[2024-01-24 12:44:39,006] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:44:39,009] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:44:39,009] [INFO] DQC Reference Directory: /var/lib/cwl/stg1b5178e2-9920-41ee-be21-be6d7638ce22/dqc_reference
[2024-01-24 12:44:40,254] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:44:40,255] [INFO] Task started: Prodigal
[2024-01-24 12:44:40,255] [INFO] Running command: gunzip -c /var/lib/cwl/stg7a14b8e8-1196-4b8f-916c-b71cd30128b7/GCF_902859785.1_LMG_18924_genomic.fna.gz | prodigal -d GCF_902859785.1_LMG_18924_genomic.fna/cds.fna -a GCF_902859785.1_LMG_18924_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:45:03,969] [INFO] Task succeeded: Prodigal
[2024-01-24 12:45:03,970] [INFO] Task started: HMMsearch
[2024-01-24 12:45:03,970] [INFO] Running command: hmmsearch --tblout GCF_902859785.1_LMG_18924_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1b5178e2-9920-41ee-be21-be6d7638ce22/dqc_reference/reference_markers.hmm GCF_902859785.1_LMG_18924_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:45:04,448] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:45:04,450] [INFO] Found 6/6 markers.
[2024-01-24 12:45:04,507] [INFO] Query marker FASTA was written to GCF_902859785.1_LMG_18924_genomic.fna/markers.fasta
[2024-01-24 12:45:04,507] [INFO] Task started: Blastn
[2024-01-24 12:45:04,508] [INFO] Running command: blastn -query GCF_902859785.1_LMG_18924_genomic.fna/markers.fasta -db /var/lib/cwl/stg1b5178e2-9920-41ee-be21-be6d7638ce22/dqc_reference/reference_markers.fasta -out GCF_902859785.1_LMG_18924_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:05,510] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:05,513] [INFO] Selected 18 target genomes.
[2024-01-24 12:45:05,514] [INFO] Target genome list was writen to GCF_902859785.1_LMG_18924_genomic.fna/target_genomes.txt
[2024-01-24 12:45:05,522] [INFO] Task started: fastANI
[2024-01-24 12:45:05,522] [INFO] Running command: fastANI --query /var/lib/cwl/stg7a14b8e8-1196-4b8f-916c-b71cd30128b7/GCF_902859785.1_LMG_18924_genomic.fna.gz --refList GCF_902859785.1_LMG_18924_genomic.fna/target_genomes.txt --output GCF_902859785.1_LMG_18924_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:45:37,827] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:37,827] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1b5178e2-9920-41ee-be21-be6d7638ce22/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:45:37,827] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1b5178e2-9920-41ee-be21-be6d7638ce22/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:45:37,842] [INFO] Found 18 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:45:37,842] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:45:37,842] [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 graminis	strain=LMG 18924	GCA_902859785.1	60548	60548	type	True	100.0	2471	2472	95	conclusive
Paraburkholderia graminis	strain=C4D1M	GCA_000172415.1	60548	60548	type	True	99.9745	2418	2472	95	conclusive
Paraburkholderia phenoliruptrix	strain=LMG 22037	GCA_902833655.1	252970	252970	suspected-type	True	88.8842	1733	2472	95	below_threshold
Paraburkholderia phenoliruptrix	strain=LMG 22037	GCA_902859825.1	252970	252970	suspected-type	True	88.866	1721	2472	95	below_threshold
Paraburkholderia dilworthii	strain=WSM3556	GCA_000472525.1	948106	948106	type	True	88.1215	1712	2472	95	below_threshold
Paraburkholderia rhynchosiae	strain=LMG 27174	GCA_902859775.1	487049	487049	type	True	87.8412	1672	2472	95	below_threshold
Paraburkholderia rhynchosiae	strain=WSM 3937	GCA_002879865.1	487049	487049	type	True	87.8184	1670	2472	95	below_threshold
Paraburkholderia kirstenboschensis	strain=LMG 28727	GCA_904848585.1	1245436	1245436	type	True	87.7534	1782	2472	95	below_threshold
Paraburkholderia caledonica	strain=NBRC 102488	GCA_000685095.1	134536	134536	type	True	87.4344	1777	2472	95	below_threshold
Paraburkholderia kirstenboschensis	strain=KB15	GCA_001636975.1	1245436	1245436	type	True	87.3972	1445	2472	95	below_threshold
Paraburkholderia caledonica	strain=LMG 19076	GCA_902833635.1	134536	134536	type	True	87.3904	1794	2472	95	below_threshold
Paraburkholderia dipogonis	strain=ICMP 19430	GCA_004402975.1	1211383	1211383	type	True	85.6169	1570	2472	95	below_threshold
Paraburkholderia aromaticivorans	strain=BN5	GCA_002278075.1	2026199	2026199	type	True	85.2926	1617	2472	95	below_threshold
Paraburkholderia haematera	strain=LMG 31837	GCA_905220975.1	2793077	2793077	type	True	84.8795	1419	2472	95	below_threshold
