[2024-01-24 12:13:23,544] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:13:23,548] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:13:23,549] [INFO] DQC Reference Directory: /var/lib/cwl/stg24b3306f-3258-4bdc-81e3-f39904b7c443/dqc_reference
[2024-01-24 12:13:26,484] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:13:26,485] [INFO] Task started: Prodigal
[2024-01-24 12:13:26,485] [INFO] Running command: gunzip -c /var/lib/cwl/stg18d490f7-ef59-41a2-b119-b3464e44e936/GCF_902459705.1_LMG_31013_genomic.fna.gz | prodigal -d GCF_902459705.1_LMG_31013_genomic.fna/cds.fna -a GCF_902459705.1_LMG_31013_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:13:44,778] [INFO] Task succeeded: Prodigal
[2024-01-24 12:13:44,779] [INFO] Task started: HMMsearch
[2024-01-24 12:13:44,779] [INFO] Running command: hmmsearch --tblout GCF_902459705.1_LMG_31013_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg24b3306f-3258-4bdc-81e3-f39904b7c443/dqc_reference/reference_markers.hmm GCF_902459705.1_LMG_31013_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:13:45,163] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:13:45,165] [INFO] Found 6/6 markers.
[2024-01-24 12:13:45,227] [INFO] Query marker FASTA was written to GCF_902459705.1_LMG_31013_genomic.fna/markers.fasta
[2024-01-24 12:13:45,227] [INFO] Task started: Blastn
[2024-01-24 12:13:45,227] [INFO] Running command: blastn -query GCF_902459705.1_LMG_31013_genomic.fna/markers.fasta -db /var/lib/cwl/stg24b3306f-3258-4bdc-81e3-f39904b7c443/dqc_reference/reference_markers.fasta -out GCF_902459705.1_LMG_31013_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:13:46,213] [INFO] Task succeeded: Blastn
[2024-01-24 12:13:46,217] [INFO] Selected 14 target genomes.
[2024-01-24 12:13:46,217] [INFO] Target genome list was writen to GCF_902459705.1_LMG_31013_genomic.fna/target_genomes.txt
[2024-01-24 12:13:46,224] [INFO] Task started: fastANI
[2024-01-24 12:13:46,224] [INFO] Running command: fastANI --query /var/lib/cwl/stg18d490f7-ef59-41a2-b119-b3464e44e936/GCF_902459705.1_LMG_31013_genomic.fna.gz --refList GCF_902459705.1_LMG_31013_genomic.fna/target_genomes.txt --output GCF_902459705.1_LMG_31013_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:14:04,895] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:04,895] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg24b3306f-3258-4bdc-81e3-f39904b7c443/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:14:04,896] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg24b3306f-3258-4bdc-81e3-f39904b7c443/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:14:04,907] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:14:04,907] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:14:04,908] [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
Pandoraea terrigena	strain=LMG 31013	GCA_902459705.1	2508292	2508292	type	True	100.0	1770	1770	95	conclusive
Pandoraea eparura	strain=LMG 31012	GCA_902459725.1	2508291	2508291	type	True	91.4403	1373	1770	95	below_threshold
Pandoraea soli	strain=LMG 31014	GCA_902459595.1	2508293	2508293	type	True	90.5633	1373	1770	95	below_threshold
Pandoraea cepalis	strain=LMG 31106	GCA_902459665.1	2508294	2508294	type	True	90.477	1391	1770	95	below_threshold
Pandoraea bronchicola	strain=LMG 20603	GCA_902459805.1	2508287	2508287	type	True	86.7634	1218	1770	95	below_threshold
Pandoraea communis	strain=LMG 31110	GCA_902459745.1	2508297	2508297	type	True	86.4396	1278	1770	95	below_threshold
Pandoraea apista	strain=DSM 16535	GCA_001465595.2	93218	93218	type	True	85.7188	1235	1770	95	below_threshold
Pandoraea nosoerga	strain=LMG 31109	GCA_902459585.1	2508296	2508296	type	True	84.8693	1127	1770	95	below_threshold
Pandoraea pnomenusa	strain=NCTC13160	GCA_900454355.1	93220	93220	type	True	84.8495	1210	1770	95	below_threshold
Burkholderia ubonensis		GCA_902499185.1	101571	101571	type	True	78.6092	560	1770	95	below_threshold
Burkholderia ubonensis	strain=LMG 20358	GCA_902833085.1	101571	101571	type	True	78.5789	569	1770	95	below_threshold
Paraburkholderia saeva	strain=LMG 31841	GCA_907164555.1	2777537	2777537	type	True	78.4418	442	1770	95	below_threshold
Paraburkholderia podalyriae	strain=WC7.3b	GCA_014397785.1	1938811	1938811	type	True	78.3839	520	1770	95	below_threshold
