[2024-01-24 14:28:18,075] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:28:18,077] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:28:18,078] [INFO] DQC Reference Directory: /var/lib/cwl/stg1f9f70be-c0e0-44c8-9e27-ebd69fbfd91e/dqc_reference
[2024-01-24 14:28:20,484] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:28:20,485] [INFO] Task started: Prodigal
[2024-01-24 14:28:20,485] [INFO] Running command: gunzip -c /var/lib/cwl/stgbd0a0db7-fdaa-4a57-9374-3581c3c341db/GCF_900019265.1_BN2475-7296_genomic.fna.gz | prodigal -d GCF_900019265.1_BN2475-7296_genomic.fna/cds.fna -a GCF_900019265.1_BN2475-7296_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:28:42,943] [INFO] Task succeeded: Prodigal
[2024-01-24 14:28:42,944] [INFO] Task started: HMMsearch
[2024-01-24 14:28:42,944] [INFO] Running command: hmmsearch --tblout GCF_900019265.1_BN2475-7296_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1f9f70be-c0e0-44c8-9e27-ebd69fbfd91e/dqc_reference/reference_markers.hmm GCF_900019265.1_BN2475-7296_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:28:43,315] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:28:43,317] [INFO] Found 6/6 markers.
[2024-01-24 14:28:43,372] [INFO] Query marker FASTA was written to GCF_900019265.1_BN2475-7296_genomic.fna/markers.fasta
[2024-01-24 14:28:43,372] [INFO] Task started: Blastn
[2024-01-24 14:28:43,373] [INFO] Running command: blastn -query GCF_900019265.1_BN2475-7296_genomic.fna/markers.fasta -db /var/lib/cwl/stg1f9f70be-c0e0-44c8-9e27-ebd69fbfd91e/dqc_reference/reference_markers.fasta -out GCF_900019265.1_BN2475-7296_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:28:44,556] [INFO] Task succeeded: Blastn
[2024-01-24 14:28:44,564] [INFO] Selected 18 target genomes.
[2024-01-24 14:28:44,565] [INFO] Target genome list was writen to GCF_900019265.1_BN2475-7296_genomic.fna/target_genomes.txt
[2024-01-24 14:28:44,572] [INFO] Task started: fastANI
[2024-01-24 14:28:44,573] [INFO] Running command: fastANI --query /var/lib/cwl/stgbd0a0db7-fdaa-4a57-9374-3581c3c341db/GCF_900019265.1_BN2475-7296_genomic.fna.gz --refList GCF_900019265.1_BN2475-7296_genomic.fna/target_genomes.txt --output GCF_900019265.1_BN2475-7296_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:29:18,924] [INFO] Task succeeded: fastANI
[2024-01-24 14:29:18,925] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1f9f70be-c0e0-44c8-9e27-ebd69fbfd91e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:29:18,925] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1f9f70be-c0e0-44c8-9e27-ebd69fbfd91e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:29:18,945] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:29:18,945] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:29:18,945] [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 ribeironis	strain=STM 7296	GCA_900019265.2	1247936	1247936	type	True	100.0	2314	2323	95	conclusive
Paraburkholderia ultramafica	strain=LMG 28614	GCA_902859915.1	1544867	1544867	type	True	89.1632	1536	2323	95	below_threshold
Paraburkholderia ginsengisoli	strain=NBRC 100965	GCA_000739735.1	311231	311231	type	True	88.2411	1492	2323	95	below_threshold
Paraburkholderia panacisoli	strain=DCY113	GCA_008369935.1	2603818	2603818	type	True	88.0524	1605	2323	95	below_threshold
Paraburkholderia fynbosensis	strain=LMG 27177	GCA_902859935.1	1200993	1200993	type	True	87.8013	1509	2323	95	below_threshold
Paraburkholderia xenovorans	strain=LB400	GCA_000013645.1	36873	36873	type	True	86.6303	1424	2323	95	below_threshold
Paraburkholderia phytofirmans	strain=PsJN	GCA_000020125.1	261302	261302	type	True	86.5543	1426	2323	95	below_threshold
Paraburkholderia dipogonis	strain=ICMP 19430	GCA_004402975.1	1211383	1211383	type	True	86.4904	1489	2323	95	below_threshold
Paraburkholderia aromaticivorans	strain=BN5	GCA_002278075.1	2026199	2026199	type	True	86.4639	1465	2323	95	below_threshold
Paraburkholderia bryophila	strain=LMG 23644	GCA_003269035.1	420952	420952	type	True	86.2168	1374	2323	95	below_threshold
Paraburkholderia nemoris	strain=LMG 31836	GCA_905221015.1	2793076	2793076	type	True	85.9174	1452	2323	95	below_threshold
Paraburkholderia domus	strain=LMG 31832	GCA_905220705.1	2793075	2793075	type	True	85.8232	1423	2323	95	below_threshold
Paraburkholderia haematera	strain=LMG 31837	GCA_905220975.1	2793077	2793077	type	True	85.754	1386	2323	95	below_threshold
Paraburkholderia podalyriae	strain=WC7.3b	GCA_014397785.1	1938811	1938811	type	True	85.4049	1454	2323	95	below_threshold
Paraburkholderia sprentiae	strain=WSM5005	GCA_000473465.1	948107	948107	type	True	85.1134	1422	2323	95	below_threshold
Paraburkholderia graminis	strain=LMG 18924	GCA_902859785.1	60548	60548	type	True	85.1068	1345	2323	95	below_threshold
