[2024-01-24 13:48:43,619] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:48:43,621] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:48:43,621] [INFO] DQC Reference Directory: /var/lib/cwl/stg86f06296-2fe2-4839-bdcd-7547c730aaa8/dqc_reference
[2024-01-24 13:48:44,826] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:48:44,827] [INFO] Task started: Prodigal
[2024-01-24 13:48:44,828] [INFO] Running command: gunzip -c /var/lib/cwl/stga85dd284-7404-4dcb-98c3-06e3cf83cfa0/GCF_003368325.1_ASM336832v1_genomic.fna.gz | prodigal -d GCF_003368325.1_ASM336832v1_genomic.fna/cds.fna -a GCF_003368325.1_ASM336832v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:11,618] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:11,618] [INFO] Task started: HMMsearch
[2024-01-24 13:49:11,618] [INFO] Running command: hmmsearch --tblout GCF_003368325.1_ASM336832v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg86f06296-2fe2-4839-bdcd-7547c730aaa8/dqc_reference/reference_markers.hmm GCF_003368325.1_ASM336832v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:11,979] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:11,980] [INFO] Found 6/6 markers.
[2024-01-24 13:49:12,039] [INFO] Query marker FASTA was written to GCF_003368325.1_ASM336832v1_genomic.fna/markers.fasta
[2024-01-24 13:49:12,040] [INFO] Task started: Blastn
[2024-01-24 13:49:12,040] [INFO] Running command: blastn -query GCF_003368325.1_ASM336832v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg86f06296-2fe2-4839-bdcd-7547c730aaa8/dqc_reference/reference_markers.fasta -out GCF_003368325.1_ASM336832v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:12,903] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:12,907] [INFO] Selected 18 target genomes.
[2024-01-24 13:49:12,907] [INFO] Target genome list was writen to GCF_003368325.1_ASM336832v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:12,913] [INFO] Task started: fastANI
[2024-01-24 13:49:12,914] [INFO] Running command: fastANI --query /var/lib/cwl/stga85dd284-7404-4dcb-98c3-06e3cf83cfa0/GCF_003368325.1_ASM336832v1_genomic.fna.gz --refList GCF_003368325.1_ASM336832v1_genomic.fna/target_genomes.txt --output GCF_003368325.1_ASM336832v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:47,433] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:47,433] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg86f06296-2fe2-4839-bdcd-7547c730aaa8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:47,433] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg86f06296-2fe2-4839-bdcd-7547c730aaa8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:47,453] [INFO] Found 18 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:49:47,453] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:49:47,453] [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 caffeinilytica	strain=CF1	GCA_003368325.1	1761016	1761016	type	True	100.0	2767	2774	95	conclusive
Paraburkholderia caffeinilytica	strain=CGMCC 1.15103	GCA_014640695.1	1761016	1761016	type	True	99.9866	2739	2774	95	conclusive
Paraburkholderia caffeinilytica	strain=LMG 28690	GCA_902859905.1	1761016	1761016	type	True	99.9815	2724	2774	95	conclusive
Paraburkholderia madseniana	strain=RP11	GCA_009690905.1	2599607	2599607	type	True	91.6635	1990	2774	95	below_threshold
Paraburkholderia nemoris	strain=LMG 31836	GCA_905221015.1	2793076	2793076	type	True	91.6146	2003	2774	95	below_threshold
Paraburkholderia elongata	strain=5N	GCA_013177735.1	2675747	2675747	type	True	90.9096	1807	2774	95	below_threshold
Paraburkholderia polaris	strain=RP-4-7	GCA_012927345.1	2728848	2728848	type	True	90.5368	1857	2774	95	below_threshold
Paraburkholderia haematera	strain=LMG 31837	GCA_905220975.1	2793077	2793077	type	True	90.29	1860	2774	95	below_threshold
Paraburkholderia domus	strain=LMG 31832	GCA_905220705.1	2793075	2793075	type	True	90.2337	1800	2774	95	below_threshold
Paraburkholderia solitsugae	strain=1N	GCA_013177695.1	2675748	2675748	type	True	90.1904	1831	2774	95	below_threshold
Paraburkholderia lacunae	strain=S27	GCA_003353175.1	2211104	2211104	type	True	87.3146	1793	2774	95	below_threshold
Paraburkholderia kirstenboschensis	strain=KB15	GCA_001636975.1	1245436	1245436	type	True	84.6326	1178	2774	95	below_threshold
Paraburkholderia podalyriae	strain=WC7.3b	GCA_014397785.1	1938811	1938811	type	True	84.2635	1434	2774	95	below_threshold
Burkholderia multivorans	strain=ATCC BAA-247	GCA_000959525.1	87883	87883	type	True	80.8601	1059	2774	95	below_threshold
Burkholderia dolosa	strain=LMG 18943	GCA_902499135.1	152500	152500	type	True	80.798	998	2774	95	below_threshold
Burkholderia multivorans	strain=NCTC13007	GCA_900446205.1	87883	87883	type	True	80.7899	1062	2774	95	below_threshold
Burkholderia contaminans	strain=LMG 23361	GCA_001758385.2	488447	488447	type	True	80.6118	1153	2774	95	below_threshold
Burkholderia perseverans	strain=INN12	GCA_022870505.1	2615214	2615214	type	True	80.3958	1060	2774	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:47,462] [INFO] DFAST Taxonomy check result was written to GCF_003368325.1_ASM336832v1_genomic.fna/tc_result.tsv
