[2024-01-25 20:04:05,554] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:04:05,556] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:04:05,556] [INFO] DQC Reference Directory: /var/lib/cwl/stg78c874af-0b8c-4a5d-a56f-537c1749b555/dqc_reference
[2024-01-25 20:04:06,654] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:04:06,655] [INFO] Task started: Prodigal
[2024-01-25 20:04:06,655] [INFO] Running command: gunzip -c /var/lib/cwl/stg7c2d99f4-415b-46fb-a273-9e116823d89c/GCF_902859945.1_LMG_28688_genomic.fna.gz | prodigal -d GCF_902859945.1_LMG_28688_genomic.fna/cds.fna -a GCF_902859945.1_LMG_28688_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:04:29,744] [INFO] Task succeeded: Prodigal
[2024-01-25 20:04:29,744] [INFO] Task started: HMMsearch
[2024-01-25 20:04:29,744] [INFO] Running command: hmmsearch --tblout GCF_902859945.1_LMG_28688_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg78c874af-0b8c-4a5d-a56f-537c1749b555/dqc_reference/reference_markers.hmm GCF_902859945.1_LMG_28688_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:04:30,050] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:04:30,051] [INFO] Found 6/6 markers.
[2024-01-25 20:04:30,111] [INFO] Query marker FASTA was written to GCF_902859945.1_LMG_28688_genomic.fna/markers.fasta
[2024-01-25 20:04:30,111] [INFO] Task started: Blastn
[2024-01-25 20:04:30,111] [INFO] Running command: blastn -query GCF_902859945.1_LMG_28688_genomic.fna/markers.fasta -db /var/lib/cwl/stg78c874af-0b8c-4a5d-a56f-537c1749b555/dqc_reference/reference_markers.fasta -out GCF_902859945.1_LMG_28688_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:04:31,102] [INFO] Task succeeded: Blastn
[2024-01-25 20:04:31,105] [INFO] Selected 13 target genomes.
[2024-01-25 20:04:31,105] [INFO] Target genome list was writen to GCF_902859945.1_LMG_28688_genomic.fna/target_genomes.txt
[2024-01-25 20:04:31,112] [INFO] Task started: fastANI
[2024-01-25 20:04:31,112] [INFO] Running command: fastANI --query /var/lib/cwl/stg7c2d99f4-415b-46fb-a273-9e116823d89c/GCF_902859945.1_LMG_28688_genomic.fna.gz --refList GCF_902859945.1_LMG_28688_genomic.fna/target_genomes.txt --output GCF_902859945.1_LMG_28688_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:04:55,566] [INFO] Task succeeded: fastANI
[2024-01-25 20:04:55,566] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg78c874af-0b8c-4a5d-a56f-537c1749b555/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:04:55,567] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg78c874af-0b8c-4a5d-a56f-537c1749b555/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:04:55,575] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 20:04:55,575] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 20:04:55,576] [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 sacchari	strain=LMG 19450	GCA_902833715.1	159450	159450	type	True	92.3816	1816	2619	95	below_threshold
Paraburkholderia sacchari	strain=LMG 19450	GCA_000785435.2	159450	159450	type	True	92.361	1828	2619	95	below_threshold
Paraburkholderia silviterrae	strain=4M-K11	GCA_004353915.1	2528715	2528715	type	True	88.957	1811	2619	95	below_threshold
Paraburkholderia pallida	strain=7MH5	GCA_004524855.1	2547399	2547399	type	True	88.8088	1819	2619	95	below_threshold
Paraburkholderia oxyphila	strain=NBRC 105797	GCA_000685075.1	614212	614212	type	True	88.6494	1825	2619	95	below_threshold
Paraburkholderia eburnea	strain=JCM 18070	GCA_002917095.1	1189126	1189126	type	True	85.7	1424	2619	95	below_threshold
Paraburkholderia tropica	strain=LMG 22274	GCA_900109265.1	92647	92647	type	True	85.6383	1506	2619	95	below_threshold
Paraburkholderia nodosa	strain=DSM 21604	GCA_000519185.1	392320	392320	type	True	85.1711	1513	2619	95	below_threshold
Paraburkholderia acidiphila	strain=7Q-K02	GCA_009789655.1	2571747	2571747	type	True	85.0	1507	2619	95	below_threshold
Paraburkholderia hiiakae	strain=LMG 27952	GCA_904848665.1	1081782	1081782	type	True	84.7749	1484	2619	95	below_threshold
Burkholderia anthina	strain=DSM 16086	GCA_016836725.1	179879	179879	suspected-type	True	81.1079	1080	2619	95	below_threshold
Burkholderia ubonensis		GCA_902499185.1	101571	101571	type	True	81.0753	1085	2619	95	below_threshold
