[2024-01-24 13:55:58,115] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:55:58,116] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:55:58,117] [INFO] DQC Reference Directory: /var/lib/cwl/stg9f27359b-be58-4115-a865-bf59e780ca47/dqc_reference
[2024-01-24 13:55:59,335] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:55:59,336] [INFO] Task started: Prodigal
[2024-01-24 13:55:59,336] [INFO] Running command: gunzip -c /var/lib/cwl/stgebe69f63-0b96-4ae7-b4b8-6a0a1c0f3b80/GCF_009690905.1_ASM969090v1_genomic.fna.gz | prodigal -d GCF_009690905.1_ASM969090v1_genomic.fna/cds.fna -a GCF_009690905.1_ASM969090v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:56:29,583] [INFO] Task succeeded: Prodigal
[2024-01-24 13:56:29,584] [INFO] Task started: HMMsearch
[2024-01-24 13:56:29,584] [INFO] Running command: hmmsearch --tblout GCF_009690905.1_ASM969090v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9f27359b-be58-4115-a865-bf59e780ca47/dqc_reference/reference_markers.hmm GCF_009690905.1_ASM969090v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:56:29,982] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:56:29,983] [INFO] Found 6/6 markers.
[2024-01-24 13:56:30,059] [INFO] Query marker FASTA was written to GCF_009690905.1_ASM969090v1_genomic.fna/markers.fasta
[2024-01-24 13:56:30,059] [INFO] Task started: Blastn
[2024-01-24 13:56:30,059] [INFO] Running command: blastn -query GCF_009690905.1_ASM969090v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9f27359b-be58-4115-a865-bf59e780ca47/dqc_reference/reference_markers.fasta -out GCF_009690905.1_ASM969090v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:56:31,000] [INFO] Task succeeded: Blastn
[2024-01-24 13:56:31,004] [INFO] Selected 11 target genomes.
[2024-01-24 13:56:31,005] [INFO] Target genome list was writen to GCF_009690905.1_ASM969090v1_genomic.fna/target_genomes.txt
[2024-01-24 13:56:31,010] [INFO] Task started: fastANI
[2024-01-24 13:56:31,010] [INFO] Running command: fastANI --query /var/lib/cwl/stgebe69f63-0b96-4ae7-b4b8-6a0a1c0f3b80/GCF_009690905.1_ASM969090v1_genomic.fna.gz --refList GCF_009690905.1_ASM969090v1_genomic.fna/target_genomes.txt --output GCF_009690905.1_ASM969090v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:56:56,376] [INFO] Task succeeded: fastANI
[2024-01-24 13:56:56,377] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9f27359b-be58-4115-a865-bf59e780ca47/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:56:56,378] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9f27359b-be58-4115-a865-bf59e780ca47/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:56:56,393] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:56:56,393] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:56:56,393] [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 madseniana	strain=RP11	GCA_009690905.1	2599607	2599607	type	True	100.0	3190	3202	95	conclusive
Paraburkholderia nemoris	strain=LMG 31836	GCA_905221015.1	2793076	2793076	type	True	94.1738	2175	3202	95	below_threshold
Paraburkholderia aspalathi	strain=LMG 27731	GCA_900116445.1	1324617	1324617	type	True	94.0261	2236	3202	95	below_threshold
Paraburkholderia sediminicola	strain=LMG 24238	GCA_902859805.1	458836	458836	type	True	93.6183	2120	3202	95	below_threshold
Paraburkholderia caffeinilytica	strain=CF1	GCA_003368325.1	1761016	1761016	type	True	91.6336	1998	3202	95	below_threshold
Paraburkholderia elongata	strain=5N	GCA_013177735.1	2675747	2675747	type	True	91.5394	2226	3202	95	below_threshold
Paraburkholderia solitsugae	strain=1N	GCA_013177695.1	2675748	2675748	type	True	91.1254	2119	3202	95	below_threshold
Paraburkholderia haematera	strain=LMG 31837	GCA_905220975.1	2793077	2793077	type	True	90.7252	1916	3202	95	below_threshold
Paraburkholderia domus	strain=LMG 31832	GCA_905220705.1	2793075	2793075	type	True	90.6752	1937	3202	95	below_threshold
Paraburkholderia kirstenboschensis	strain=KB15	GCA_001636975.1	1245436	1245436	type	True	84.2035	1282	3202	95	below_threshold
Paraburkholderia podalyriae	strain=WC7.3b	GCA_014397785.1	1938811	1938811	type	True	83.8592	1521	3202	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:56:56,395] [INFO] DFAST Taxonomy check result was written to GCF_009690905.1_ASM969090v1_genomic.fna/tc_result.tsv
[2024-01-24 13:56:56,396] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:56:56,396] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:56:56,396] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9f27359b-be58-4115-a865-bf59e780ca47/dqc_reference/checkm_data
[2024-01-24 13:56:56,397] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:56:56,494] [INFO] Task started: CheckM
[2024-01-24 13:56:56,494] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009690905.1_ASM969090v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009690905.1_ASM969090v1_genomic.fna/checkm_input GCF_009690905.1_ASM969090v1_genomic.fna/checkm_result
[2024-01-24 13:58:19,814] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:19,816] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:19,842] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:19,843] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:19,843] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009690905.1_ASM969090v1_genomic.fna/markers.fasta)
[2024-01-24 13:58:19,844] [INFO] Task started: Blastn
[2024-01-24 13:58:19,844] [INFO] Running command: blastn -query GCF_009690905.1_ASM969090v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9f27359b-be58-4115-a865-bf59e780ca47/dqc_reference/reference_markers_gtdb.fasta -out GCF_009690905.1_ASM969090v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:21,569] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:21,573] [INFO] Selected 11 target genomes.
[2024-01-24 13:58:21,573] [INFO] Target genome list was writen to GCF_009690905.1_ASM969090v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:21,582] [INFO] Task started: fastANI
[2024-01-24 13:58:21,583] [INFO] Running command: fastANI --query /var/lib/cwl/stgebe69f63-0b96-4ae7-b4b8-6a0a1c0f3b80/GCF_009690905.1_ASM969090v1_genomic.fna.gz --refList GCF_009690905.1_ASM969090v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009690905.1_ASM969090v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:58:47,912] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:47,922] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:58:47,922] [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_009690905.1	s__Paraburkholderia madseniana	100.0	3190	3202	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	98.82	98.82	0.85	0.85	2	conclusive
GCF_900116445.1	s__Paraburkholderia aspalathi	94.015	2237	3202	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	96.47	95.19	0.81	0.72	20	-
GCF_900230185.1	s__Paraburkholderia sp900230185	93.8243	2388	3202	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902859805.1	s__Paraburkholderia sediminicola	93.6182	2120	3202	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	91.6336	1998	3202	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	100.00	100.00	1.00	1.00	3	-
GCF_013177735.1	s__Paraburkholderia sp013177735	91.5328	2227	3202	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	91.1439	2116	3202	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	90.9607	1762	3202	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	90.9236	2038	3202	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_905220975.1	s__Paraburkholderia sp905220975	90.7252	1916	3202	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	90.2673	2003	3202	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 13:58:47,924] [INFO] GTDB search result was written to GCF_009690905.1_ASM969090v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:58:47,925] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:58:47,928] [INFO] DFAST_QC result json was written to GCF_009690905.1_ASM969090v1_genomic.fna/dqc_result.json
[2024-01-24 13:58:47,928] [INFO] DFAST_QC completed!
[2024-01-24 13:58:47,928] [INFO] Total running time: 0h2m50s