acidiphila	strain=7Q-K02	GCA_009789655.1	2571747	2571747	type	True	91.1551	1813	2615	95	below_threshold
Paraburkholderia silviterrae	strain=4M-K11	GCA_004353915.1	2528715	2528715	type	True	85.4591	1507	2615	95	below_threshold
Paraburkholderia pallida	strain=7MH5	GCA_004524855.1	2547399	2547399	type	True	85.4027	1563	2615	95	below_threshold
Paraburkholderia caballeronis	strain=LMG 26416	GCA_900109675.1	416943	416943	type	True	82.9167	1341	2615	95	below_threshold
Paraburkholderia caballeronis	strain=TNe-841	GCA_900104845.1	416943	416943	type	True	82.9073	1356	2615	95	below_threshold
Paraburkholderia podalyriae	strain=WC7.3b	GCA_014397785.1	1938811	1938811	type	True	81.1683	1245	2615	95	below_threshold
Burkholderia mallei	strain=ATCC 23344	GCA_000011705.1	13373	13373	type	True	81.0164	963	2615	95	below_threshold
Paraburkholderia gardini	strain=LMG 32171	GCA_907164575.1	2823469	2823469	type	True	81.0117	1035	2615	95	below_threshold
Burkholderia perseverans	strain=INN12	GCA_022870505.1	2615214	2615214	type	True	80.9927	1127	2615	95	below_threshold
Burkholderia pseudomallei	strain=WRAIR 286	GCA_006538545.1	28450	28450	type	True	80.9474	1037	2615	95	below_threshold
Burkholderia pseudomallei	strain=ATCC 23343	GCA_001182285.1	28450	28450	type	True	80.947	1054	2615	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:31:57,885] [INFO] DFAST Taxonomy check result was written to GCF_000739775.1_ASM73977v1_genomic.fna/tc_result.tsv
[2024-01-24 12:31:57,887] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:31:57,887] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:31:57,888] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stged6feb69-7b22-4c14-a1a1-6d00593da9e9/dqc_reference/checkm_data
[2024-01-24 12:31:57,890] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:31:57,971] [INFO] Task started: CheckM
[2024-01-24 12:31:57,971] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000739775.1_ASM73977v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000739775.1_ASM73977v1_genomic.fna/checkm_input GCF_000739775.1_ASM73977v1_genomic.fna/checkm_result
[2024-01-24 12:33:07,625] [INFO] Task succeeded: CheckM
[2024-01-24 12:33:07,627] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:33:07,646] [INFO] ===== Completeness check finished =====
[2024-01-24 12:33:07,647] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:33:07,647] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000739775.1_ASM73977v1_genomic.fna/markers.fasta)
[2024-01-24 12:33:07,647] [INFO] Task started: Blastn
[2024-01-24 12:33:07,648] [INFO] Running command: blastn -query GCF_000739775.1_ASM73977v1_genomic.fna/markers.fasta -db /var/lib/cwl/stged6feb69-7b22-4c14-a1a1-6d00593da9e9/dqc_reference/reference_markers_gtdb.fasta -out GCF_000739775.1_ASM73977v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:33:09,314] [INFO] Task succeeded: Blastn
[2024-01-24 12:33:09,318] [INFO] Selected 10 target genomes.
[2024-01-24 12:33:09,318] [INFO] Target genome list was writen to GCF_000739775.1_ASM73977v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:33:09,326] [INFO] Task started: fastANI
[2024-01-24 12:33:09,326] [INFO] Running command: fastANI --query /var/lib/cwl/stg7334c9bc-24e7-433a-8ff0-2be5ebda796d/GCF_000739775.1_ASM73977v1_genomic.fna.gz --refList GCF_000739775.1_ASM73977v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000739775.1_ASM73977v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:33:27,471] [INFO] Task succeeded: fastANI
[2024-01-24 12:33:27,484] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:33:27,484] [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_000739775.1	s__Paraburkholderia heleia	100.0	2612	2615	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.5542	N/A	N/A	N/A	N/A	1	conclusive
GCF_003096715.1	s__Paraburkholderia silvatlantica	95.554	2006	2615	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.5542	99.65	99.23	0.96	0.92	5	-
GCF_000519185.1	s__Paraburkholderia nodosa	93.0953	1987	2615	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001718195.1	s__Paraburkholderia nodosa_A	92.7963	1921	2615	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	92.6782	1934	2615	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	91.1733	1811	2615	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104845.1	s__Paraburkholderia caballeronis	82.8933	1358	2615	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	99.48	98.95	0.97	0.92	9	-
GCF_000011705.1	s__Burkholderia mallei	80.994	967	2615	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	99.31	98.71	0.94	0.78	1780	-
GCF_902499135.1	s__Burkholderia dolosa	80.9863	1013	2615	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	99.52	98.66	0.97	0.91	15	-
GCF_902859895.1	s__Pararobbsia alpina	78.5668	594	2615	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pararobbsia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:33:27,485] [INFO] GTDB search result was written to GCF_000739775.1_ASM73977v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:33:27,486] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:33:27,489] [INFO] DFAST_QC result json was written to GCF_000739775.1_ASM73977v1_genomic.fna/dqc_result.json
[2024-01-24 12:33:27,490] [INFO] DFAST_QC completed!
[2024-01-24 12:33:27,490] [INFO] Total running time: 0h2m24s