Paraburkholderia graminis	strain=C4D1M	GCA_000172415.1	60548	60548	type	True	85.0071	1328	2323	95	below_threshold
Paraburkholderia kirstenboschensis	strain=KB15	GCA_001636975.1	1245436	1245436	type	True	84.34	1121	2323	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:29:18,947] [INFO] DFAST Taxonomy check result was written to GCF_900019265.1_BN2475-7296_genomic.fna/tc_result.tsv
[2024-01-24 14:29:18,948] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:29:18,948] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:29:18,948] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1f9f70be-c0e0-44c8-9e27-ebd69fbfd91e/dqc_reference/checkm_data
[2024-01-24 14:29:18,949] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:29:19,021] [INFO] Task started: CheckM
[2024-01-24 14:29:19,021] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900019265.1_BN2475-7296_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900019265.1_BN2475-7296_genomic.fna/checkm_input GCF_900019265.1_BN2475-7296_genomic.fna/checkm_result
[2024-01-24 14:30:25,143] [INFO] Task succeeded: CheckM
[2024-01-24 14:30:25,145] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:30:25,167] [INFO] ===== Completeness check finished =====
[2024-01-24 14:30:25,168] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:30:25,168] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900019265.1_BN2475-7296_genomic.fna/markers.fasta)
[2024-01-24 14:30:25,169] [INFO] Task started: Blastn
[2024-01-24 14:30:25,169] [INFO] Running command: blastn -query GCF_900019265.1_BN2475-7296_genomic.fna/markers.fasta -db /var/lib/cwl/stg1f9f70be-c0e0-44c8-9e27-ebd69fbfd91e/dqc_reference/reference_markers_gtdb.fasta -out GCF_900019265.1_BN2475-7296_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:30:27,261] [INFO] Task succeeded: Blastn
[2024-01-24 14:30:27,265] [INFO] Selected 13 target genomes.
[2024-01-24 14:30:27,265] [INFO] Target genome list was writen to GCF_900019265.1_BN2475-7296_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:30:27,275] [INFO] Task started: fastANI
[2024-01-24 14:30:27,275] [INFO] Running command: fastANI --query /var/lib/cwl/stgbd0a0db7-fdaa-4a57-9374-3581c3c341db/GCF_900019265.1_BN2475-7296_genomic.fna.gz --refList GCF_900019265.1_BN2475-7296_genomic.fna/target_genomes_gtdb.txt --output GCF_900019265.1_BN2475-7296_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:30:54,006] [INFO] Task succeeded: fastANI
[2024-01-24 14:30:54,018] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:30:54,019] [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_900019265.1	s__Paraburkholderia ribeironis	100.0	2314	2323	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_902859915.1	s__Paraburkholderia ultramafica	89.1505	1537	2323	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000739735.1	s__Paraburkholderia ginsengisoli	88.2355	1493	2323	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_008369935.1	s__Paraburkholderia panacisoli	88.0452	1608	2323	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012275575.1	s__Paraburkholderia sp012275575	87.6974	1407	2323	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004339745.1	s__Paraburkholderia sp004339745	86.8473	1500	2323	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000020125.1	s__Paraburkholderia phytofirmans	86.5627	1425	2323	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	95.77	95.72	0.82	0.81	3	-
GCF_002278075.1	s__Paraburkholderia aromaticivorans	86.4801	1464	2323	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003002025.1	s__Paraburkholderia sp003002025	86.3488	1456	2323	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	97.08	96.80	0.83	0.80	5	-
GCF_900177725.1	s__Paraburkholderia susongensis	86.2726	1423	2323	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003269035.1	s__Paraburkholderia bryophila	86.2309	1372	2323	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	98.31	96.63	0.94	0.89	3	-
GCF_011752995.1	s__Paraburkholderia sp011752995	85.9901	1312	2323	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	99.23	99.21	0.92	0.90	4	-
GCF_000172415.1	s__Paraburkholderia graminis	85.0048	1328	2323	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	98.52	98.23	0.90	0.89	12	-
--------------------------------------------------------------------------------
[2024-01-24 14:30:54,021] [INFO] GTDB search result was written to GCF_900019265.1_BN2475-7296_genomic.fna/result_gtdb.tsv
[2024-01-24 14:30:54,021] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:30:54,025] [INFO] DFAST_QC result json was written to GCF_900019265.1_BN2475-7296_genomic.fna/dqc_result.json
[2024-01-24 14:30:54,026] [INFO] DFAST_QC completed!
[2024-01-24 14:30:54,026] [INFO] Total running time: 0h2m36s