[2024-01-24 15:10:40,029] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:10:40,032] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:10:40,032] [INFO] DQC Reference Directory: /var/lib/cwl/stge9c86e0a-1613-4296-8536-23088ae26785/dqc_reference
[2024-01-24 15:10:41,404] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:10:41,405] [INFO] Task started: Prodigal
[2024-01-24 15:10:41,406] [INFO] Running command: gunzip -c /var/lib/cwl/stg34d8bba4-92b9-43b2-b4a1-d4be74f0bb2d/GCF_003402575.1_ASM340257v1_genomic.fna.gz | prodigal -d GCF_003402575.1_ASM340257v1_genomic.fna/cds.fna -a GCF_003402575.1_ASM340257v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:10:48,360] [INFO] Task succeeded: Prodigal
[2024-01-24 15:10:48,361] [INFO] Task started: HMMsearch
[2024-01-24 15:10:48,361] [INFO] Running command: hmmsearch --tblout GCF_003402575.1_ASM340257v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge9c86e0a-1613-4296-8536-23088ae26785/dqc_reference/reference_markers.hmm GCF_003402575.1_ASM340257v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:10:48,641] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:10:48,642] [INFO] Found 6/6 markers.
[2024-01-24 15:10:48,671] [INFO] Query marker FASTA was written to GCF_003402575.1_ASM340257v1_genomic.fna/markers.fasta
[2024-01-24 15:10:48,672] [INFO] Task started: Blastn
[2024-01-24 15:10:48,672] [INFO] Running command: blastn -query GCF_003402575.1_ASM340257v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge9c86e0a-1613-4296-8536-23088ae26785/dqc_reference/reference_markers.fasta -out GCF_003402575.1_ASM340257v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:10:49,394] [INFO] Task succeeded: Blastn
[2024-01-24 15:10:49,397] [INFO] Selected 32 target genomes.
[2024-01-24 15:10:49,397] [INFO] Target genome list was writen to GCF_003402575.1_ASM340257v1_genomic.fna/target_genomes.txt
[2024-01-24 15:10:49,410] [INFO] Task started: fastANI
[2024-01-24 15:10:49,411] [INFO] Running command: fastANI --query /var/lib/cwl/stg34d8bba4-92b9-43b2-b4a1-d4be74f0bb2d/GCF_003402575.1_ASM340257v1_genomic.fna.gz --refList GCF_003402575.1_ASM340257v1_genomic.fna/target_genomes.txt --output GCF_003402575.1_ASM340257v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:11:13,632] [INFO] Task succeeded: fastANI
[2024-01-24 15:11:13,633] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge9c86e0a-1613-4296-8536-23088ae26785/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:11:13,633] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge9c86e0a-1613-4296-8536-23088ae26785/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:11:13,644] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 15:11:13,644] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 15:11:13,644] [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	78.2206	94	873	95	below_threshold
Burkholderia dolosa	strain=FDAARGOS_1463	GCA_019930785.1	152500	152500	type	True	78.0564	61	873	95	below_threshold
Sutterella faecalis	strain=KGMB03119	GCA_006337085.1	2584944	2584944	type	True	78.0306	104	873	95	below_threshold
Sutterella wadsworthensis	strain=FDAARGOS_1159	GCA_016724805.1	40545	40545	type	True	77.9338	75	873	95	below_threshold
Burkholderia oklahomensis	strain=LMG 23618	GCA_900608545.1	342113	342113	type	True	77.0735	72	873	95	below_threshold
Burkholderia oklahomensis	strain=C6786	GCA_001522135.2	342113	342113	type	True	77.0468	73	873	95	below_threshold
Sutterella parvirubra	strain=YIT 11816	GCA_000250875.1	437898	437898	type	True	76.8541	95	873	95	below_threshold
Sutterella wadsworthensis	strain=DSM 14016	GCA_003315195.1	40545	40545	type	True	76.7169	68	873	95	below_threshold
Burkholderia dolosa	strain=LMG 18943	GCA_902499135.1	152500	152500	type	True	76.4306	54	873	95	below_threshold
Burkholderia oklahomensis	strain=C6786	GCA_000170375.1	342113	342113	type	True	76.103	64	873	95	below_threshold
Duganella aceris	strain=SAP-35	GCA_011090165.1	2703883	2703883	type	True	75.7229	50	873	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:11:13,646] [INFO] DFAST Taxonomy check result was written to GCF_003402575.1_ASM340257v1_genomic.fna/tc_result.tsv
[2024-01-24 15:11:13,647] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:11:13,647] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:11:13,647] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge9c86e0a-1613-4296-8536-23088ae26785/dqc_reference/checkm_data