[2024-01-24 13:49:47,463] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:47,463] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:47,463] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg86f06296-2fe2-4839-bdcd-7547c730aaa8/dqc_reference/checkm_data
[2024-01-24 13:49:47,465] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:47,550] [INFO] Task started: CheckM
[2024-01-24 13:49:47,550] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003368325.1_ASM336832v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003368325.1_ASM336832v1_genomic.fna/checkm_input GCF_003368325.1_ASM336832v1_genomic.fna/checkm_result
[2024-01-24 13:51:02,985] [INFO] Task succeeded: CheckM
[2024-01-24 13:51:02,986] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:51:03,011] [INFO] ===== Completeness check finished =====
[2024-01-24 13:51:03,011] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:51:03,012] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003368325.1_ASM336832v1_genomic.fna/markers.fasta)
[2024-01-24 13:51:03,012] [INFO] Task started: Blastn
[2024-01-24 13:51:03,012] [INFO] Running command: blastn -query GCF_003368325.1_ASM336832v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg86f06296-2fe2-4839-bdcd-7547c730aaa8/dqc_reference/reference_markers_gtdb.fasta -out GCF_003368325.1_ASM336832v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:51:04,445] [INFO] Task succeeded: Blastn
[2024-01-24 13:51:04,448] [INFO] Selected 17 target genomes.
[2024-01-24 13:51:04,448] [INFO] Target genome list was writen to GCF_003368325.1_ASM336832v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:51:04,477] [INFO] Task started: fastANI
[2024-01-24 13:51:04,478] [INFO] Running command: fastANI --query /var/lib/cwl/stga85dd284-7404-4dcb-98c3-06e3cf83cfa0/GCF_003368325.1_ASM336832v1_genomic.fna.gz --refList GCF_003368325.1_ASM336832v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003368325.1_ASM336832v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:51:38,845] [INFO] Task succeeded: fastANI
[2024-01-24 13:51:38,859] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:51:38,859] [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_003368325.1	s__Paraburkholderia caffeinilytica	100.0	2768	2774	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	100.00	100.00	1.00	1.00	3	conclusive
GCF_900230185.1	s__Paraburkholderia sp900230185	91.7894	2161	2774	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009690905.1	s__Paraburkholderia madseniana	91.6449	1993	2774	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	98.82	98.82	0.85	0.85	2	-
GCF_902859805.1	s__Paraburkholderia sediminicola	91.3341	2063	2774	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013177735.1	s__Paraburkholderia sp013177735	90.9011	1808	2774	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012927345.1	s__Paraburkholderia sp012927345	90.5313	1858	2774	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001634365.1	s__Paraburkholderia sp001634365	90.4947	1626	2774	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_905220835.1	s__Paraburkholderia sp905220835	90.2684	1793	2774	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	99.73	99.56	0.96	0.94	13	-
GCF_013177695.1	s__Paraburkholderia sp013177695	90.1917	1830	2774	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142905.1	s__Paraburkholderia sp900142905	90.0784	1893	2774	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	98.29	98.24	0.83	0.82	6	-
GCF_003610295.1	s__Paraburkholderia sp003610295	90.0531	1855	2774	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013409845.1	s__Paraburkholderia metrosideri_A	89.0204	1688	2774	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	100.00	100.00	1.00	1.00	4	-
GCF_003353175.1	s__Paraburkholderia lacunae	87.2907	1795	2774	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142195.1	s__Paraburkholderia terricola	87.0369	1596	2774	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	99.26	98.60	0.95	0.92	6	-
GCF_001718835.1	s__Burkholderia cepacia_F	80.8312	1101	2774	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013403875.1	s__Burkholderia guangdongensis	80.6676	952	2774	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000987075.1	s__Burkholderia contaminans	80.62	1166	2774	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	97.97	95.20	0.90	0.82	86	-
--------------------------------------------------------------------------------
[2024-01-24 13:51:38,861] [INFO] GTDB search result was written to GCF_003368325.1_ASM336832v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:51:38,862] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:51:38,865] [INFO] DFAST_QC result json was written to GCF_003368325.1_ASM336832v1_genomic.fna/dqc_result.json
[2024-01-24 13:51:38,866] [INFO] DFAST_QC completed!
[2024-01-24 13:51:38,866] [INFO] Total running time: 0h2m55s