[2024-01-24 13:45:57,003] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:45:57,004] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:45:57,005] [INFO] DQC Reference Directory: /var/lib/cwl/stg5beb22d7-d1c7-401a-969c-2d14247bbff4/dqc_reference
[2024-01-24 13:45:58,307] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:45:58,308] [INFO] Task started: Prodigal
[2024-01-24 13:45:58,308] [INFO] Running command: gunzip -c /var/lib/cwl/stg907d7dd1-768c-4d27-9a28-db0555b4cf5a/GCF_902833905.1_Paraburkholderia_tuberum_LMG_21444_genomic.fna.gz | prodigal -d GCF_902833905.1_Paraburkholderia_tuberum_LMG_21444_genomic.fna/cds.fna -a GCF_902833905.1_Paraburkholderia_tuberum_LMG_21444_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:25,719] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:25,720] [INFO] Task started: HMMsearch
[2024-01-24 13:46:25,720] [INFO] Running command: hmmsearch --tblout GCF_902833905.1_Paraburkholderia_tuberum_LMG_21444_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5beb22d7-d1c7-401a-969c-2d14247bbff4/dqc_reference/reference_markers.hmm GCF_902833905.1_Paraburkholderia_tuberum_LMG_21444_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:26,251] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:26,253] [INFO] Found 6/6 markers.
[2024-01-24 13:46:26,326] [INFO] Query marker FASTA was written to GCF_902833905.1_Paraburkholderia_tuberum_LMG_21444_genomic.fna/markers.fasta
[2024-01-24 13:46:26,327] [INFO] Task started: Blastn
[2024-01-24 13:46:26,327] [INFO] Running command: blastn -query GCF_902833905.1_Paraburkholderia_tuberum_LMG_21444_genomic.fna/markers.fasta -db /var/lib/cwl/stg5beb22d7-d1c7-401a-969c-2d14247bbff4/dqc_reference/reference_markers.fasta -out GCF_902833905.1_Paraburkholderia_tuberum_LMG_21444_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:27,386] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:27,389] [INFO] Selected 11 target genomes.
[2024-01-24 13:46:27,389] [INFO] Target genome list was writen to GCF_902833905.1_Paraburkholderia_tuberum_LMG_21444_genomic.fna/target_genomes.txt
[2024-01-24 13:46:27,399] [INFO] Task started: fastANI
[2024-01-24 13:46:27,399] [INFO] Running command: fastANI --query /var/lib/cwl/stg907d7dd1-768c-4d27-9a28-db0555b4cf5a/GCF_902833905.1_Paraburkholderia_tuberum_LMG_21444_genomic.fna.gz --refList GCF_902833905.1_Paraburkholderia_tuberum_LMG_21444_genomic.fna/target_genomes.txt --output GCF_902833905.1_Paraburkholderia_tuberum_LMG_21444_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:52,857] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:52,857] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5beb22d7-d1c7-401a-969c-2d14247bbff4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:52,858] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5beb22d7-d1c7-401a-969c-2d14247bbff4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:52,867] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:46:52,868] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:46:52,868] [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 tuberum	strain=LMG 21444	GCA_902833905.1	157910	157910	type	True	100.0	2828	2838	95	conclusive
Paraburkholderia atlantica	strain=CNPSo 3155	GCA_009362785.1	2654982	2654982	type	True	92.3942	1938	2838	95	below_threshold
Paraburkholderia youngii	strain=JPY169	GCA_013366925.1	2782701	2782701	type	True	92.3156	1997	2838	95	below_threshold
Paraburkholderia podalyriae	strain=WC7.3b	GCA_014397785.1	1938811	1938811	type	True	92.3061	1979	2838	95	below_threshold
Paraburkholderia sprentiae	strain=WSM5005	GCA_000473465.1	948107	948107	type	True	91.6578	1896	2838	95	below_threshold
Paraburkholderia sprentiae	strain=WSM5005	GCA_001865575.2	948107	948107	type	True	91.6484	1905	2838	95	below_threshold
Paraburkholderia monticola	strain=JC2948	GCA_001580545.1	1399968	1399968	type	True	91.0	1783	2838	95	below_threshold
Paraburkholderia haematera	strain=LMG 31837	GCA_905220975.1	2793077	2793077	type	True	84.2169	1367	2838	95	below_threshold
Paraburkholderia nemoris	strain=LMG 31836	GCA_905221015.1	2793076	2793076	type	True	83.9478	1466	2838	95	below_threshold