[2024-01-24 15:11:13,649] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:11:13,682] [INFO] Task started: CheckM
[2024-01-24 15:11:13,682] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003402575.1_ASM340257v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003402575.1_ASM340257v1_genomic.fna/checkm_input GCF_003402575.1_ASM340257v1_genomic.fna/checkm_result
[2024-01-24 15:11:40,945] [INFO] Task succeeded: CheckM
[2024-01-24 15:11:40,946] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:11:40,966] [INFO] ===== Completeness check finished =====
[2024-01-24 15:11:40,967] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:11:40,967] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003402575.1_ASM340257v1_genomic.fna/markers.fasta)
[2024-01-24 15:11:40,967] [INFO] Task started: Blastn
[2024-01-24 15:11:40,968] [INFO] Running command: blastn -query GCF_003402575.1_ASM340257v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge9c86e0a-1613-4296-8536-23088ae26785/dqc_reference/reference_markers_gtdb.fasta -out GCF_003402575.1_ASM340257v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:11:41,976] [INFO] Task succeeded: Blastn
[2024-01-24 15:11:41,985] [INFO] Selected 19 target genomes.
[2024-01-24 15:11:41,985] [INFO] Target genome list was writen to GCF_003402575.1_ASM340257v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:11:42,004] [INFO] Task started: fastANI
[2024-01-24 15:11:42,004] [INFO] Running command: fastANI --query /var/lib/cwl/stg34d8bba4-92b9-43b2-b4a1-d4be74f0bb2d/GCF_003402575.1_ASM340257v1_genomic.fna.gz --refList GCF_003402575.1_ASM340257v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003402575.1_ASM340257v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:11:58,536] [INFO] Task succeeded: fastANI
[2024-01-24 15:11:58,554] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:11:58,554] [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_003402575.1	s__Mesosutterella multiformis	100.0	868	873	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Mesosutterella	95.0	99.16	98.62	0.94	0.88	11	conclusive
GCF_001182045.1	s__Mesosutterella massiliensis	94.0938	740	873	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Mesosutterella	95.0	99.88	99.78	0.99	0.98	5	-
GCA_902797695.1	s__Mesosutterella sp902797695	79.1176	265	873	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Mesosutterella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003854935.1	s__Cupriavidus pauculus_C	77.5906	53	873	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002902945.1	s__Paraburkholderia caribensis	77.5364	60	873	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	98.86	96.01	0.91	0.80	9	-
GCF_016899755.1	s__Sutterella massiliensis	77.0273	69	873	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Sutterella	95.0	98.18	98.18	0.90	0.90	2	-
GCF_009183815.1	s__Sutterella seckii_A	76.911	100	873	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Sutterella	95.0	98.09	95.34	0.87	0.81	4	-
GCA_905215795.1	s__Sutterella sp905215795	76.7853	61	873	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Sutterella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905202595.1	s__Sutterella sp905202595	76.6978	76	873	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Sutterella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003315195.1	s__Sutterella wadsworthensis	76.6332	67	873	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Sutterella	95.0	98.28	97.53	0.92	0.89	35	-
GCF_001544755.2	s__Caballeronia catudaia	75.9098	57	873	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001544695.2	s__Caballeronia arvi	75.8629	57	873	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011090165.1	s__Duganella aceris	75.7229	50	873	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:11:58,559] [INFO] GTDB search result was written to GCF_003402575.1_ASM340257v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:11:58,559] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:11:58,563] [INFO] DFAST_QC result json was written to GCF_003402575.1_ASM340257v1_genomic.fna/dqc_result.json
[2024-01-24 15:11:58,563] [INFO] DFAST_QC completed!
[2024-01-24 15:11:58,563] [INFO] Total running time: 0h1m19s