[2024-01-24 10:47:24,226] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:24,232] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:24,232] [INFO] DQC Reference Directory: /var/lib/cwl/stgc76635c8-8654-4124-9b1b-99418c78f285/dqc_reference
[2024-01-24 10:47:26,303] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:26,304] [INFO] Task started: Prodigal
[2024-01-24 10:47:26,305] [INFO] Running command: gunzip -c /var/lib/cwl/stg4140693c-fa98-4c28-83f8-354d226c867b/GCF_902459595.1_LMG_31014_genomic.fna.gz | prodigal -d GCF_902459595.1_LMG_31014_genomic.fna/cds.fna -a GCF_902459595.1_LMG_31014_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:42,860] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:42,860] [INFO] Task started: HMMsearch
[2024-01-24 10:47:42,861] [INFO] Running command: hmmsearch --tblout GCF_902459595.1_LMG_31014_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc76635c8-8654-4124-9b1b-99418c78f285/dqc_reference/reference_markers.hmm GCF_902459595.1_LMG_31014_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:43,164] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:43,166] [INFO] Found 6/6 markers.
[2024-01-24 10:47:43,206] [INFO] Query marker FASTA was written to GCF_902459595.1_LMG_31014_genomic.fna/markers.fasta
[2024-01-24 10:47:43,206] [INFO] Task started: Blastn
[2024-01-24 10:47:43,207] [INFO] Running command: blastn -query GCF_902459595.1_LMG_31014_genomic.fna/markers.fasta -db /var/lib/cwl/stgc76635c8-8654-4124-9b1b-99418c78f285/dqc_reference/reference_markers.fasta -out GCF_902459595.1_LMG_31014_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:44,128] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:44,131] [INFO] Selected 13 target genomes.
[2024-01-24 10:47:44,132] [INFO] Target genome list was writen to GCF_902459595.1_LMG_31014_genomic.fna/target_genomes.txt
[2024-01-24 10:47:44,137] [INFO] Task started: fastANI
[2024-01-24 10:47:44,137] [INFO] Running command: fastANI --query /var/lib/cwl/stg4140693c-fa98-4c28-83f8-354d226c867b/GCF_902459595.1_LMG_31014_genomic.fna.gz --refList GCF_902459595.1_LMG_31014_genomic.fna/target_genomes.txt --output GCF_902459595.1_LMG_31014_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:48:00,407] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:00,407] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc76635c8-8654-4124-9b1b-99418c78f285/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:48:00,408] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc76635c8-8654-4124-9b1b-99418c78f285/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:48:00,425] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 10:48:00,425] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 10:48:00,426] [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
Pandoraea soli	strain=LMG 31014	GCA_902459595.1	2508293	2508293	type	True	100.0	1627	1627	95	inconclusive
Pandoraea cepalis	strain=LMG 31106	GCA_902459665.1	2508294	2508294	type	True	95.8105	1461	1627	95	inconclusive
Pandoraea eparura	strain=LMG 31012	GCA_902459725.1	2508291	2508291	type	True	91.0348	1404	1627	95	below_threshold
Pandoraea terrigena	strain=LMG 31013	GCA_902459705.1	2508292	2508292	type	True	90.542	1375	1627	95	below_threshold
Pandoraea bronchicola	strain=LMG 20603	GCA_902459805.1	2508287	2508287	type	True	86.7421	1217	1627	95	below_threshold
Pandoraea communis	strain=LMG 31110	GCA_902459745.1	2508297	2508297	type	True	86.3303	1270	1627	95	below_threshold
Pandoraea capi	strain=LMG 20602	GCA_902459735.1	2508286	2508286	type	True	84.9594	1197	1627	95	below_threshold
Pandoraea morbifera	strain=LMG 31116	GCA_902459575.1	2508300	2508300	type	True	84.845	1187	1627	95	below_threshold
Burkholderia ubonensis		GCA_902499185.1	101571	101571	type	True	78.4896	563	1627	95	below_threshold
Burkholderia anthina	strain=DSM 16086	GCA_016836725.1	179879	179879	suspected-type	True	78.4874	561	1627	95	below_threshold
Burkholderia ubonensis	strain=LMG 20358	GCA_902833085.1	101571	101571	type	True	78.4536	563	1627	95	below_threshold
Paraburkholderia gardini	strain=LMG 32171	GCA_907164575.1	2823469	2823469	type	True	78.3752	452	1627	95	below_threshold