Paraburkholderia nemoris	strain=LMG 31836	GCA_905221015.1	2793076	2793076	type	True	84.8038	1512	2472	95	below_threshold
Paraburkholderia domus	strain=LMG 31832	GCA_905220705.1	2793075	2793075	type	True	84.5945	1445	2472	95	below_threshold
Paraburkholderia fungorum	strain=ATCC BAA-463	GCA_000961515.1	134537	134537	suspected-type	True	84.5078	1509	2472	95	below_threshold
Paraburkholderia podalyriae	strain=WC7.3b	GCA_014397785.1	1938811	1938811	type	True	84.2596	1430	2472	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:45:37,844] [INFO] DFAST Taxonomy check result was written to GCF_902859785.1_LMG_18924_genomic.fna/tc_result.tsv
[2024-01-24 12:45:37,844] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:45:37,845] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:45:37,845] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1b5178e2-9920-41ee-be21-be6d7638ce22/dqc_reference/checkm_data
[2024-01-24 12:45:37,846] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:45:37,914] [INFO] Task started: CheckM
[2024-01-24 12:45:37,915] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_902859785.1_LMG_18924_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_902859785.1_LMG_18924_genomic.fna/checkm_input GCF_902859785.1_LMG_18924_genomic.fna/checkm_result
[2024-01-24 12:46:43,795] [INFO] Task succeeded: CheckM
[2024-01-24 12:46:43,796] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:46:43,818] [INFO] ===== Completeness check finished =====
[2024-01-24 12:46:43,819] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:46:43,819] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_902859785.1_LMG_18924_genomic.fna/markers.fasta)
[2024-01-24 12:46:43,819] [INFO] Task started: Blastn
[2024-01-24 12:46:43,819] [INFO] Running command: blastn -query GCF_902859785.1_LMG_18924_genomic.fna/markers.fasta -db /var/lib/cwl/stg1b5178e2-9920-41ee-be21-be6d7638ce22/dqc_reference/reference_markers_gtdb.fasta -out GCF_902859785.1_LMG_18924_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:46:45,720] [INFO] Task succeeded: Blastn
[2024-01-24 12:46:45,726] [INFO] Selected 11 target genomes.
[2024-01-24 12:46:45,726] [INFO] Target genome list was writen to GCF_902859785.1_LMG_18924_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:46:45,745] [INFO] Task started: fastANI
[2024-01-24 12:46:45,745] [INFO] Running command: fastANI --query /var/lib/cwl/stg7a14b8e8-1196-4b8f-916c-b71cd30128b7/GCF_902859785.1_LMG_18924_genomic.fna.gz --refList GCF_902859785.1_LMG_18924_genomic.fna/target_genomes_gtdb.txt --output GCF_902859785.1_LMG_18924_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:47:06,065] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:06,079] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:47:06,079] [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_000172415.1	s__Paraburkholderia graminis	99.9745	2418	2472	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	98.52	98.23	0.90	0.89	12	conclusive
GCF_000472445.1	s__Paraburkholderia sp000472445	89.2785	1692	2472	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	88.8743	1720	2472	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	99.08	98.23	0.90	0.84	7	-
GCF_000472525.1	s__Paraburkholderia dilworthii	88.1279	1711	2472	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000148685.1	s__Paraburkholderia sp000148685	87.8994	1786	2472	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	98.01	98.00	0.91	0.91	4	-
GCF_000472545.1	s__Paraburkholderia sp000472545	87.8754	1822	2472	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	87.8169	1670	2472	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_904848585.1	s__Paraburkholderia kirstenboschensis	87.7465	1784	2472	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	99.97	99.97	1.00	1.00	2	-
GCF_000685095.1	s__Paraburkholderia caledonica	87.4261	1778	2472	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	97.03	95.65	0.88	0.80	10	-
GCF_004339745.1	s__Paraburkholderia sp004339745	85.5938	1622	2472	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002278075.1	s__Paraburkholderia aromaticivorans	85.2993	1614	2472	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 12:47:06,081] [INFO] GTDB search result was written to GCF_902859785.1_LMG_18924_genomic.fna/result_gtdb.tsv
[2024-01-24 12:47:06,082] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:47:06,085] [INFO] DFAST_QC result json was written to GCF_902859785.1_LMG_18924_genomic.fna/dqc_result.json
[2024-01-24 12:47:06,086] [INFO] DFAST_QC completed!
[2024-01-24 12:47:06,086] [INFO] Total running time: 0h2m27s