[2024-01-24 12:51:06,220] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:51:06,222] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:51:06,222] [INFO] DQC Reference Directory: /var/lib/cwl/stg68af6aed-e15c-4461-9791-cb6d7600b5a8/dqc_reference
[2024-01-24 12:51:07,400] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:51:07,401] [INFO] Task started: Prodigal
[2024-01-24 12:51:07,401] [INFO] Running command: gunzip -c /var/lib/cwl/stgb5ee0f7e-9b82-4228-81ca-488c1e552470/GCF_002278075.1_ASM227807v1_genomic.fna.gz | prodigal -d GCF_002278075.1_ASM227807v1_genomic.fna/cds.fna -a GCF_002278075.1_ASM227807v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:51:35,161] [INFO] Task succeeded: Prodigal
[2024-01-24 12:51:35,161] [INFO] Task started: HMMsearch
[2024-01-24 12:51:35,161] [INFO] Running command: hmmsearch --tblout GCF_002278075.1_ASM227807v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg68af6aed-e15c-4461-9791-cb6d7600b5a8/dqc_reference/reference_markers.hmm GCF_002278075.1_ASM227807v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:51:35,500] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:51:35,502] [INFO] Found 6/6 markers.
[2024-01-24 12:51:35,564] [INFO] Query marker FASTA was written to GCF_002278075.1_ASM227807v1_genomic.fna/markers.fasta
[2024-01-24 12:51:35,565] [INFO] Task started: Blastn
[2024-01-24 12:51:35,565] [INFO] Running command: blastn -query GCF_002278075.1_ASM227807v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg68af6aed-e15c-4461-9791-cb6d7600b5a8/dqc_reference/reference_markers.fasta -out GCF_002278075.1_ASM227807v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:51:36,513] [INFO] Task succeeded: Blastn
[2024-01-24 12:51:36,517] [INFO] Selected 15 target genomes.
[2024-01-24 12:51:36,517] [INFO] Target genome list was writen to GCF_002278075.1_ASM227807v1_genomic.fna/target_genomes.txt
[2024-01-24 12:51:36,539] [INFO] Task started: fastANI
[2024-01-24 12:51:36,539] [INFO] Running command: fastANI --query /var/lib/cwl/stgb5ee0f7e-9b82-4228-81ca-488c1e552470/GCF_002278075.1_ASM227807v1_genomic.fna.gz --refList GCF_002278075.1_ASM227807v1_genomic.fna/target_genomes.txt --output GCF_002278075.1_ASM227807v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:52:05,222] [INFO] Task succeeded: fastANI
[2024-01-24 12:52:05,222] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg68af6aed-e15c-4461-9791-cb6d7600b5a8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:52:05,222] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg68af6aed-e15c-4461-9791-cb6d7600b5a8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:52:05,234] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:52:05,234] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:52:05,234] [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 aromaticivorans	strain=BN5	GCA_002278075.1	2026199	2026199	type	True	100.0	2962	2966	95	conclusive
Paraburkholderia xenovorans	strain=LB400	GCA_000013645.1	36873	36873	type	True	91.0864	2038	2966	95	below_threshold
Paraburkholderia xenovorans	strain=LB400	GCA_000756045.1	36873	36873	type	True	91.0817	2034	2966	95	below_threshold
Paraburkholderia phytofirmans	strain=PsJN	GCA_000020125.1	261302	261302	type	True	89.4835	1913	2966	95	below_threshold
Paraburkholderia dipogonis	strain=ICMP 19430	GCA_004402975.1	1211383	1211383	type	True	89.3314	1926	2966	95	below_threshold
Paraburkholderia ultramafica	strain=LMG 28614	GCA_902859915.1	1544867	1544867	type	True	87.5874	1611	2966	95	below_threshold
Paraburkholderia ginsengisoli	strain=NBRC 100965	GCA_000739735.1	311231	311231	type	True	87.1141	1638	2966	95	below_threshold
Paraburkholderia bryophila	strain=LMG 23644	GCA_003269035.1	420952	420952	type	True	86.6946	1718	2966	95	below_threshold
Paraburkholderia panacisoli	strain=DCY113	GCA_008369935.1	2603818	2603818	type	True	86.6691	1798	2966	95	below_threshold
Paraburkholderia nemoris	strain=LMG 31836	GCA_905221015.1	2793076	2793076	type	True	86.5657	1792	2966	95	below_threshold
Paraburkholderia haematera	strain=LMG 31837	GCA_905220975.1	2793077	2793077	type	True	86.4761	1637	2966	95	below_threshold
Paraburkholderia domus	strain=LMG 31832	GCA_905220705.1	2793075	2793075	type	True	86.3341	1749	2966	95	below_threshold
