[2023-06-13 21:20:32,957] [INFO] DFAST_QC pipeline started.
[2023-06-13 21:20:32,959] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 21:20:32,959] [INFO] DQC Reference Directory: /var/lib/cwl/stgae5c053d-2924-4b5b-8a79-780b0c5c6606/dqc_reference
[2023-06-13 21:20:34,245] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 21:20:34,246] [INFO] Task started: Prodigal
[2023-06-13 21:20:34,246] [INFO] Running command: gunzip -c /var/lib/cwl/stgbaa9b7cc-96b8-4639-b778-3779c6a9ea9f/GCA_947464545.1_RE-9nov16-115_genomic.fna.gz | prodigal -d GCA_947464545.1_RE-9nov16-115_genomic.fna/cds.fna -a GCA_947464545.1_RE-9nov16-115_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 21:20:42,345] [INFO] Task succeeded: Prodigal
[2023-06-13 21:20:42,345] [INFO] Task started: HMMsearch
[2023-06-13 21:20:42,345] [INFO] Running command: hmmsearch --tblout GCA_947464545.1_RE-9nov16-115_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgae5c053d-2924-4b5b-8a79-780b0c5c6606/dqc_reference/reference_markers.hmm GCA_947464545.1_RE-9nov16-115_genomic.fna/protein.faa > /dev/null
[2023-06-13 21:20:42,616] [INFO] Task succeeded: HMMsearch
[2023-06-13 21:20:42,617] [INFO] Found 6/6 markers.
[2023-06-13 21:20:42,662] [INFO] Query marker FASTA was written to GCA_947464545.1_RE-9nov16-115_genomic.fna/markers.fasta
[2023-06-13 21:20:42,662] [INFO] Task started: Blastn
[2023-06-13 21:20:42,662] [INFO] Running command: blastn -query GCA_947464545.1_RE-9nov16-115_genomic.fna/markers.fasta -db /var/lib/cwl/stgae5c053d-2924-4b5b-8a79-780b0c5c6606/dqc_reference/reference_markers.fasta -out GCA_947464545.1_RE-9nov16-115_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 21:20:43,294] [INFO] Task succeeded: Blastn
[2023-06-13 21:20:43,298] [INFO] Selected 32 target genomes.
[2023-06-13 21:20:43,298] [INFO] Target genome list was writen to GCA_947464545.1_RE-9nov16-115_genomic.fna/target_genomes.txt
[2023-06-13 21:20:43,302] [INFO] Task started: fastANI
[2023-06-13 21:20:43,302] [INFO] Running command: fastANI --query /var/lib/cwl/stgbaa9b7cc-96b8-4639-b778-3779c6a9ea9f/GCA_947464545.1_RE-9nov16-115_genomic.fna.gz --refList GCA_947464545.1_RE-9nov16-115_genomic.fna/target_genomes.txt --output GCA_947464545.1_RE-9nov16-115_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 21:21:12,167] [INFO] Task succeeded: fastANI
[2023-06-13 21:21:12,167] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgae5c053d-2924-4b5b-8a79-780b0c5c6606/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 21:21:12,168] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgae5c053d-2924-4b5b-8a79-780b0c5c6606/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 21:21:12,179] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 21:21:12,179] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 21:21:12,179] [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
Luteitalea pratensis	strain=DSM 100886; HEG_-6_39	GCA_001618865.1	1855912	1855912	type	True	76.9393	184	992	95	below_threshold
Fulvimonas soli	strain=DSM 14263	GCA_003148905.1	155197	155197	type	True	75.1194	76	992	95	below_threshold
Immundisolibacter cernigliae	strain=TR3.2	GCA_001697225.1	1810504	1810504	type	True	75.1185	50	992	95	below_threshold
Fulvimonas soli	strain=LMG 19981	GCA_006352285.1	155197	155197	type	True	75.1148	73	992	95	below_threshold
Solimonas variicoloris	strain=DSM 15731	GCA_000382285.1	254408	254408	type	True	75.0649	92	992	95	below_threshold
Paraburkholderia guartelaensis	strain=CNPSo 3008	GCA_004353905.1	2546446	2546446	type	True	75.035	61	992	95	below_threshold
Pseudoduganella umbonata	strain=CECT 7753	GCA_014192225.1	864828	864828	type	True	75.0271	80	992	95	below_threshold
Corallococcus soli	strain=ZKHCc1 1396	GCA_014930455.1	2710757	2710757	type	True	74.9695	80	992	95	below_threshold
Myxococcus fulvus	strain=DSM 16525	GCA_900111765.1	33	33	type	True	74.9613	86	992	95	below_threshold
Paraburkholderia hiiakae	strain=LMG 27952	GCA_904848665.1	1081782	1081782	type	True	74.9612	60	992	95	below_threshold
Paraburkholderia pallida	strain=7MH5	GCA_004524855.1	2547399	2547399	type	True	74.9518	70	992	95	below_threshold
Oharaeibacter diazotrophicus	strain=DSM 102969	GCA_004362745.1	1920512	1920512	type	True	74.8765	112	992	95	below_threshold
Nocardia alba	strain=DSM 44684	GCA_004339125.1	225051	225051	type	True	74.8676	66	992	95	below_threshold
Nocardia alba	strain=NBRC 108234	GCA_001612665.1	225051	225051	type	True	74.866	67	992	95	below_threshold
Pyxidicoccus fallax	strain=DSM 14698	GCA_012933655.1	394095	394095	type	True	74.8237	109	992	95	below_threshold
Paraburkholderia silviterrae	strain=4M-K11	GCA_004353915.1	2528715	2528715	type	True	74.7795	71	992	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 21:21:12,182] [INFO] DFAST Taxonomy check result was written to GCA_947464545.1_RE-9nov16-115_genomic.fna/tc_result.tsv
[2023-06-13 21:21:12,182] [INFO] ===== Taxonomy check completed =====
[2023-06-13 21:21:12,182] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 21:21:12,182] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgae5c053d-2924-4b5b-8a79-780b0c5c6606/dqc_reference/checkm_data
