[2024-01-24 13:36:44,598] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:36:44,599] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:36:44,599] [INFO] DQC Reference Directory: /var/lib/cwl/stg00f59acd-6251-48ea-ac4d-bcf8d9c440f8/dqc_reference
[2024-01-24 13:36:45,999] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:36:46,000] [INFO] Task started: Prodigal
[2024-01-24 13:36:46,000] [INFO] Running command: gunzip -c /var/lib/cwl/stg44689336-6204-4f40-b625-f4e6a74a888e/GCF_014397785.1_ASM1439778v1_genomic.fna.gz | prodigal -d GCF_014397785.1_ASM1439778v1_genomic.fna/cds.fna -a GCF_014397785.1_ASM1439778v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:37:14,979] [INFO] Task succeeded: Prodigal
[2024-01-24 13:37:14,979] [INFO] Task started: HMMsearch
[2024-01-24 13:37:14,979] [INFO] Running command: hmmsearch --tblout GCF_014397785.1_ASM1439778v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg00f59acd-6251-48ea-ac4d-bcf8d9c440f8/dqc_reference/reference_markers.hmm GCF_014397785.1_ASM1439778v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:37:15,385] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:37:15,386] [INFO] Found 6/6 markers.
[2024-01-24 13:37:15,456] [INFO] Query marker FASTA was written to GCF_014397785.1_ASM1439778v1_genomic.fna/markers.fasta
[2024-01-24 13:37:15,456] [INFO] Task started: Blastn
[2024-01-24 13:37:15,456] [INFO] Running command: blastn -query GCF_014397785.1_ASM1439778v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg00f59acd-6251-48ea-ac4d-bcf8d9c440f8/dqc_reference/reference_markers.fasta -out GCF_014397785.1_ASM1439778v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:16,584] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:16,588] [INFO] Selected 11 target genomes.
[2024-01-24 13:37:16,588] [INFO] Target genome list was writen to GCF_014397785.1_ASM1439778v1_genomic.fna/target_genomes.txt
[2024-01-24 13:37:16,667] [INFO] Task started: fastANI
[2024-01-24 13:37:16,667] [INFO] Running command: fastANI --query /var/lib/cwl/stg44689336-6204-4f40-b625-f4e6a74a888e/GCF_014397785.1_ASM1439778v1_genomic.fna.gz --refList GCF_014397785.1_ASM1439778v1_genomic.fna/target_genomes.txt --output GCF_014397785.1_ASM1439778v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:40,089] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:40,090] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg00f59acd-6251-48ea-ac4d-bcf8d9c440f8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:40,090] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg00f59acd-6251-48ea-ac4d-bcf8d9c440f8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:40,100] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:37:40,100] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:37:40,100] [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 podalyriae	strain=WC7.3b	GCA_014397785.1	1938811	1938811	type	True	100.0	2968	2976	95	conclusive
Paraburkholderia sprentiae	strain=WSM5005	GCA_001865575.2	948107	948107	type	True	93.079	2008	2976	95	below_threshold
Paraburkholderia sprentiae	strain=WSM5005	GCA_000473465.1	948107	948107	type	True	93.0148	2014	2976	95	below_threshold
Paraburkholderia tuberum	strain=LMG 21444	GCA_902833905.1	157910	157910	type	True	92.4601	1960	2976	95	below_threshold
Paraburkholderia atlantica	strain=CNPSo 3155	GCA_009362785.1	2654982	2654982	type	True	91.0632	1857	2976	95	below_threshold
Paraburkholderia youngii	strain=JPY169	GCA_013366925.1	2782701	2782701	type	True	91.0158	1933	2976	95	below_threshold
Paraburkholderia monticola	strain=JC2948	GCA_001580545.1	1399968	1399968	type	True	90.6878	1715	2976	95	below_threshold
Paraburkholderia nemoris	strain=LMG 31836	GCA_905221015.1	2793076	2793076	type	True	83.9376	1452	2976	95	below_threshold
Paraburkholderia haematera	strain=LMG 31837	GCA_905220975.1	2793077	2793077	type	True	83.9047	1388	2976	95	below_threshold