Burkholderia perseverans	strain=INN12	GCA_022870505.1	2615214	2615214	type	True	78.2141	590	1627	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:48:00,427] [INFO] DFAST Taxonomy check result was written to GCF_902459595.1_LMG_31014_genomic.fna/tc_result.tsv
[2024-01-24 10:48:00,428] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:48:00,428] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:48:00,428] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc76635c8-8654-4124-9b1b-99418c78f285/dqc_reference/checkm_data
[2024-01-24 10:48:00,429] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:48:00,477] [INFO] Task started: CheckM
[2024-01-24 10:48:00,477] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_902459595.1_LMG_31014_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_902459595.1_LMG_31014_genomic.fna/checkm_input GCF_902459595.1_LMG_31014_genomic.fna/checkm_result
[2024-01-24 10:48:52,048] [INFO] Task succeeded: CheckM
[2024-01-24 10:48:52,050] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:48:52,072] [INFO] ===== Completeness check finished =====
[2024-01-24 10:48:52,073] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:48:52,073] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_902459595.1_LMG_31014_genomic.fna/markers.fasta)
[2024-01-24 10:48:52,074] [INFO] Task started: Blastn
[2024-01-24 10:48:52,074] [INFO] Running command: blastn -query GCF_902459595.1_LMG_31014_genomic.fna/markers.fasta -db /var/lib/cwl/stgc76635c8-8654-4124-9b1b-99418c78f285/dqc_reference/reference_markers_gtdb.fasta -out GCF_902459595.1_LMG_31014_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:53,829] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:53,833] [INFO] Selected 10 target genomes.
[2024-01-24 10:48:53,833] [INFO] Target genome list was writen to GCF_902459595.1_LMG_31014_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:48:53,841] [INFO] Task started: fastANI
[2024-01-24 10:48:53,841] [INFO] Running command: fastANI --query /var/lib/cwl/stg4140693c-fa98-4c28-83f8-354d226c867b/GCF_902459595.1_LMG_31014_genomic.fna.gz --refList GCF_902459595.1_LMG_31014_genomic.fna/target_genomes_gtdb.txt --output GCF_902459595.1_LMG_31014_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:49:06,753] [INFO] Task succeeded: fastANI
[2024-01-24 10:49:06,762] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:49:06,763] [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_902459665.1	s__Pandoraea cepalis	95.8105	1461	1627	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	97.00	95.81	0.88	0.85	6	conclusive
GCF_902459725.1	s__Pandoraea eparura	91.0175	1406	1627	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902459705.1	s__Pandoraea terrigena	90.5477	1374	1627	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902459805.1	s__Pandoraea bronchicola	86.7375	1218	1627	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902459745.1	s__Pandoraea communis	86.347	1268	1627	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0166	98.36	97.48	0.89	0.87	3	-
GCF_902459555.1	s__Pandoraea horticolens	86.2012	1249	1627	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0166	N/A	N/A	N/A	N/A	1	-
GCF_000807775.2	s__Pandoraea fibrosis	86.1213	1246	1627	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	99.41	98.83	0.97	0.94	3	-
GCF_000767615.3	s__Pandoraea pnomenusa	84.9813	1194	1627	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	99.00	95.12	0.95	0.92	14	-
GCF_902459735.1	s__Pandoraea capi	84.9594	1197	1627	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	96.45	96.45	0.90	0.90	2	-
GCF_000814845.2	s__Pandoraea sputorum	84.7954	1189	1627	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	99.03	97.40	0.96	0.92	5	-
--------------------------------------------------------------------------------
[2024-01-24 10:49:06,766] [INFO] GTDB search result was written to GCF_902459595.1_LMG_31014_genomic.fna/result_gtdb.tsv
[2024-01-24 10:49:06,766] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:49:06,772] [INFO] DFAST_QC result json was written to GCF_902459595.1_LMG_31014_genomic.fna/dqc_result.json
[2024-01-24 10:49:06,772] [INFO] DFAST_QC completed!
[2024-01-24 10:49:06,772] [INFO] Total running time: 0h1m43s