[2023-06-18 14:01:47,516] [INFO] DFAST_QC pipeline started.
[2023-06-18 14:01:47,519] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 14:01:47,519] [INFO] DQC Reference Directory: /var/lib/cwl/stgeffd9514-3285-44dc-b924-1a9313b20d53/dqc_reference
[2023-06-18 14:01:48,812] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 14:01:48,813] [INFO] Task started: Prodigal
[2023-06-18 14:01:48,813] [INFO] Running command: gunzip -c /var/lib/cwl/stg8a89da79-46e1-4e70-b446-655631e02d5e/GCA_018262625.1_ASM1826262v1_genomic.fna.gz | prodigal -d GCA_018262625.1_ASM1826262v1_genomic.fna/cds.fna -a GCA_018262625.1_ASM1826262v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 14:01:55,671] [INFO] Task succeeded: Prodigal
[2023-06-18 14:01:55,672] [INFO] Task started: HMMsearch
[2023-06-18 14:01:55,672] [INFO] Running command: hmmsearch --tblout GCA_018262625.1_ASM1826262v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgeffd9514-3285-44dc-b924-1a9313b20d53/dqc_reference/reference_markers.hmm GCA_018262625.1_ASM1826262v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 14:01:55,936] [INFO] Task succeeded: HMMsearch
[2023-06-18 14:01:55,937] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg8a89da79-46e1-4e70-b446-655631e02d5e/GCA_018262625.1_ASM1826262v1_genomic.fna.gz]
[2023-06-18 14:01:55,969] [INFO] Query marker FASTA was written to GCA_018262625.1_ASM1826262v1_genomic.fna/markers.fasta
[2023-06-18 14:01:55,969] [INFO] Task started: Blastn
[2023-06-18 14:01:55,969] [INFO] Running command: blastn -query GCA_018262625.1_ASM1826262v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeffd9514-3285-44dc-b924-1a9313b20d53/dqc_reference/reference_markers.fasta -out GCA_018262625.1_ASM1826262v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 14:01:56,655] [INFO] Task succeeded: Blastn
[2023-06-18 14:01:56,659] [INFO] Selected 20 target genomes.
[2023-06-18 14:01:56,660] [INFO] Target genome list was writen to GCA_018262625.1_ASM1826262v1_genomic.fna/target_genomes.txt
[2023-06-18 14:01:56,664] [INFO] Task started: fastANI
[2023-06-18 14:01:56,664] [INFO] Running command: fastANI --query /var/lib/cwl/stg8a89da79-46e1-4e70-b446-655631e02d5e/GCA_018262625.1_ASM1826262v1_genomic.fna.gz --refList GCA_018262625.1_ASM1826262v1_genomic.fna/target_genomes.txt --output GCA_018262625.1_ASM1826262v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 14:02:12,537] [INFO] Task succeeded: fastANI
[2023-06-18 14:02:12,537] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgeffd9514-3285-44dc-b924-1a9313b20d53/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 14:02:12,538] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgeffd9514-3285-44dc-b924-1a9313b20d53/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 14:02:12,552] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 14:02:12,553] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-18 14:02:12,553] [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
Cupriavidus nantongensis	strain=X1	GCA_001598055.1	1796606	1796606	type	True	76.6404	108	634	95	below_threshold
Rubrivivax benzoatilyticus	strain=JA2	GCA_000420125.1	316997	316997	type	True	76.5058	101	634	95	below_threshold
Rubrivivax benzoatilyticus	strain=JA2	GCA_000190375.2	316997	316997	type	True	76.4863	102	634	95	below_threshold
Cupriavidus gilardii	strain=ATCC 700815	GCA_013004615.1	82541	82541	type	True	76.4564	93	634	95	below_threshold
Cupriavidus gilardii	strain=CCUG 38401	GCA_008801915.1	82541	82541	type	True	76.4027	95	634	95	below_threshold
Burkholderia dolosa	strain=FDAARGOS_1463	GCA_019930785.1	152500	152500	type	True	76.3353	99	634	95	below_threshold
Massilia arenosa	strain=MC02	GCA_004614185.1	2561931	2561931	type	True	76.271	68	634	95	below_threshold
Burkholderia dolosa	strain=LMG 18943	GCA_902499135.1	152500	152500	type	True	76.267	99	634	95	below_threshold
Derxia gummosa	strain=DSM 723	GCA_000482785.1	203699	203699	type	True	76.2645	86	634	95	below_threshold
Thauera phenylacetica	strain=B4P	GCA_000310225.1	164400	164400	type	True	76.2548	101	634	95	below_threshold
Aromatoleum anaerobium	strain=LuFRes1	GCA_012910705.2	182180	182180	type	True	76.2352	81	634	95	below_threshold
Cupriavidus agavae	strain=ASC-9842	GCA_004217045.1	1001822	1001822	type	True	76.2255	96	634	95	below_threshold
Thauera aminoaromatica	strain=S2	GCA_000310185.1	164330	164330	type	True	76.1739	86	634	95	below_threshold
Cupriavidus plantarum	strain=LMG 26296	GCA_905397285.1	942865	942865	type	True	76.1655	79	634	95	below_threshold
Burkholderia oklahomensis	strain=C6786	GCA_000170375.1	342113	342113	type	True	76.0954	93	634	95	below_threshold
Burkholderia oklahomensis	strain=C6786	GCA_001522135.2	342113	342113	type	True	76.0551	99	634	95	below_threshold
Burkholderia oklahomensis	strain=LMG 23618	GCA_900608545.1	342113	342113	type	True	76.0481	101	634	95	below_threshold
