[2024-01-24 12:00:36,713] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:00:36,716] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:00:36,716] [INFO] DQC Reference Directory: /var/lib/cwl/stgf09bf727-d58e-4fd2-b0ce-8a1b4304834c/dqc_reference
[2024-01-24 12:00:39,378] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:00:39,379] [INFO] Task started: Prodigal
[2024-01-24 12:00:39,380] [INFO] Running command: gunzip -c /var/lib/cwl/stgf2e0e83b-1c7a-4702-a0dc-ee4c7eb0a589/GCF_905220705.1_LMG_31832_genomic.fna.gz | prodigal -d GCF_905220705.1_LMG_31832_genomic.fna/cds.fna -a GCF_905220705.1_LMG_31832_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:01:07,029] [INFO] Task succeeded: Prodigal
[2024-01-24 12:01:07,030] [INFO] Task started: HMMsearch
[2024-01-24 12:01:07,030] [INFO] Running command: hmmsearch --tblout GCF_905220705.1_LMG_31832_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf09bf727-d58e-4fd2-b0ce-8a1b4304834c/dqc_reference/reference_markers.hmm GCF_905220705.1_LMG_31832_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:01:07,405] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:01:07,407] [INFO] Found 6/6 markers.
[2024-01-24 12:01:07,472] [INFO] Query marker FASTA was written to GCF_905220705.1_LMG_31832_genomic.fna/markers.fasta
[2024-01-24 12:01:07,473] [INFO] Task started: Blastn
[2024-01-24 12:01:07,473] [INFO] Running command: blastn -query GCF_905220705.1_LMG_31832_genomic.fna/markers.fasta -db /var/lib/cwl/stgf09bf727-d58e-4fd2-b0ce-8a1b4304834c/dqc_reference/reference_markers.fasta -out GCF_905220705.1_LMG_31832_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:01:08,393] [INFO] Task succeeded: Blastn
[2024-01-24 12:01:08,397] [INFO] Selected 13 target genomes.
[2024-01-24 12:01:08,398] [INFO] Target genome list was writen to GCF_905220705.1_LMG_31832_genomic.fna/target_genomes.txt
[2024-01-24 12:01:08,404] [INFO] Task started: fastANI
[2024-01-24 12:01:08,404] [INFO] Running command: fastANI --query /var/lib/cwl/stgf2e0e83b-1c7a-4702-a0dc-ee4c7eb0a589/GCF_905220705.1_LMG_31832_genomic.fna.gz --refList GCF_905220705.1_LMG_31832_genomic.fna/target_genomes.txt --output GCF_905220705.1_LMG_31832_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:01:35,909] [INFO] Task succeeded: fastANI
[2024-01-24 12:01:35,910] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf09bf727-d58e-4fd2-b0ce-8a1b4304834c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:01:35,910] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf09bf727-d58e-4fd2-b0ce-8a1b4304834c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:01:35,925] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:01:35,926] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:01:35,926] [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 domus	strain=LMG 31832	GCA_905220705.1	2793075	2793075	type	True	100.0	2865	2869	95	conclusive
Paraburkholderia solitsugae	strain=1N	GCA_013177695.1	2675748	2675748	type	True	91.7534	2008	2869	95	below_threshold
Paraburkholderia elongata	strain=5N	GCA_013177735.1	2675747	2675747	type	True	91.0324	1907	2869	95	below_threshold
Paraburkholderia polaris	strain=RP-4-7	GCA_012927345.1	2728848	2728848	type	True	90.9959	2024	2869	95	below_threshold
Paraburkholderia madseniana	strain=RP11	GCA_009690905.1	2599607	2599607	type	True	90.6809	1939	2869	95	below_threshold
Paraburkholderia haematera	strain=LMG 31837	GCA_905220975.1	2793077	2793077	type	True	90.6092	1970	2869	95	below_threshold
Paraburkholderia nemoris	strain=LMG 31836	GCA_905221015.1	2793076	2793076	type	True	90.4195	1982	2869	95	below_threshold
Paraburkholderia aspalathi	strain=LMG 27731	GCA_900116445.1	1324617	1324617	type	True	90.3292	2011	2869	95	below_threshold
Paraburkholderia caffeinilytica	strain=CF1	GCA_003368325.1	1761016	1761016	type	True	90.1354	1842	2869	95	below_threshold
Paraburkholderia agricolaris	strain=BaQS159	GCA_009455635.1	2152888	2152888	type	True	89.2902	1920	2869	95	below_threshold
Paraburkholderia fungorum	strain=ATCC BAA-463	GCA_000961515.1	134537	134537	suspected-type	True	88.8815	1948	2869	95	below_threshold
Paraburkholderia kirstenboschensis	strain=KB15	GCA_001636975.1	1245436	1245436	type	True	84.0184	1200	2869	95	below_threshold
