[2024-01-24 12:07:18,592] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:07:18,594] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:07:18,594] [INFO] DQC Reference Directory: /var/lib/cwl/stg00885593-936f-4864-ac8e-7d819c6da12c/dqc_reference
[2024-01-24 12:07:19,818] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:07:19,819] [INFO] Task started: Prodigal
[2024-01-24 12:07:19,820] [INFO] Running command: gunzip -c /var/lib/cwl/stgee8b973a-2d57-4aa5-a330-3ffd1b5c7186/GCF_001544835.2_Burkholderia_sp._LMG_29320_genomic.fna.gz | prodigal -d GCF_001544835.2_Burkholderia_sp._LMG_29320_genomic.fna/cds.fna -a GCF_001544835.2_Burkholderia_sp._LMG_29320_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:07:42,146] [INFO] Task succeeded: Prodigal
[2024-01-24 12:07:42,147] [INFO] Task started: HMMsearch
[2024-01-24 12:07:42,147] [INFO] Running command: hmmsearch --tblout GCF_001544835.2_Burkholderia_sp._LMG_29320_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg00885593-936f-4864-ac8e-7d819c6da12c/dqc_reference/reference_markers.hmm GCF_001544835.2_Burkholderia_sp._LMG_29320_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:07:42,507] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:07:42,508] [INFO] Found 6/6 markers.
[2024-01-24 12:07:42,569] [INFO] Query marker FASTA was written to GCF_001544835.2_Burkholderia_sp._LMG_29320_genomic.fna/markers.fasta
[2024-01-24 12:07:42,569] [INFO] Task started: Blastn
[2024-01-24 12:07:42,569] [INFO] Running command: blastn -query GCF_001544835.2_Burkholderia_sp._LMG_29320_genomic.fna/markers.fasta -db /var/lib/cwl/stg00885593-936f-4864-ac8e-7d819c6da12c/dqc_reference/reference_markers.fasta -out GCF_001544835.2_Burkholderia_sp._LMG_29320_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:43,628] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:43,639] [INFO] Selected 15 target genomes.
[2024-01-24 12:07:43,640] [INFO] Target genome list was writen to GCF_001544835.2_Burkholderia_sp._LMG_29320_genomic.fna/target_genomes.txt
[2024-01-24 12:07:43,648] [INFO] Task started: fastANI
[2024-01-24 12:07:43,648] [INFO] Running command: fastANI --query /var/lib/cwl/stgee8b973a-2d57-4aa5-a330-3ffd1b5c7186/GCF_001544835.2_Burkholderia_sp._LMG_29320_genomic.fna.gz --refList GCF_001544835.2_Burkholderia_sp._LMG_29320_genomic.fna/target_genomes.txt --output GCF_001544835.2_Burkholderia_sp._LMG_29320_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:08:14,573] [INFO] Task succeeded: fastANI
[2024-01-24 12:08:14,573] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg00885593-936f-4864-ac8e-7d819c6da12c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:08:14,574] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg00885593-936f-4864-ac8e-7d819c6da12c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:08:14,590] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:08:14,590] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:08:14,590] [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
Caballeronia fortuita		GCA_001544835.2	1777138	1777138	type	True	100.0	2426	2428	95	conclusive
Caballeronia temeraria		GCA_001544795.2	1777137	1777137	type	True	90.0532	1963	2428	95	below_threshold
Caballeronia zhejiangensis	strain=OP-1	GCA_000698575.1	871203	871203	type	True	89.977	1827	2428	95	below_threshold
Caballeronia novacaledonica	strain=LMG 28615	GCA_900258035.1	1544861	1544861	type	True	89.2737	1637	2428	95	below_threshold
Caballeronia glebae		GCA_001545035.2	1777143	1777143	type	True	89.2163	1783	2428	95	below_threshold
Caballeronia calidae		GCA_900044055.2	1777139	1777139	type	True	88.7232	1694	2428	95	below_threshold
Caballeronia pedi		GCA_001544915.2	1777141	1777141	type	True	88.4979	1783	2428	95	below_threshold
Caballeronia cordobensis	strain=LMG 27620	GCA_001278535.1	1353886	1353886	type	True	88.1282	1816	2428	95	below_threshold
Caballeronia cordobensis		GCA_001544575.2	1353886	1353886	type	True	88.1232	1781	2428	95	below_threshold
Caballeronia arvi		GCA_001544695.2	1777135	1777135	type	True	88.0787	1783	2428	95	below_threshold
Paraburkholderia gardini	strain=LMG 32171	GCA_907164575.1	2823469	2823469	type	True	81.3053	943	2428	95	below_threshold
Paraburkholderia azotifigens	strain=NF 2-5-3	GCA_007995085.1	2057004	2057004	type	True	81.294	1212	2428	95	below_threshold
Paraburkholderia saeva	strain=LMG 31841	GCA_907164555.1	2777537	2777537	type	True	80.9403	974	2428	95	below_threshold