Derxia lacustris	strain=HL-12	GCA_002105195.1	764842	764842	type	True	75.9144	103	634	95	below_threshold
Massilia forsythiae	strain=GN2-R2	GCA_012849555.1	2728020	2728020	type	True	75.7993	83	634	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-18 14:02:12,556] [INFO] DFAST Taxonomy check result was written to GCA_018262625.1_ASM1826262v1_genomic.fna/tc_result.tsv
[2023-06-18 14:02:12,557] [INFO] ===== Taxonomy check completed =====
[2023-06-18 14:02:12,557] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 14:02:12,557] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgeffd9514-3285-44dc-b924-1a9313b20d53/dqc_reference/checkm_data
[2023-06-18 14:02:12,559] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 14:02:12,589] [INFO] Task started: CheckM
[2023-06-18 14:02:12,589] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018262625.1_ASM1826262v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018262625.1_ASM1826262v1_genomic.fna/checkm_input GCA_018262625.1_ASM1826262v1_genomic.fna/checkm_result
[2023-06-18 14:02:38,422] [INFO] Task succeeded: CheckM
[2023-06-18 14:02:38,423] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 43.42%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 14:02:38,443] [INFO] ===== Completeness check finished =====
[2023-06-18 14:02:38,443] [INFO] ===== Start GTDB Search =====
[2023-06-18 14:02:38,444] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018262625.1_ASM1826262v1_genomic.fna/markers.fasta)
[2023-06-18 14:02:38,444] [INFO] Task started: Blastn
[2023-06-18 14:02:38,444] [INFO] Running command: blastn -query GCA_018262625.1_ASM1826262v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeffd9514-3285-44dc-b924-1a9313b20d53/dqc_reference/reference_markers_gtdb.fasta -out GCA_018262625.1_ASM1826262v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 14:02:39,305] [INFO] Task succeeded: Blastn
[2023-06-18 14:02:39,309] [INFO] Selected 15 target genomes.
[2023-06-18 14:02:39,310] [INFO] Target genome list was writen to GCA_018262625.1_ASM1826262v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 14:02:39,336] [INFO] Task started: fastANI
[2023-06-18 14:02:39,336] [INFO] Running command: fastANI --query /var/lib/cwl/stg8a89da79-46e1-4e70-b446-655631e02d5e/GCA_018262625.1_ASM1826262v1_genomic.fna.gz --refList GCA_018262625.1_ASM1826262v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018262625.1_ASM1826262v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 14:02:47,553] [INFO] Task succeeded: fastANI
[2023-06-18 14:02:47,575] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-18 14:02:47,575] [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
GCA_016716275.1	s__JADJWR01 sp016716275	78.5542	191	634	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__JADJWR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016861185.1	s__DSNY01 sp016861185	78.3257	189	634	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__DSNY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011056935.1	s__DSNY01 sp011056935	78.0695	192	634	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__DSNY01	95.0	98.37	98.37	0.91	0.91	2	-
GCA_013813185.1	s__JACCZX01 sp013813185	77.3844	55	634	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__JACCZX01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000190375.1	s__Rubrivivax benzoatilyticus	76.5241	100	634	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	99.67	98.73	0.98	0.95	5	-
GCA_013695705.1	s__JACCZX01 sp013695705	76.5209	54	634	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__JACCZX01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002354895.1	s__Thauera sp002354895	76.5182	80	634	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018971105.1	s__Rubrivivax sp018971105	76.309	94	634	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000482785.1	s__Derxia gummosa	76.2453	87	634	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Derxia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005882215.1	s__VBCK01 sp005882215	76.2341	71	634	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__VBCK01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014379395.1	s__Janthinobacterium sp014379395	76.2176	53	634	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Janthinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903644065.1	s__CAHJXF01 sp903644065	76.194	76	634	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__CAHJXF01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-18 14:02:47,577] [INFO] GTDB search result was written to GCA_018262625.1_ASM1826262v1_genomic.fna/result_gtdb.tsv
[2023-06-18 14:02:47,578] [INFO] ===== GTDB Search completed =====
[2023-06-18 14:02:47,581] [INFO] DFAST_QC result json was written to GCA_018262625.1_ASM1826262v1_genomic.fna/dqc_result.json
[2023-06-18 14:02:47,582] [INFO] DFAST_QC completed!
[2023-06-18 14:02:47,582] [INFO] Total running time: 0h1m0s