[2024-01-25 19:36:35,613] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:36:35,614] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:36:35,614] [INFO] DQC Reference Directory: /var/lib/cwl/stg8eb7b8e0-06a5-43bc-b4e6-4a3fa43b9fc3/dqc_reference
[2024-01-25 19:36:36,719] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:36:36,720] [INFO] Task started: Prodigal
[2024-01-25 19:36:36,720] [INFO] Running command: gunzip -c /var/lib/cwl/stgaf4f4df3-c13d-4772-9ae1-f3b609302148/GCF_002362315.1_ASM236231v1_genomic.fna.gz | prodigal -d GCF_002362315.1_ASM236231v1_genomic.fna/cds.fna -a GCF_002362315.1_ASM236231v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:37:02,966] [INFO] Task succeeded: Prodigal
[2024-01-25 19:37:02,966] [INFO] Task started: HMMsearch
[2024-01-25 19:37:02,966] [INFO] Running command: hmmsearch --tblout GCF_002362315.1_ASM236231v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8eb7b8e0-06a5-43bc-b4e6-4a3fa43b9fc3/dqc_reference/reference_markers.hmm GCF_002362315.1_ASM236231v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:37:03,257] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:37:03,258] [INFO] Found 6/6 markers.
[2024-01-25 19:37:03,311] [INFO] Query marker FASTA was written to GCF_002362315.1_ASM236231v1_genomic.fna/markers.fasta
[2024-01-25 19:37:03,312] [INFO] Task started: Blastn
[2024-01-25 19:37:03,312] [INFO] Running command: blastn -query GCF_002362315.1_ASM236231v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8eb7b8e0-06a5-43bc-b4e6-4a3fa43b9fc3/dqc_reference/reference_markers.fasta -out GCF_002362315.1_ASM236231v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:37:04,169] [INFO] Task succeeded: Blastn
[2024-01-25 19:37:04,173] [INFO] Selected 12 target genomes.
[2024-01-25 19:37:04,173] [INFO] Target genome list was writen to GCF_002362315.1_ASM236231v1_genomic.fna/target_genomes.txt
[2024-01-25 19:37:04,176] [INFO] Task started: fastANI
[2024-01-25 19:37:04,176] [INFO] Running command: fastANI --query /var/lib/cwl/stgaf4f4df3-c13d-4772-9ae1-f3b609302148/GCF_002362315.1_ASM236231v1_genomic.fna.gz --refList GCF_002362315.1_ASM236231v1_genomic.fna/target_genomes.txt --output GCF_002362315.1_ASM236231v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:37:25,017] [INFO] Task succeeded: fastANI
[2024-01-25 19:37:25,018] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8eb7b8e0-06a5-43bc-b4e6-4a3fa43b9fc3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:37:25,018] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8eb7b8e0-06a5-43bc-b4e6-4a3fa43b9fc3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:37:25,026] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:37:25,026] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:37:25,027] [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
Paraburkholderia acidicola	strain=ATCC 31363	GCA_002362315.1	1912599	1912599	type	True	100.0	2385	2385	95	conclusive
Paraburkholderia megapolitana	strain=LMG 23650	GCA_900113825.1	420953	420953	type	True	92.6179	2025	2385	95	below_threshold
Paraburkholderia megapolitana	strain=LMG 23650	GCA_007556815.1	420953	420953	type	True	92.611	2048	2385	95	below_threshold
Paraburkholderia flava	strain=LD6	GCA_004359985.1	2547393	2547393	type	True	84.5535	1464	2385	95	below_threshold
Paraburkholderia sartisoli	strain=LMG 24000	GCA_900107685.1	83784	83784	type	True	82.5272	1030	2385	95	below_threshold
Paraburkholderia monticola	strain=JC2948	GCA_001580545.1	1399968	1399968	type	True	82.4105	1126	2385	95	below_threshold
Paraburkholderia lacunae	strain=S27	GCA_003353175.1	2211104	2211104	type	True	82.2778	1131	2385	95	below_threshold
Paraburkholderia gardini	strain=LMG 32171	GCA_907164575.1	2823469	2823469	type	True	82.2178	1035	2385	95	below_threshold
Paraburkholderia podalyriae	strain=WC7.3b	GCA_014397785.1	1938811	1938811	type	True	82.2066	1116	2385	95	below_threshold
Paraburkholderia saeva	strain=LMG 31841	GCA_907164555.1	2777537	2777537	type	True	82.1473	1031	2385	95	below_threshold
Paraburkholderia ribeironis	strain=STM 7296	GCA_900019265.2	1247936	1247936	type	True	82.047	1049	2385	95	below_threshold
Paraburkholderia azotifigens	strain=NF 2-5-3	GCA_007995085.1	2057004	2057004	type	True	81.8542	1156	2385	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:37:25,028] [INFO] DFAST Taxonomy check result was written to GCF_002362315.1_ASM236231v1_genomic.fna/tc_result.tsv