Paraburkholderia haematera	strain=LMG 31837	GCA_905220975.1	2793077	2793077	type	True	77.9729	466	1770	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:14:04,909] [INFO] DFAST Taxonomy check result was written to GCF_902459705.1_LMG_31013_genomic.fna/tc_result.tsv
[2024-01-24 12:14:04,910] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:14:04,910] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:14:04,910] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg24b3306f-3258-4bdc-81e3-f39904b7c443/dqc_reference/checkm_data
[2024-01-24 12:14:04,911] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:14:04,962] [INFO] Task started: CheckM
[2024-01-24 12:14:04,962] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_902459705.1_LMG_31013_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_902459705.1_LMG_31013_genomic.fna/checkm_input GCF_902459705.1_LMG_31013_genomic.fna/checkm_result
[2024-01-24 12:15:04,412] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:04,414] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:04,437] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:04,438] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:04,438] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_902459705.1_LMG_31013_genomic.fna/markers.fasta)
[2024-01-24 12:15:04,438] [INFO] Task started: Blastn
[2024-01-24 12:15:04,438] [INFO] Running command: blastn -query GCF_902459705.1_LMG_31013_genomic.fna/markers.fasta -db /var/lib/cwl/stg24b3306f-3258-4bdc-81e3-f39904b7c443/dqc_reference/reference_markers_gtdb.fasta -out GCF_902459705.1_LMG_31013_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:06,382] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:06,387] [INFO] Selected 11 target genomes.
[2024-01-24 12:15:06,387] [INFO] Target genome list was writen to GCF_902459705.1_LMG_31013_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:06,394] [INFO] Task started: fastANI
[2024-01-24 12:15:06,395] [INFO] Running command: fastANI --query /var/lib/cwl/stg18d490f7-ef59-41a2-b119-b3464e44e936/GCF_902459705.1_LMG_31013_genomic.fna.gz --refList GCF_902459705.1_LMG_31013_genomic.fna/target_genomes_gtdb.txt --output GCF_902459705.1_LMG_31013_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:15:20,568] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:20,578] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:15:20,579] [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_902459705.1	s__Pandoraea terrigena	100.0	1770	1770	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_902459725.1	s__Pandoraea eparura	91.451	1372	1770	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902459665.1	s__Pandoraea cepalis	90.477	1391	1770	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	97.00	95.81	0.88	0.85	6	-
GCF_902459805.1	s__Pandoraea bronchicola	86.7489	1220	1770	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902459745.1	s__Pandoraea communis	86.4346	1279	1770	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0166	98.36	97.48	0.89	0.87	3	-
GCF_001465595.2	s__Pandoraea apista	85.7188	1235	1770	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	99.24	99.05	0.93	0.91	21	-
GCF_902459735.1	s__Pandoraea capi	85.0619	1193	1770	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	96.45	96.45	0.90	0.90	2	-
GCF_000815105.2	s__Pandoraea pulmonicola	85.0106	1208	1770	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	100.00	100.00	1.00	1.00	2	-
GCF_902459585.1	s__Pandoraea nosoerga	84.8541	1128	1770	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	99.66	99.29	0.94	0.91	4	-
GCF_000767615.3	s__Pandoraea pnomenusa	84.8338	1233	1770	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	99.00	95.12	0.95	0.92	14	-
GCF_902459615.1	s__Pandoraea commovens	84.7758	1239	1770	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:15:20,580] [INFO] GTDB search result was written to GCF_902459705.1_LMG_31013_genomic.fna/result_gtdb.tsv
[2024-01-24 12:15:20,584] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:15:20,592] [INFO] DFAST_QC result json was written to GCF_902459705.1_LMG_31013_genomic.fna/dqc_result.json
[2024-01-24 12:15:20,593] [INFO] DFAST_QC completed!
[2024-01-24 12:15:20,593] [INFO] Total running time: 0h1m57s