Paraburkholderia pallida	strain=7MH5	GCA_004524855.1	2547399	2547399	type	True	80.4642	1050	2428	95	below_threshold
Paraburkholderia silviterrae	strain=4M-K11	GCA_004353915.1	2528715	2528715	type	True	80.3844	995	2428	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:08:14,593] [INFO] DFAST Taxonomy check result was written to GCF_001544835.2_Burkholderia_sp._LMG_29320_genomic.fna/tc_result.tsv
[2024-01-24 12:08:14,593] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:08:14,593] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:08:14,594] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg00885593-936f-4864-ac8e-7d819c6da12c/dqc_reference/checkm_data
[2024-01-24 12:08:14,595] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:08:14,668] [INFO] Task started: CheckM
[2024-01-24 12:08:14,668] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001544835.2_Burkholderia_sp._LMG_29320_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001544835.2_Burkholderia_sp._LMG_29320_genomic.fna/checkm_input GCF_001544835.2_Burkholderia_sp._LMG_29320_genomic.fna/checkm_result
[2024-01-24 12:09:18,021] [INFO] Task succeeded: CheckM
[2024-01-24 12:09:18,022] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:09:18,052] [INFO] ===== Completeness check finished =====
[2024-01-24 12:09:18,052] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:09:18,052] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001544835.2_Burkholderia_sp._LMG_29320_genomic.fna/markers.fasta)
[2024-01-24 12:09:18,053] [INFO] Task started: Blastn
[2024-01-24 12:09:18,053] [INFO] Running command: blastn -query GCF_001544835.2_Burkholderia_sp._LMG_29320_genomic.fna/markers.fasta -db /var/lib/cwl/stg00885593-936f-4864-ac8e-7d819c6da12c/dqc_reference/reference_markers_gtdb.fasta -out GCF_001544835.2_Burkholderia_sp._LMG_29320_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:09:20,021] [INFO] Task succeeded: Blastn
[2024-01-24 12:09:20,026] [INFO] Selected 11 target genomes.
[2024-01-24 12:09:20,026] [INFO] Target genome list was writen to GCF_001544835.2_Burkholderia_sp._LMG_29320_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:09:20,092] [INFO] Task started: fastANI
[2024-01-24 12:09:20,093] [INFO] Running command: fastANI --query /var/lib/cwl/stgee8b973a-2d57-4aa5-a330-3ffd1b5c7186/GCF_001544835.2_Burkholderia_sp._LMG_29320_genomic.fna.gz --refList GCF_001544835.2_Burkholderia_sp._LMG_29320_genomic.fna/target_genomes_gtdb.txt --output GCF_001544835.2_Burkholderia_sp._LMG_29320_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:09:44,456] [INFO] Task succeeded: fastANI
[2024-01-24 12:09:44,476] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:09:44,476] [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_001544835.2	s__Caballeronia fortuita	100.0	2426	2428	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001544795.2	s__Caballeronia temeraria	90.0499	1963	2428	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000698575.1	s__Caballeronia zhejiangensis	89.9632	1830	2428	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia	95.0	99.44	99.18	0.93	0.92	4	-
GCF_900258035.1	s__Caballeronia novacaledonica	89.2873	1635	2428	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001545035.1	s__Caballeronia glebae	89.22	1782	2428	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000648925.1	s__Caballeronia jiangsuensis	89.1253	1730	2428	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia	95.0	96.41	96.41	0.81	0.81	2	-
GCA_001580565.1	s__Caballeronia megalochromosomata	88.9849	1757	2428	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900044055.2	s__Caballeronia calidae	88.7256	1692	2428	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001544915.2	s__Caballeronia pedi	88.5116	1781	2428	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001544575.2	s__Caballeronia cordobensis	88.1161	1781	2428	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia	95.0	98.18	97.54	0.94	0.91	5	-
GCF_001544695.2	s__Caballeronia arvi	88.0871	1781	2428	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:09:44,478] [INFO] GTDB search result was written to GCF_001544835.2_Burkholderia_sp._LMG_29320_genomic.fna/result_gtdb.tsv
[2024-01-24 12:09:44,479] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:09:44,484] [INFO] DFAST_QC result json was written to GCF_001544835.2_Burkholderia_sp._LMG_29320_genomic.fna/dqc_result.json
[2024-01-24 12:09:44,484] [INFO] DFAST_QC completed!
[2024-01-24 12:09:44,484] [INFO] Total running time: 0h2m26s