[2023-06-13 21:21:12,183] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 21:21:12,220] [INFO] Task started: CheckM
[2023-06-13 21:21:12,220] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947464545.1_RE-9nov16-115_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947464545.1_RE-9nov16-115_genomic.fna/checkm_input GCA_947464545.1_RE-9nov16-115_genomic.fna/checkm_result
[2023-06-13 21:21:38,256] [INFO] Task succeeded: CheckM
[2023-06-13 21:21:38,257] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.98%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 21:21:38,279] [INFO] ===== Completeness check finished =====
[2023-06-13 21:21:38,279] [INFO] ===== Start GTDB Search =====
[2023-06-13 21:21:38,280] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947464545.1_RE-9nov16-115_genomic.fna/markers.fasta)
[2023-06-13 21:21:38,280] [INFO] Task started: Blastn
[2023-06-13 21:21:38,280] [INFO] Running command: blastn -query GCA_947464545.1_RE-9nov16-115_genomic.fna/markers.fasta -db /var/lib/cwl/stgae5c053d-2924-4b5b-8a79-780b0c5c6606/dqc_reference/reference_markers_gtdb.fasta -out GCA_947464545.1_RE-9nov16-115_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 21:21:39,282] [INFO] Task succeeded: Blastn
[2023-06-13 21:21:39,285] [INFO] Selected 19 target genomes.
[2023-06-13 21:21:39,285] [INFO] Target genome list was writen to GCA_947464545.1_RE-9nov16-115_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 21:21:39,292] [INFO] Task started: fastANI
[2023-06-13 21:21:39,292] [INFO] Running command: fastANI --query /var/lib/cwl/stgbaa9b7cc-96b8-4639-b778-3779c6a9ea9f/GCA_947464545.1_RE-9nov16-115_genomic.fna.gz --refList GCA_947464545.1_RE-9nov16-115_genomic.fna/target_genomes_gtdb.txt --output GCA_947464545.1_RE-9nov16-115_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 21:21:55,892] [INFO] Task succeeded: fastANI
[2023-06-13 21:21:55,904] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 21:21:55,904] [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_018268955.1	s__WHSN01 sp018268955	80.3982	538	992	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__WHSN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902825985.1	s__WHSN01 sp902825985	78.181	388	992	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__WHSN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017883165.1	s__JADGOC01 sp017883165	77.9638	265	992	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__JADGOC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009380045.1	s__WHSN01 sp009380045	77.7247	270	992	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__WHSN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001917905.1	s__Gp6-AA45 sp001917905	77.6589	241	992	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__Gp6-AA45	95.0	99.03	98.94	0.79	0.79	3	-
GCA_016195265.1	s__Gp6-AA45 sp016195265	77.5869	297	992	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__Gp6-AA45	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003223775.1	s__Gp6-AA45 sp003223775	77.4639	236	992	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__Gp6-AA45	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003222395.1	s__Gp6-AA45 sp003222395	77.2512	311	992	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__Gp6-AA45	95.0	99.74	99.72	0.98	0.98	4	-
GCA_003222535.1	s__Gp6-AA45 sp003222535	77.2401	325	992	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__Gp6-AA45	95.0	99.30	99.28	0.90	0.90	3	-
GCA_016195295.1	s__Gp6-AA45 sp016195295	77.0535	203	992	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__Gp6-AA45	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001767195.1	s__Gp6-AA40 sp001767195	77.0258	172	992	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__Gp6-AA40	95.0	99.78	99.78	0.93	0.93	2	-
GCA_016184455.1	s__Gp6-AA40 sp016184455	76.9767	202	992	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__Gp6-AA40	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016789685.1	s__JAEUQQ01 sp016789685	76.8893	195	992	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__JAFNAJ01;g__JAEUQQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003170135.1	s__Fen-181 sp003170135	76.7918	190	992	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__Fen-181;g__Fen-181	95.0	99.94	99.94	0.97	0.97	2	-
GCA_017305835.1	s__RCIO01 sp017305835	74.954	89	992	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__RCIO01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_904848665.1	s__Paraburkholderia hiiakae	74.953	61	992	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004353915.1	s__Paraburkholderia sp004353915	74.7687	73	992	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 21:21:55,906] [INFO] GTDB search result was written to GCA_947464545.1_RE-9nov16-115_genomic.fna/result_gtdb.tsv
[2023-06-13 21:21:55,907] [INFO] ===== GTDB Search completed =====
[2023-06-13 21:21:55,910] [INFO] DFAST_QC result json was written to GCA_947464545.1_RE-9nov16-115_genomic.fna/dqc_result.json
[2023-06-13 21:21:55,910] [INFO] DFAST_QC completed!
[2023-06-13 21:21:55,910] [INFO] Total running time: 0h1m23s