[2024-01-24 11:20:04,202] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:20:04,204] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:20:04,204] [INFO] DQC Reference Directory: /var/lib/cwl/stg3e604054-caea-4289-9f9d-2d634939a89d/dqc_reference
[2024-01-24 11:20:05,337] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:20:05,338] [INFO] Task started: Prodigal
[2024-01-24 11:20:05,338] [INFO] Running command: gunzip -c /var/lib/cwl/stg5b2474d5-4422-48fe-a3d5-a1ad9167daec/GCF_902859805.1_LMG_24238_genomic.fna.gz | prodigal -d GCF_902859805.1_LMG_24238_genomic.fna/cds.fna -a GCF_902859805.1_LMG_24238_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:20:31,780] [INFO] Task succeeded: Prodigal
[2024-01-24 11:20:31,780] [INFO] Task started: HMMsearch
[2024-01-24 11:20:31,780] [INFO] Running command: hmmsearch --tblout GCF_902859805.1_LMG_24238_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3e604054-caea-4289-9f9d-2d634939a89d/dqc_reference/reference_markers.hmm GCF_902859805.1_LMG_24238_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:20:32,092] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:20:32,093] [INFO] Found 6/6 markers.
[2024-01-24 11:20:32,152] [INFO] Query marker FASTA was written to GCF_902859805.1_LMG_24238_genomic.fna/markers.fasta
[2024-01-24 11:20:32,152] [INFO] Task started: Blastn
[2024-01-24 11:20:32,152] [INFO] Running command: blastn -query GCF_902859805.1_LMG_24238_genomic.fna/markers.fasta -db /var/lib/cwl/stg3e604054-caea-4289-9f9d-2d634939a89d/dqc_reference/reference_markers.fasta -out GCF_902859805.1_LMG_24238_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:20:33,034] [INFO] Task succeeded: Blastn
[2024-01-24 11:20:33,037] [INFO] Selected 11 target genomes.
[2024-01-24 11:20:33,038] [INFO] Target genome list was writen to GCF_902859805.1_LMG_24238_genomic.fna/target_genomes.txt
[2024-01-24 11:20:33,041] [INFO] Task started: fastANI
[2024-01-24 11:20:33,041] [INFO] Running command: fastANI --query /var/lib/cwl/stg5b2474d5-4422-48fe-a3d5-a1ad9167daec/GCF_902859805.1_LMG_24238_genomic.fna.gz --refList GCF_902859805.1_LMG_24238_genomic.fna/target_genomes.txt --output GCF_902859805.1_LMG_24238_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:20:55,922] [INFO] Task succeeded: fastANI
[2024-01-24 11:20:55,923] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3e604054-caea-4289-9f9d-2d634939a89d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:20:55,923] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3e604054-caea-4289-9f9d-2d634939a89d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:20:55,932] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:20:55,932] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:20:55,932] [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 sediminicola	strain=LMG 24238	GCA_902859805.1	458836	458836	type	True	100.0	2857	2860	95	conclusive
Paraburkholderia aspalathi	strain=LMG 27731	GCA_900116445.1	1324617	1324617	type	True	94.0324	2346	2860	95	below_threshold
Paraburkholderia nemoris	strain=LMG 31836	GCA_905221015.1	2793076	2793076	type	True	93.9932	2259	2860	95	below_threshold
Paraburkholderia madseniana	strain=RP11	GCA_009690905.1	2599607	2599607	type	True	93.5864	2123	2860	95	below_threshold
Paraburkholderia polaris	strain=RP-4-7	GCA_012927345.1	2728848	2728848	type	True	90.6289	2027	2860	95	below_threshold
Paraburkholderia solitsugae	strain=1N	GCA_013177695.1	2675748	2675748	type	True	90.2591	1971	2860	95	below_threshold
Paraburkholderia domus	strain=LMG 31832	GCA_905220705.1	2793075	2793075	type	True	90.1993	1975	2860	95	below_threshold
Paraburkholderia haematera	strain=LMG 31837	GCA_905220975.1	2793077	2793077	type	True	90.1027	1954	2860	95	below_threshold
Paraburkholderia agricolaris	strain=BaQS159	GCA_009455635.1	2152888	2152888	type	True	89.1379	1993	2860	95	below_threshold
Paraburkholderia kirstenboschensis	strain=KB15	GCA_001636975.1	1245436	1245436	type	True	84.2895	1200	2860	95	below_threshold
