[2024-01-24 15:18:25,269] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:18:25,272] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:18:25,272] [INFO] DQC Reference Directory: /var/lib/cwl/stgbdeaa927-0262-43f4-94e1-85d9593527f1/dqc_reference
[2024-01-24 15:18:26,585] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:18:26,586] [INFO] Task started: Prodigal
[2024-01-24 15:18:26,586] [INFO] Running command: gunzip -c /var/lib/cwl/stgb6bf27d1-54d9-4063-91f3-2d4c2a5eeb88/GCF_904848585.1_LMG_28727_genomic.fna.gz | prodigal -d GCF_904848585.1_LMG_28727_genomic.fna/cds.fna -a GCF_904848585.1_LMG_28727_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:18:54,647] [INFO] Task succeeded: Prodigal
[2024-01-24 15:18:54,647] [INFO] Task started: HMMsearch
[2024-01-24 15:18:54,647] [INFO] Running command: hmmsearch --tblout GCF_904848585.1_LMG_28727_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbdeaa927-0262-43f4-94e1-85d9593527f1/dqc_reference/reference_markers.hmm GCF_904848585.1_LMG_28727_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:18:55,023] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:18:55,024] [INFO] Found 6/6 markers.
[2024-01-24 15:18:55,099] [INFO] Query marker FASTA was written to GCF_904848585.1_LMG_28727_genomic.fna/markers.fasta
[2024-01-24 15:18:55,100] [INFO] Task started: Blastn
[2024-01-24 15:18:55,100] [INFO] Running command: blastn -query GCF_904848585.1_LMG_28727_genomic.fna/markers.fasta -db /var/lib/cwl/stgbdeaa927-0262-43f4-94e1-85d9593527f1/dqc_reference/reference_markers.fasta -out GCF_904848585.1_LMG_28727_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:18:56,188] [INFO] Task succeeded: Blastn
[2024-01-24 15:18:56,201] [INFO] Selected 12 target genomes.
[2024-01-24 15:18:56,202] [INFO] Target genome list was writen to GCF_904848585.1_LMG_28727_genomic.fna/target_genomes.txt
[2024-01-24 15:18:56,211] [INFO] Task started: fastANI
[2024-01-24 15:18:56,211] [INFO] Running command: fastANI --query /var/lib/cwl/stgb6bf27d1-54d9-4063-91f3-2d4c2a5eeb88/GCF_904848585.1_LMG_28727_genomic.fna.gz --refList GCF_904848585.1_LMG_28727_genomic.fna/target_genomes.txt --output GCF_904848585.1_LMG_28727_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:19:19,367] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:19,368] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbdeaa927-0262-43f4-94e1-85d9593527f1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:19:19,369] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbdeaa927-0262-43f4-94e1-85d9593527f1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:19:19,383] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 15:19:19,383] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:19:19,384] [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 kirstenboschensis	strain=LMG 28727	GCA_904848585.1	1245436	1245436	type	True	100.0	2813	2816	95	conclusive
Paraburkholderia kirstenboschensis	strain=KB15	GCA_001636975.1	1245436	1245436	type	True	99.7301	2256	2816	95	conclusive
Paraburkholderia caledonica	strain=NBRC 102488	GCA_000685095.1	134536	134536	type	True	93.1139	2006	2816	95	below_threshold
Paraburkholderia caledonica	strain=LMG 19076	GCA_902833635.1	134536	134536	type	True	93.1047	2002	2816	95	below_threshold
Paraburkholderia dilworthii	strain=WSM3556	GCA_000472525.1	948106	948106	type	True	90.1578	1900	2816	95	below_threshold
Paraburkholderia rhynchosiae	strain=LMG 27174	GCA_902859775.1	487049	487049	type	True	88.424	1768	2816	95	below_threshold
Paraburkholderia graminis	strain=LMG 18924	GCA_902859785.1	60548	60548	type	True	87.7025	1785	2816	95	below_threshold
Paraburkholderia graminis	strain=C4D1M	GCA_000172415.1	60548	60548	type	True	87.606	1766	2816	95	below_threshold
Paraburkholderia nemoris	strain=LMG 31836	GCA_905221015.1	2793076	2793076	type	True	84.4999	1541	2816	95	below_threshold
Paraburkholderia haematera	strain=LMG 31837	GCA_905220975.1	2793077	2793077	type	True	84.351	1442	2816	95	below_threshold
Paraburkholderia domus	strain=LMG 31832	GCA_905220705.1	2793075	2793075	type	True	84.338	1479	2816	95	below_threshold
