[2023-06-28 19:03:55,746] [INFO] DFAST_QC pipeline started.
[2023-06-28 19:03:55,761] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 19:03:55,762] [INFO] DQC Reference Directory: /var/lib/cwl/stg31ba13bf-b70e-41cb-94c0-49da5d00078f/dqc_reference
[2023-06-28 19:03:57,145] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 19:03:57,146] [INFO] Task started: Prodigal
[2023-06-28 19:03:57,146] [INFO] Running command: gunzip -c /var/lib/cwl/stg76dd9392-b773-416c-a77b-659305ca6cf1/GCA_017936545.1_ASM1793654v1_genomic.fna.gz | prodigal -d GCA_017936545.1_ASM1793654v1_genomic.fna/cds.fna -a GCA_017936545.1_ASM1793654v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 19:04:02,540] [INFO] Task succeeded: Prodigal
[2023-06-28 19:04:02,540] [INFO] Task started: HMMsearch
[2023-06-28 19:04:02,540] [INFO] Running command: hmmsearch --tblout GCA_017936545.1_ASM1793654v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg31ba13bf-b70e-41cb-94c0-49da5d00078f/dqc_reference/reference_markers.hmm GCA_017936545.1_ASM1793654v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 19:04:02,824] [INFO] Task succeeded: HMMsearch
[2023-06-28 19:04:02,826] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg76dd9392-b773-416c-a77b-659305ca6cf1/GCA_017936545.1_ASM1793654v1_genomic.fna.gz]
[2023-06-28 19:04:02,855] [INFO] Query marker FASTA was written to GCA_017936545.1_ASM1793654v1_genomic.fna/markers.fasta
[2023-06-28 19:04:02,856] [INFO] Task started: Blastn
[2023-06-28 19:04:02,856] [INFO] Running command: blastn -query GCA_017936545.1_ASM1793654v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg31ba13bf-b70e-41cb-94c0-49da5d00078f/dqc_reference/reference_markers.fasta -out GCA_017936545.1_ASM1793654v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 19:04:03,685] [INFO] Task succeeded: Blastn
[2023-06-28 19:04:03,690] [INFO] Selected 23 target genomes.
[2023-06-28 19:04:03,690] [INFO] Target genome list was writen to GCA_017936545.1_ASM1793654v1_genomic.fna/target_genomes.txt
[2023-06-28 19:04:03,697] [INFO] Task started: fastANI
[2023-06-28 19:04:03,697] [INFO] Running command: fastANI --query /var/lib/cwl/stg76dd9392-b773-416c-a77b-659305ca6cf1/GCA_017936545.1_ASM1793654v1_genomic.fna.gz --refList GCA_017936545.1_ASM1793654v1_genomic.fna/target_genomes.txt --output GCA_017936545.1_ASM1793654v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 19:04:22,550] [INFO] Task succeeded: fastANI
[2023-06-28 19:04:22,551] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg31ba13bf-b70e-41cb-94c0-49da5d00078f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 19:04:22,551] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg31ba13bf-b70e-41cb-94c0-49da5d00078f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 19:04:22,564] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 19:04:22,564] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 19:04:22,564] [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
Sutterella megalosphaeroides	strain=6FBBBH3	GCA_003609995.1	2494234	2494234	type	True	79.0515	206	675	95	below_threshold
Sutterella parvirubra	strain=YIT 11816	GCA_000250875.1	437898	437898	type	True	78.9714	188	675	95	below_threshold
Sutterella faecalis	strain=KGMB03119	GCA_006337085.1	2584944	2584944	type	True	78.6001	211	675	95	below_threshold
Sutterella wadsworthensis	strain=DSM 14016	GCA_003315195.1	40545	40545	type	True	77.72	133	675	95	below_threshold
Sutterella wadsworthensis	strain=FDAARGOS_1159	GCA_016724805.1	40545	40545	type	True	77.6066	136	675	95	below_threshold
Burkholderia contaminans	strain=LMG 23361	GCA_001758385.2	488447	488447	type	True	76.0186	61	675	95	below_threshold
Burkholderia seminalis	strain=LMG 24067	GCA_902832885.1	488731	488731	type	True	75.7439	69	675	95	below_threshold
Massilia agri	strain=JCM 31661	GCA_024753255.1	1886785	1886785	type	True	75.6494	50	675	95	below_threshold
Burkholderia perseverans	strain=INN12	GCA_022870505.1	2615214	2615214	type	True	75.528	74	675	95	below_threshold
Paraburkholderia caballeronis	strain=LMG 26416	GCA_900109675.1	416943	416943	type	True	75.5175	64	675	95	below_threshold
Paraburkholderia caballeronis	strain=TNe-841	GCA_900104845.1	416943	416943	type	True	75.5108	62	675	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 19:04:22,567] [INFO] DFAST Taxonomy check result was written to GCA_017936545.1_ASM1793654v1_genomic.fna/tc_result.tsv
[2023-06-28 19:04:22,567] [INFO] ===== Taxonomy check completed =====