Paraburkholderia domus	strain=LMG 31832	GCA_905220705.1	2793075	2793075	type	True	83.8386	1432	2976	95	below_threshold
Paraburkholderia kirstenboschensis	strain=KB15	GCA_001636975.1	1245436	1245436	type	True	83.7915	1261	2976	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:40,103] [INFO] DFAST Taxonomy check result was written to GCF_014397785.1_ASM1439778v1_genomic.fna/tc_result.tsv
[2024-01-24 13:37:40,103] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:40,103] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:40,104] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg00f59acd-6251-48ea-ac4d-bcf8d9c440f8/dqc_reference/checkm_data
[2024-01-24 13:37:40,105] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:40,190] [INFO] Task started: CheckM
[2024-01-24 13:37:40,190] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014397785.1_ASM1439778v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014397785.1_ASM1439778v1_genomic.fna/checkm_input GCF_014397785.1_ASM1439778v1_genomic.fna/checkm_result
[2024-01-24 13:38:55,653] [INFO] Task succeeded: CheckM
[2024-01-24 13:38:55,654] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:38:55,674] [INFO] ===== Completeness check finished =====
[2024-01-24 13:38:55,674] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:38:55,675] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014397785.1_ASM1439778v1_genomic.fna/markers.fasta)
[2024-01-24 13:38:55,675] [INFO] Task started: Blastn
[2024-01-24 13:38:55,675] [INFO] Running command: blastn -query GCF_014397785.1_ASM1439778v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg00f59acd-6251-48ea-ac4d-bcf8d9c440f8/dqc_reference/reference_markers_gtdb.fasta -out GCF_014397785.1_ASM1439778v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:38:57,642] [INFO] Task succeeded: Blastn
[2024-01-24 13:38:57,646] [INFO] Selected 8 target genomes.
[2024-01-24 13:38:57,646] [INFO] Target genome list was writen to GCF_014397785.1_ASM1439778v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:38:57,661] [INFO] Task started: fastANI
[2024-01-24 13:38:57,662] [INFO] Running command: fastANI --query /var/lib/cwl/stg44689336-6204-4f40-b625-f4e6a74a888e/GCF_014397785.1_ASM1439778v1_genomic.fna.gz --refList GCF_014397785.1_ASM1439778v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014397785.1_ASM1439778v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:39:15,165] [INFO] Task succeeded: fastANI
[2024-01-24 13:39:15,173] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:39:15,173] [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_014397785.1	s__Paraburkholderia sp014397785	100.0	2968	2976	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_001865575.1	s__Paraburkholderia sprentiae	93.0482	2014	2976	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	99.96	99.96	0.99	0.99	2	-
GCF_902833905.1	s__Paraburkholderia tuberum	92.4395	1962	2976	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	97.72	96.26	0.82	0.75	13	-
GCF_004197395.1	s__Paraburkholderia sp004197395	91.2869	1849	2976	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009362785.1	s__Paraburkholderia atlantica	91.0342	1860	2976	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	91.0229	1932	2976	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	97.48	97.40	0.88	0.87	5	-
GCA_000173575.1	s__Paraburkholderia sp000173575	90.8125	1642	2976	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	90.6736	1718	2976	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 13:39:15,175] [INFO] GTDB search result was written to GCF_014397785.1_ASM1439778v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:39:15,175] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:39:15,179] [INFO] DFAST_QC result json was written to GCF_014397785.1_ASM1439778v1_genomic.fna/dqc_result.json
[2024-01-24 13:39:15,180] [INFO] DFAST_QC completed!
[2024-01-24 13:39:15,180] [INFO] Total running time: 0h2m31s