[2024-01-24 15:10:41,181] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:10:41,183] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:10:41,183] [INFO] DQC Reference Directory: /var/lib/cwl/stg11ca61d7-f47e-4502-acc6-c7e09cffad98/dqc_reference
[2024-01-24 15:10:42,526] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:10:42,527] [INFO] Task started: Prodigal
[2024-01-24 15:10:42,527] [INFO] Running command: gunzip -c /var/lib/cwl/stg47944ebb-cd4b-4324-adba-63acb01511ab/GCF_010499255.1_ASM1049925v1_genomic.fna.gz | prodigal -d GCF_010499255.1_ASM1049925v1_genomic.fna/cds.fna -a GCF_010499255.1_ASM1049925v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:10:52,263] [INFO] Task succeeded: Prodigal
[2024-01-24 15:10:52,264] [INFO] Task started: HMMsearch
[2024-01-24 15:10:52,264] [INFO] Running command: hmmsearch --tblout GCF_010499255.1_ASM1049925v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg11ca61d7-f47e-4502-acc6-c7e09cffad98/dqc_reference/reference_markers.hmm GCF_010499255.1_ASM1049925v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:10:52,551] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:10:52,553] [INFO] Found 6/6 markers.
[2024-01-24 15:10:52,590] [INFO] Query marker FASTA was written to GCF_010499255.1_ASM1049925v1_genomic.fna/markers.fasta
[2024-01-24 15:10:52,590] [INFO] Task started: Blastn
[2024-01-24 15:10:52,590] [INFO] Running command: blastn -query GCF_010499255.1_ASM1049925v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg11ca61d7-f47e-4502-acc6-c7e09cffad98/dqc_reference/reference_markers.fasta -out GCF_010499255.1_ASM1049925v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:10:53,374] [INFO] Task succeeded: Blastn
[2024-01-24 15:10:53,378] [INFO] Selected 24 target genomes.
[2024-01-24 15:10:53,379] [INFO] Target genome list was writen to GCF_010499255.1_ASM1049925v1_genomic.fna/target_genomes.txt
[2024-01-24 15:10:53,397] [INFO] Task started: fastANI
[2024-01-24 15:10:53,397] [INFO] Running command: fastANI --query /var/lib/cwl/stg47944ebb-cd4b-4324-adba-63acb01511ab/GCF_010499255.1_ASM1049925v1_genomic.fna.gz --refList GCF_010499255.1_ASM1049925v1_genomic.fna/target_genomes.txt --output GCF_010499255.1_ASM1049925v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:11:11,212] [INFO] Task succeeded: fastANI
[2024-01-24 15:11:11,213] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg11ca61d7-f47e-4502-acc6-c7e09cffad98/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:11:11,213] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg11ca61d7-f47e-4502-acc6-c7e09cffad98/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:11:11,240] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:11:11,240] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:11:11,240] [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
Sheuella amnicola	strain=NBD-18	GCA_010499255.1	2707330	2707330	type	True	100.0	1046	1047	95	conclusive
Pusillimonas minor	strain=YC-7-48	GCA_014237865.1	2697024	2697024	type	True	78.6636	67	1047	95	below_threshold
Zwartia hollandica	strain=LF4-65	GCA_019923725.1	324606	324606	type	True	77.761	119	1047	95	below_threshold
Bordetella hinzii	strain=NCTC13199	GCA_900637615.1	103855	103855	type	True	77.1379	74	1047	95	below_threshold
Achromobacter marplatensis	strain=CECT 7342	GCA_003315095.1	470868	470868	type	True	77.132	86	1047	95	below_threshold
Achromobacter marplatensis	strain=LMG 26219	GCA_902859635.1	470868	470868	type	True	77.0992	85	1047	95	below_threshold
Achromobacter piechaudii	strain=LMG 1873	GCA_902859685.1	72556	72556	type	True	77.028	92	1047	95	below_threshold
Bordetella hinzii	strain=LMG 13501	GCA_001548475.1	103855	103855	type	True	77.0035	72	1047	95	below_threshold
Orrella marina	strain=HZ20	GCA_003058465.1	2163011	2163011	type	True	76.9658	56	1047	95	below_threshold
Achromobacter marplatensis	strain=B2	GCA_002209535.1	470868	470868	type	True	76.7949	82	1047	95	below_threshold
Achromobacter piechaudii	strain=NBRC 102461	GCA_001571245.1	72556	72556	type	True	76.7766	92	1047	95	below_threshold
Pusillimonas harenae	strain=DSM 25667	GCA_013416515.1	657015	657015	type	True	76.608	61	1047	95	below_threshold
Pusillimonas ginsengisoli	strain=KCTC 22046	GCA_004153455.1	453575	453575	type	True	76.5194	65	1047	95	below_threshold
Bordetella bronchialis	strain=AU3182	GCA_001676705.1	463025	463025	type	True	76.4992	70	1047	95	below_threshold
Alcaligenes pakistanensis	strain=KCTC 42083	GCA_014652815.1	1482717	1482717	type	True	76.4955	56	1047	95	below_threshold
Pigmentiphaga litoralis	strain=KCTC 22165	GCA_014651835.1	516702	516702	type	True	75.9344	60	1047	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:11:11,242] [INFO] DFAST Taxonomy check result was written to GCF_010499255.1_ASM1049925v1_genomic.fna/tc_result.tsv
[2024-01-24 15:11:11,243] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:11:11,243] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:11:11,243] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg11ca61d7-f47e-4502-acc6-c7e09cffad98/dqc_reference/checkm_data
[2024-01-24 15:11:11,245] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:11:11,290] [INFO] Task started: CheckM
[2024-01-24 15:11:11,291] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010499255.1_ASM1049925v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010499255.1_ASM1049925v1_genomic.fna/checkm_input GCF_010499255.1_ASM1049925v1_genomic.fna/checkm_result
[2024-01-24 15:11:46,479] [INFO] Task succeeded: CheckM
[2024-01-24 15:11:46,481] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:11:46,500] [INFO] ===== Completeness check finished =====
[2024-01-24 15:11:46,501] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:11:46,501] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010499255.1_ASM1049925v1_genomic.fna/markers.fasta)
[2024-01-24 15:11:46,501] [INFO] Task started: Blastn
[2024-01-24 15:11:46,502] [INFO] Running command: blastn -query GCF_010499255.1_ASM1049925v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg11ca61d7-f47e-4502-acc6-c7e09cffad98/dqc_reference/reference_markers_gtdb.fasta -out GCF_010499255.1_ASM1049925v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:11:47,721] [INFO] Task succeeded: Blastn
[2024-01-24 15:11:47,725] [INFO] Selected 24 target genomes.