Paraburkholderia podalyriae	strain=WC7.3b	GCA_014397785.1	1938811	1938811	type	True	83.9729	1566	2816	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:19:19,385] [INFO] DFAST Taxonomy check result was written to GCF_904848585.1_LMG_28727_genomic.fna/tc_result.tsv
[2024-01-24 15:19:19,386] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:19:19,386] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:19:19,386] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbdeaa927-0262-43f4-94e1-85d9593527f1/dqc_reference/checkm_data
[2024-01-24 15:19:19,387] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:19:19,466] [INFO] Task started: CheckM
[2024-01-24 15:19:19,467] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_904848585.1_LMG_28727_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_904848585.1_LMG_28727_genomic.fna/checkm_input GCF_904848585.1_LMG_28727_genomic.fna/checkm_result
[2024-01-24 15:20:34,134] [INFO] Task succeeded: CheckM
[2024-01-24 15:20:34,136] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:20:34,159] [INFO] ===== Completeness check finished =====
[2024-01-24 15:20:34,159] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:20:34,160] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_904848585.1_LMG_28727_genomic.fna/markers.fasta)
[2024-01-24 15:20:34,160] [INFO] Task started: Blastn
[2024-01-24 15:20:34,160] [INFO] Running command: blastn -query GCF_904848585.1_LMG_28727_genomic.fna/markers.fasta -db /var/lib/cwl/stgbdeaa927-0262-43f4-94e1-85d9593527f1/dqc_reference/reference_markers_gtdb.fasta -out GCF_904848585.1_LMG_28727_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:20:36,083] [INFO] Task succeeded: Blastn
[2024-01-24 15:20:36,087] [INFO] Selected 9 target genomes.
[2024-01-24 15:20:36,088] [INFO] Target genome list was writen to GCF_904848585.1_LMG_28727_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:20:36,096] [INFO] Task started: fastANI
[2024-01-24 15:20:36,096] [INFO] Running command: fastANI --query /var/lib/cwl/stgb6bf27d1-54d9-4063-91f3-2d4c2a5eeb88/GCF_904848585.1_LMG_28727_genomic.fna.gz --refList GCF_904848585.1_LMG_28727_genomic.fna/target_genomes_gtdb.txt --output GCF_904848585.1_LMG_28727_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:20:54,956] [INFO] Task succeeded: fastANI
[2024-01-24 15:20:54,972] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:20:54,972] [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_904848585.1	s__Paraburkholderia kirstenboschensis	100.0	2813	2816	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	99.97	99.97	1.00	1.00	2	conclusive
GCF_000685095.1	s__Paraburkholderia caledonica	93.1002	2008	2816	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	97.03	95.65	0.88	0.80	10	-
GCF_000472525.1	s__Paraburkholderia dilworthii	90.1659	1899	2816	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002879865.1	s__Paraburkholderia rhynchosiae	88.416	1768	2816	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000172415.1	s__Paraburkholderia graminis	87.6049	1766	2816	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	98.52	98.23	0.90	0.89	12	-
GCF_000472445.1	s__Paraburkholderia sp000472445	87.3555	1623	2816	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902859825.1	s__Paraburkholderia phenoliruptrix	86.9464	1684	2816	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	99.08	98.23	0.90	0.84	7	-
GCF_000148685.1	s__Paraburkholderia sp000148685	86.2899	1729	2816	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	98.01	98.00	0.91	0.91	4	-
GCF_013366925.1	s__Paraburkholderia youngii	83.4697	1464	2816	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	97.48	97.40	0.88	0.87	5	-
--------------------------------------------------------------------------------
[2024-01-24 15:20:54,974] [INFO] GTDB search result was written to GCF_904848585.1_LMG_28727_genomic.fna/result_gtdb.tsv
[2024-01-24 15:20:54,975] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:20:54,981] [INFO] DFAST_QC result json was written to GCF_904848585.1_LMG_28727_genomic.fna/dqc_result.json
[2024-01-24 15:20:54,981] [INFO] DFAST_QC completed!
[2024-01-24 15:20:54,981] [INFO] Total running time: 0h2m30s