Paraburkholderia domus	strain=LMG 31832	GCA_905220705.1	2793075	2793075	type	True	83.941	1453	2838	95	below_threshold
Paraburkholderia kirstenboschensis	strain=KB15	GCA_001636975.1	1245436	1245436	type	True	83.7575	1232	2838	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:52,869] [INFO] DFAST Taxonomy check result was written to GCF_902833905.1_Paraburkholderia_tuberum_LMG_21444_genomic.fna/tc_result.tsv
[2024-01-24 13:46:52,870] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:52,870] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:52,870] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5beb22d7-d1c7-401a-969c-2d14247bbff4/dqc_reference/checkm_data
[2024-01-24 13:46:52,871] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:52,956] [INFO] Task started: CheckM
[2024-01-24 13:46:52,956] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_902833905.1_Paraburkholderia_tuberum_LMG_21444_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_902833905.1_Paraburkholderia_tuberum_LMG_21444_genomic.fna/checkm_input GCF_902833905.1_Paraburkholderia_tuberum_LMG_21444_genomic.fna/checkm_result
[2024-01-24 13:48:06,134] [INFO] Task succeeded: CheckM
[2024-01-24 13:48:06,136] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:48:06,159] [INFO] ===== Completeness check finished =====
[2024-01-24 13:48:06,159] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:48:06,160] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_902833905.1_Paraburkholderia_tuberum_LMG_21444_genomic.fna/markers.fasta)
[2024-01-24 13:48:06,160] [INFO] Task started: Blastn
[2024-01-24 13:48:06,160] [INFO] Running command: blastn -query GCF_902833905.1_Paraburkholderia_tuberum_LMG_21444_genomic.fna/markers.fasta -db /var/lib/cwl/stg5beb22d7-d1c7-401a-969c-2d14247bbff4/dqc_reference/reference_markers_gtdb.fasta -out GCF_902833905.1_Paraburkholderia_tuberum_LMG_21444_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:48:08,112] [INFO] Task succeeded: Blastn
[2024-01-24 13:48:08,119] [INFO] Selected 8 target genomes.
[2024-01-24 13:48:08,119] [INFO] Target genome list was writen to GCF_902833905.1_Paraburkholderia_tuberum_LMG_21444_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:48:08,130] [INFO] Task started: fastANI
[2024-01-24 13:48:08,131] [INFO] Running command: fastANI --query /var/lib/cwl/stg907d7dd1-768c-4d27-9a28-db0555b4cf5a/GCF_902833905.1_Paraburkholderia_tuberum_LMG_21444_genomic.fna.gz --refList GCF_902833905.1_Paraburkholderia_tuberum_LMG_21444_genomic.fna/target_genomes_gtdb.txt --output GCF_902833905.1_Paraburkholderia_tuberum_LMG_21444_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:48:25,672] [INFO] Task succeeded: fastANI
[2024-01-24 13:48:25,685] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:48:25,685] [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_902833905.1	s__Paraburkholderia tuberum	100.0	2828	2838	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	97.72	96.26	0.82	0.75	13	conclusive
GCF_009362785.1	s__Paraburkholderia atlantica	92.4226	1935	2838	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	98.68	97.45	0.92	0.86	7	-
GCF_013366925.1	s__Paraburkholderia youngii	92.3052	1998	2838	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	97.48	97.40	0.88	0.87	5	-
GCF_014397785.1	s__Paraburkholderia sp014397785	92.2844	1982	2838	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	92.2699	1921	2838	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001865575.1	s__Paraburkholderia sprentiae	91.7097	1898	2838	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	99.96	99.96	0.99	0.99	2	-
GCA_000173575.1	s__Paraburkholderia sp000173575	91.145	1634	2838	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	91.0069	1782	2838	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 13:48:25,687] [INFO] GTDB search result was written to GCF_902833905.1_Paraburkholderia_tuberum_LMG_21444_genomic.fna/result_gtdb.tsv
[2024-01-24 13:48:25,687] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:48:25,690] [INFO] DFAST_QC result json was written to GCF_902833905.1_Paraburkholderia_tuberum_LMG_21444_genomic.fna/dqc_result.json
[2024-01-24 13:48:25,690] [INFO] DFAST_QC completed!
[2024-01-24 13:48:25,690] [INFO] Total running time: 0h2m29s