Paraburkholderia podalyriae	strain=WC7.3b	GCA_014397785.1	1938811	1938811	type	True	83.8153	1417	2860	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:20:55,934] [INFO] DFAST Taxonomy check result was written to GCF_902859805.1_LMG_24238_genomic.fna/tc_result.tsv
[2024-01-24 11:20:55,934] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:20:55,934] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:20:55,934] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3e604054-caea-4289-9f9d-2d634939a89d/dqc_reference/checkm_data
[2024-01-24 11:20:55,935] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:20:56,011] [INFO] Task started: CheckM
[2024-01-24 11:20:56,011] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_902859805.1_LMG_24238_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_902859805.1_LMG_24238_genomic.fna/checkm_input GCF_902859805.1_LMG_24238_genomic.fna/checkm_result
[2024-01-24 11:22:07,491] [INFO] Task succeeded: CheckM
[2024-01-24 11:22:07,493] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:22:07,512] [INFO] ===== Completeness check finished =====
[2024-01-24 11:22:07,513] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:22:07,513] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_902859805.1_LMG_24238_genomic.fna/markers.fasta)
[2024-01-24 11:22:07,513] [INFO] Task started: Blastn
[2024-01-24 11:22:07,513] [INFO] Running command: blastn -query GCF_902859805.1_LMG_24238_genomic.fna/markers.fasta -db /var/lib/cwl/stg3e604054-caea-4289-9f9d-2d634939a89d/dqc_reference/reference_markers_gtdb.fasta -out GCF_902859805.1_LMG_24238_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:22:09,109] [INFO] Task succeeded: Blastn
[2024-01-24 11:22:09,112] [INFO] Selected 10 target genomes.
[2024-01-24 11:22:09,112] [INFO] Target genome list was writen to GCF_902859805.1_LMG_24238_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:22:09,120] [INFO] Task started: fastANI
[2024-01-24 11:22:09,120] [INFO] Running command: fastANI --query /var/lib/cwl/stg5b2474d5-4422-48fe-a3d5-a1ad9167daec/GCF_902859805.1_LMG_24238_genomic.fna.gz --refList GCF_902859805.1_LMG_24238_genomic.fna/target_genomes_gtdb.txt --output GCF_902859805.1_LMG_24238_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:22:31,205] [INFO] Task succeeded: fastANI
[2024-01-24 11:22:31,214] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:22:31,214] [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_902859805.1	s__Paraburkholderia sediminicola	100.0	2857	2860	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_900116445.1	s__Paraburkholderia aspalathi	94.0324	2346	2860	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	96.47	95.19	0.81	0.72	20	-
GCF_009690905.1	s__Paraburkholderia madseniana	93.6	2121	2860	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	98.82	98.82	0.85	0.85	2	-
GCF_900230185.1	s__Paraburkholderia sp900230185	93.3264	2324	2860	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003368325.1	s__Paraburkholderia caffeinilytica	91.3219	2075	2860	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	100.00	100.00	1.00	1.00	3	-
GCF_012927345.1	s__Paraburkholderia sp012927345	90.6209	2028	2860	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013177695.1	s__Paraburkholderia sp013177695	90.2598	1970	2860	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	90.1727	2096	2860	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	98.29	98.24	0.83	0.82	6	-
GCF_905220975.1	s__Paraburkholderia sp905220975	90.1107	1953	2860	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003610895.1	s__Paraburkholderia fungorum_B	89.1981	2044	2860	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:22:31,216] [INFO] GTDB search result was written to GCF_902859805.1_LMG_24238_genomic.fna/result_gtdb.tsv
[2024-01-24 11:22:31,216] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:22:31,219] [INFO] DFAST_QC result json was written to GCF_902859805.1_LMG_24238_genomic.fna/dqc_result.json
[2024-01-24 11:22:31,219] [INFO] DFAST_QC completed!
[2024-01-24 11:22:31,219] [INFO] Total running time: 0h2m27s