Paraburkholderia metrosideri	strain=LMG 28140	GCA_904848625.1	580937	580937	type	True	85.4915	1569	2966	95	below_threshold
Paraburkholderia kirstenboschensis	strain=KB15	GCA_001636975.1	1245436	1245436	type	True	84.7817	1308	2966	95	below_threshold
Paraburkholderia podalyriae	strain=WC7.3b	GCA_014397785.1	1938811	1938811	type	True	84.4229	1498	2966	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:52:05,236] [INFO] DFAST Taxonomy check result was written to GCF_002278075.1_ASM227807v1_genomic.fna/tc_result.tsv
[2024-01-24 12:52:05,237] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:52:05,237] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:52:05,237] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg68af6aed-e15c-4461-9791-cb6d7600b5a8/dqc_reference/checkm_data
[2024-01-24 12:52:05,238] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:52:05,314] [INFO] Task started: CheckM
[2024-01-24 12:52:05,314] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002278075.1_ASM227807v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002278075.1_ASM227807v1_genomic.fna/checkm_input GCF_002278075.1_ASM227807v1_genomic.fna/checkm_result
[2024-01-24 12:53:23,484] [INFO] Task succeeded: CheckM
[2024-01-24 12:53:23,485] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:53:23,507] [INFO] ===== Completeness check finished =====
[2024-01-24 12:53:23,507] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:53:23,507] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002278075.1_ASM227807v1_genomic.fna/markers.fasta)
[2024-01-24 12:53:23,508] [INFO] Task started: Blastn
[2024-01-24 12:53:23,508] [INFO] Running command: blastn -query GCF_002278075.1_ASM227807v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg68af6aed-e15c-4461-9791-cb6d7600b5a8/dqc_reference/reference_markers_gtdb.fasta -out GCF_002278075.1_ASM227807v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:53:25,374] [INFO] Task succeeded: Blastn
[2024-01-24 12:53:25,377] [INFO] Selected 9 target genomes.
[2024-01-24 12:53:25,378] [INFO] Target genome list was writen to GCF_002278075.1_ASM227807v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:53:25,490] [INFO] Task started: fastANI
[2024-01-24 12:53:25,490] [INFO] Running command: fastANI --query /var/lib/cwl/stgb5ee0f7e-9b82-4228-81ca-488c1e552470/GCF_002278075.1_ASM227807v1_genomic.fna.gz --refList GCF_002278075.1_ASM227807v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002278075.1_ASM227807v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:53:44,615] [INFO] Task succeeded: fastANI
[2024-01-24 12:53:44,623] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:53:44,623] [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_002278075.1	s__Paraburkholderia aromaticivorans	100.0	2963	2966	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_900104795.1	s__Paraburkholderia sp900104795	91.5586	2223	2966	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	98.49	98.44	0.88	0.86	5	-
GCF_902459535.1	s__Paraburkholderia sp000178415	91.2019	2034	2966	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	99.44	99.44	0.87	0.87	2	-
GCF_000013645.1	s__Paraburkholderia xenovorans	91.0797	2037	2966	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	99.29	98.59	0.95	0.90	3	-
GCF_004339745.1	s__Paraburkholderia sp004339745	89.8495	2020	2966	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012689525.1	s__Paraburkholderia aromaticivorans_A	89.6103	2013	2966	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	89.5018	1911	2966	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	95.77	95.72	0.82	0.81	3	-
GCF_003002025.1	s__Paraburkholderia sp003002025	89.1775	1896	2966	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	97.08	96.80	0.83	0.80	5	-
GCF_902859915.1	s__Paraburkholderia ultramafica	87.6111	1608	2966	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 12:53:44,625] [INFO] GTDB search result was written to GCF_002278075.1_ASM227807v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:53:44,626] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:53:44,629] [INFO] DFAST_QC result json was written to GCF_002278075.1_ASM227807v1_genomic.fna/dqc_result.json
[2024-01-24 12:53:44,629] [INFO] DFAST_QC completed!
[2024-01-24 12:53:44,629] [INFO] Total running time: 0h2m38s