Paraburkholderia podalyriae	strain=WC7.3b	GCA_014397785.1	1938811	1938811	type	True	83.7327	1433	2869	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:01:35,927] [INFO] DFAST Taxonomy check result was written to GCF_905220705.1_LMG_31832_genomic.fna/tc_result.tsv
[2024-01-24 12:01:35,928] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:01:35,928] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:01:35,928] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf09bf727-d58e-4fd2-b0ce-8a1b4304834c/dqc_reference/checkm_data
[2024-01-24 12:01:35,929] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:01:36,020] [INFO] Task started: CheckM
[2024-01-24 12:01:36,021] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_905220705.1_LMG_31832_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_905220705.1_LMG_31832_genomic.fna/checkm_input GCF_905220705.1_LMG_31832_genomic.fna/checkm_result
[2024-01-24 12:02:50,209] [INFO] Task succeeded: CheckM
[2024-01-24 12:02:50,211] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:02:50,238] [INFO] ===== Completeness check finished =====
[2024-01-24 12:02:50,239] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:02:50,239] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_905220705.1_LMG_31832_genomic.fna/markers.fasta)
[2024-01-24 12:02:50,240] [INFO] Task started: Blastn
[2024-01-24 12:02:50,240] [INFO] Running command: blastn -query GCF_905220705.1_LMG_31832_genomic.fna/markers.fasta -db /var/lib/cwl/stgf09bf727-d58e-4fd2-b0ce-8a1b4304834c/dqc_reference/reference_markers_gtdb.fasta -out GCF_905220705.1_LMG_31832_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:02:51,940] [INFO] Task succeeded: Blastn
[2024-01-24 12:02:51,945] [INFO] Selected 12 target genomes.
[2024-01-24 12:02:51,945] [INFO] Target genome list was writen to GCF_905220705.1_LMG_31832_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:02:51,954] [INFO] Task started: fastANI
[2024-01-24 12:02:51,954] [INFO] Running command: fastANI --query /var/lib/cwl/stgf2e0e83b-1c7a-4702-a0dc-ee4c7eb0a589/GCF_905220705.1_LMG_31832_genomic.fna.gz --refList GCF_905220705.1_LMG_31832_genomic.fna/target_genomes_gtdb.txt --output GCF_905220705.1_LMG_31832_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:03:18,490] [INFO] Task succeeded: fastANI
[2024-01-24 12:03:18,507] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:03:18,507] [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_905220835.1	s__Paraburkholderia sp905220835	99.561	2540	2869	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	99.73	99.56	0.96	0.94	13	conclusive
GCF_013177695.1	s__Paraburkholderia sp013177695	91.7184	2013	2869	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142905.1	s__Paraburkholderia sp900142905	91.6695	2152	2869	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	98.29	98.24	0.83	0.82	6	-
GCF_013177735.1	s__Paraburkholderia sp013177735	90.9926	1912	2869	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012927345.1	s__Paraburkholderia sp012927345	90.988	2025	2869	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900230185.1	s__Paraburkholderia sp900230185	90.7049	2105	2869	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009690905.1	s__Paraburkholderia madseniana	90.68	1939	2869	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	98.82	98.82	0.85	0.85	2	-
GCF_905220975.1	s__Paraburkholderia sp905220975	90.5969	1972	2869	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001634365.1	s__Paraburkholderia sp001634365	90.4064	1725	2869	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116445.1	s__Paraburkholderia aspalathi	90.3437	2009	2869	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	96.47	95.19	0.81	0.72	20	-
GCF_003610295.1	s__Paraburkholderia sp003610295	90.0433	1958	2869	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003610895.1	s__Paraburkholderia fungorum_B	89.2356	1946	2869	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 12:03:18,509] [INFO] GTDB search result was written to GCF_905220705.1_LMG_31832_genomic.fna/result_gtdb.tsv
[2024-01-24 12:03:18,510] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:03:18,514] [INFO] DFAST_QC result json was written to GCF_905220705.1_LMG_31832_genomic.fna/dqc_result.json
[2024-01-24 12:03:18,514] [INFO] DFAST_QC completed!
[2024-01-24 12:03:18,514] [INFO] Total running time: 0h2m42s