[2023-06-28 19:04:22,567] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 19:04:22,568] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg31ba13bf-b70e-41cb-94c0-49da5d00078f/dqc_reference/checkm_data
[2023-06-28 19:04:22,569] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 19:04:22,594] [INFO] Task started: CheckM
[2023-06-28 19:04:22,594] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017936545.1_ASM1793654v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017936545.1_ASM1793654v1_genomic.fna/checkm_input GCA_017936545.1_ASM1793654v1_genomic.fna/checkm_result
[2023-06-28 19:04:45,058] [INFO] Task succeeded: CheckM
[2023-06-28 19:04:45,059] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 19:04:45,082] [INFO] ===== Completeness check finished =====
[2023-06-28 19:04:45,082] [INFO] ===== Start GTDB Search =====
[2023-06-28 19:04:45,083] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017936545.1_ASM1793654v1_genomic.fna/markers.fasta)
[2023-06-28 19:04:45,083] [INFO] Task started: Blastn
[2023-06-28 19:04:45,083] [INFO] Running command: blastn -query GCA_017936545.1_ASM1793654v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg31ba13bf-b70e-41cb-94c0-49da5d00078f/dqc_reference/reference_markers_gtdb.fasta -out GCA_017936545.1_ASM1793654v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 19:04:46,393] [INFO] Task succeeded: Blastn
[2023-06-28 19:04:46,397] [INFO] Selected 12 target genomes.
[2023-06-28 19:04:46,397] [INFO] Target genome list was writen to GCA_017936545.1_ASM1793654v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 19:04:46,419] [INFO] Task started: fastANI
[2023-06-28 19:04:46,420] [INFO] Running command: fastANI --query /var/lib/cwl/stg76dd9392-b773-416c-a77b-659305ca6cf1/GCA_017936545.1_ASM1793654v1_genomic.fna.gz --refList GCA_017936545.1_ASM1793654v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017936545.1_ASM1793654v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 19:04:51,926] [INFO] Task succeeded: fastANI
[2023-06-28 19:04:51,942] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 19:04:51,943] [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_017936545.1	s__Sutterella sp017936545	100.0	670	675	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Sutterella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000297775.1	s__Sutterella wadsworthensis_A	80.9282	299	675	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Sutterella	95.0	98.94	98.60	0.92	0.86	8	-
GCA_900764215.1	s__Sutterella sp900764215	80.4667	253	675	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Sutterella	95.0	99.09	99.09	0.76	0.76	2	-
GCA_900543805.1	s__Sutterella merdavium	79.4441	213	675	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Sutterella	95.0	98.29	97.30	0.92	0.87	4	-
GCA_900754475.1	s__Sutterella sp900754475	79.1284	188	675	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Sutterella	95.0	98.47	98.47	0.94	0.94	2	-
GCF_003609995.1	s__Sutterella megalosphaeroides	79.061	205	675	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Sutterella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905213905.1	s__Sutterella sp905213905	78.9527	201	675	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Sutterella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016899755.1	s__Sutterella massiliensis	78.8473	203	675	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Sutterella	95.0	98.18	98.18	0.90	0.90	2	-
GCA_905186105.1	s__Sutterella sp905186105	78.651	127	675	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Sutterella	95.0	97.95	97.93	0.89	0.89	3	-
GCF_006337085.1	s__Sutterella faecalis	78.55	213	675	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Sutterella	95.0	99.36	97.93	0.96	0.93	5	-
GCA_905198475.1	s__Sutterella sp905198475	78.3815	196	675	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Sutterella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905194315.1	s__Sutterella sp905194315	77.5212	144	675	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Sutterella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 19:04:51,945] [INFO] GTDB search result was written to GCA_017936545.1_ASM1793654v1_genomic.fna/result_gtdb.tsv
[2023-06-28 19:04:51,945] [INFO] ===== GTDB Search completed =====
[2023-06-28 19:04:51,949] [INFO] DFAST_QC result json was written to GCA_017936545.1_ASM1793654v1_genomic.fna/dqc_result.json
[2023-06-28 19:04:51,949] [INFO] DFAST_QC completed!
[2023-06-28 19:04:51,949] [INFO] Total running time: 0h0m56s