[2024-01-24 15:11:47,725] [INFO] Target genome list was writen to GCF_010499255.1_ASM1049925v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:11:47,750] [INFO] Task started: fastANI
[2024-01-24 15:11:47,750] [INFO] Running command: fastANI --query /var/lib/cwl/stg47944ebb-cd4b-4324-adba-63acb01511ab/GCF_010499255.1_ASM1049925v1_genomic.fna.gz --refList GCF_010499255.1_ASM1049925v1_genomic.fna/target_genomes_gtdb.txt --output GCF_010499255.1_ASM1049925v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:12:03,837] [INFO] Task succeeded: fastANI
[2024-01-24 15:12:03,856] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:12:03,857] [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_010499255.1	s__NBD-18 sp003507735	100.0	1046	1047	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__NBD-18	95.0	99.47	99.47	0.95	0.95	2	conclusive
GCF_902859725.1	s__Achromobacter mucicolens	78.3059	97	1047	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	97.28	95.42	0.92	0.89	13	-
GCA_002292845.1	s__NBD-18 sp002292845	77.4695	84	1047	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__NBD-18	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903847325.1	s__NBD-18 sp903847325	77.45	167	1047	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__NBD-18	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903958565.1	s__NBD-18 sp903958565	77.3468	116	1047	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__NBD-18	95.0	99.16	98.92	0.86	0.85	5	-
GCA_002737415.1	s__NBD-18 sp002737415	77.3355	92	1047	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__NBD-18	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903929925.1	s__NBD-18 sp903929925	77.3003	81	1047	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__NBD-18	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013205565.1	s__NBD-18 sp013205565	77.2681	89	1047	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__NBD-18	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903894155.1	s__NBD-18 sp903894155	77.1768	131	1047	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__NBD-18	95.0	99.08	98.85	0.85	0.83	4	-
GCA_903821335.1	s__NBD-18 sp903821335	77.0514	157	1047	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__NBD-18	95.0	99.43	99.29	0.86	0.84	5	-
GCF_004339425.1	s__Candidimonas_A sp004339425	77.0318	66	1047	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Candidimonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003123725.1	s__Corticimicrobacter populi	77.0028	55	1047	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Corticimicrobacter	95.0	96.49	96.49	0.90	0.90	2	-
GCF_001704295.1	s__Bordetella_C sp001704295	76.9004	69	1047	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009763255.1	s__Bordetella_A sp009763255	76.8511	76	1047	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella_A	95.0	97.90	97.90	0.93	0.93	2	-
GCF_001571245.1	s__Achromobacter piechaudii	76.7766	92	1047	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	99.00	98.18	0.96	0.93	8	-
GCF_000067205.1	s__Bordetella_A petrii	76.5671	84	1047	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004153455.1	s__Pusillimonas_B ginsengisoli	76.5194	65	1047	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pusillimonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001676705.1	s__Bordetella_C bronchialis	76.4992	70	1047	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella_C	95.0	99.23	99.23	0.97	0.97	2	-
GCF_002261185.1	s__Bordetella_A sp002261185	76.4896	100	1047	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella_A	95.0	98.69	98.69	0.95	0.95	2	-
GCA_903903735.1	s__NBD-18 sp903903735	76.4756	73	1047	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__NBD-18	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:12:03,858] [INFO] GTDB search result was written to GCF_010499255.1_ASM1049925v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:12:03,859] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:12:03,868] [INFO] DFAST_QC result json was written to GCF_010499255.1_ASM1049925v1_genomic.fna/dqc_result.json
[2024-01-24 15:12:03,869] [INFO] DFAST_QC completed!
[2024-01-24 15:12:03,869] [INFO] Total running time: 0h1m23s