Burkholderia ubonensis	strain=LMG 20358	GCA_902833085.1	101571	101571	type	True	80.9981	1108	2619	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:04:55,589] [INFO] DFAST Taxonomy check result was written to GCF_902859945.1_LMG_28688_genomic.fna/tc_result.tsv
[2024-01-25 20:04:55,589] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:04:55,589] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:04:55,590] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg78c874af-0b8c-4a5d-a56f-537c1749b555/dqc_reference/checkm_data
[2024-01-25 20:04:55,590] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:04:55,664] [INFO] Task started: CheckM
[2024-01-25 20:04:55,664] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_902859945.1_LMG_28688_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_902859945.1_LMG_28688_genomic.fna/checkm_input GCF_902859945.1_LMG_28688_genomic.fna/checkm_result
[2024-01-25 20:06:00,317] [INFO] Task succeeded: CheckM
[2024-01-25 20:06:00,318] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:06:00,335] [INFO] ===== Completeness check finished =====
[2024-01-25 20:06:00,336] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:06:00,336] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_902859945.1_LMG_28688_genomic.fna/markers.fasta)
[2024-01-25 20:06:00,336] [INFO] Task started: Blastn
[2024-01-25 20:06:00,337] [INFO] Running command: blastn -query GCF_902859945.1_LMG_28688_genomic.fna/markers.fasta -db /var/lib/cwl/stg78c874af-0b8c-4a5d-a56f-537c1749b555/dqc_reference/reference_markers_gtdb.fasta -out GCF_902859945.1_LMG_28688_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:06:02,207] [INFO] Task succeeded: Blastn
[2024-01-25 20:06:02,210] [INFO] Selected 10 target genomes.
[2024-01-25 20:06:02,210] [INFO] Target genome list was writen to GCF_902859945.1_LMG_28688_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:06:02,217] [INFO] Task started: fastANI
[2024-01-25 20:06:02,217] [INFO] Running command: fastANI --query /var/lib/cwl/stg7c2d99f4-415b-46fb-a273-9e116823d89c/GCF_902859945.1_LMG_28688_genomic.fna.gz --refList GCF_902859945.1_LMG_28688_genomic.fna/target_genomes_gtdb.txt --output GCF_902859945.1_LMG_28688_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:06:23,128] [INFO] Task succeeded: fastANI
[2024-01-25 20:06:23,135] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:06:23,136] [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_902859945.1	s__Paraburkholderia caffeinitolerans	100.0	2611	2619	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	99.86	99.86	0.95	0.95	2	conclusive
GCF_000785435.2	s__Paraburkholderia sacchari	92.3706	1826	2619	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	98.05	96.11	0.93	0.86	3	-
GCF_004353915.1	s__Paraburkholderia sp004353915	88.9315	1814	2619	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000685075.1	s__Paraburkholderia oxyphila	88.669	1822	2619	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	95.32	95.32	0.74	0.74	2	-
GCF_002917095.1	s__Paraburkholderia eburnea	85.6843	1426	2619	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	99.11	98.22	0.96	0.92	3	-
GCF_000519185.1	s__Paraburkholderia nodosa	85.1675	1513	2619	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003268775.1	s__Paraburkholderia unamae	85.1392	1520	2619	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	98.69	98.69	0.91	0.91	2	-
GCF_003096715.1	s__Paraburkholderia silvatlantica	85.0731	1378	2619	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.5542	99.65	99.23	0.96	0.92	5	-
GCF_004353905.1	s__Paraburkholderia guartelaensis	85.0299	1537	2619	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011753055.1	s__Paraburkholderia sp011753055	85.0221	1432	2619	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:06:23,137] [INFO] GTDB search result was written to GCF_902859945.1_LMG_28688_genomic.fna/result_gtdb.tsv
[2024-01-25 20:06:23,138] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:06:23,140] [INFO] DFAST_QC result json was written to GCF_902859945.1_LMG_28688_genomic.fna/dqc_result.json
[2024-01-25 20:06:23,141] [INFO] DFAST_QC completed!
[2024-01-25 20:06:23,141] [INFO] Total running time: 0h2m18s