[2024-01-25 19:37:25,028] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:37:25,028] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:37:25,029] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8eb7b8e0-06a5-43bc-b4e6-4a3fa43b9fc3/dqc_reference/checkm_data
[2024-01-25 19:37:25,029] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:37:25,092] [INFO] Task started: CheckM
[2024-01-25 19:37:25,093] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002362315.1_ASM236231v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002362315.1_ASM236231v1_genomic.fna/checkm_input GCF_002362315.1_ASM236231v1_genomic.fna/checkm_result
[2024-01-25 19:38:39,433] [INFO] Task succeeded: CheckM
[2024-01-25 19:38:39,434] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:38:39,452] [INFO] ===== Completeness check finished =====
[2024-01-25 19:38:39,452] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:38:39,453] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002362315.1_ASM236231v1_genomic.fna/markers.fasta)
[2024-01-25 19:38:39,453] [INFO] Task started: Blastn
[2024-01-25 19:38:39,453] [INFO] Running command: blastn -query GCF_002362315.1_ASM236231v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8eb7b8e0-06a5-43bc-b4e6-4a3fa43b9fc3/dqc_reference/reference_markers_gtdb.fasta -out GCF_002362315.1_ASM236231v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:38:41,074] [INFO] Task succeeded: Blastn
[2024-01-25 19:38:41,077] [INFO] Selected 15 target genomes.
[2024-01-25 19:38:41,077] [INFO] Target genome list was writen to GCF_002362315.1_ASM236231v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:38:41,087] [INFO] Task started: fastANI
[2024-01-25 19:38:41,087] [INFO] Running command: fastANI --query /var/lib/cwl/stgaf4f4df3-c13d-4772-9ae1-f3b609302148/GCF_002362315.1_ASM236231v1_genomic.fna.gz --refList GCF_002362315.1_ASM236231v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002362315.1_ASM236231v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:39:07,193] [INFO] Task succeeded: fastANI
[2024-01-25 19:39:07,205] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:39:07,206] [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_002362315.1	s__Paraburkholderia acidophila	100.0	2385	2385	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_007556815.1	s__Paraburkholderia megapolitana	92.6062	2049	2385	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	99.99	99.99	1.00	1.00	2	-
GCF_004359985.1	s__Paraburkholderia sp004359985	84.5588	1463	2385	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011752995.1	s__Paraburkholderia sp011752995	82.6195	1087	2385	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	99.23	99.21	0.92	0.90	4	-
GCF_012927125.1	s__Paraburkholderia sp012927125	82.5764	1151	2385	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001580545.1	s__Paraburkholderia monticola	82.4229	1123	2385	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004197395.1	s__Paraburkholderia sp004197395	82.3592	1156	2385	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902859915.1	s__Paraburkholderia ultramafica	82.3567	1091	2385	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003353175.1	s__Paraburkholderia lacunae	82.2656	1132	2385	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013366925.1	s__Paraburkholderia youngii	82.151	1135	2385	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	97.48	97.40	0.88	0.87	5	-
GCF_900019265.1	s__Paraburkholderia ribeironis	82.0714	1044	2385	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104845.1	s__Paraburkholderia caballeronis	81.9096	1041	2385	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	99.48	98.95	0.97	0.92	9	-
GCF_001634365.1	s__Paraburkholderia sp001634365	81.9094	1047	2385	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003610295.1	s__Paraburkholderia sp003610295	81.8182	1132	2385	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000687455.2	s__Burkholderia sp000687455	81.1311	780	2385	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:39:07,207] [INFO] GTDB search result was written to GCF_002362315.1_ASM236231v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:39:07,207] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:39:07,211] [INFO] DFAST_QC result json was written to GCF_002362315.1_ASM236231v1_genomic.fna/dqc_result.json
[2024-01-25 19:39:07,211] [INFO] DFAST_QC completed!
[2024-01-25 19:39:07,211] [INFO] Total running time: 0h2m32s