[2024-01-24 13:37:25,948] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:37:25,952] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:37:25,952] [INFO] DQC Reference Directory: /var/lib/cwl/stg1b1a30c2-3035-40b0-ab8a-bd7ff4e4bd02/dqc_reference
[2024-01-24 13:37:27,235] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:37:27,237] [INFO] Task started: Prodigal
[2024-01-24 13:37:27,237] [INFO] Running command: gunzip -c /var/lib/cwl/stg89636649-0234-4a57-80dd-97ac00d923fc/GCF_902833665.1_Paraburkholderia_phymatum_LMG_21445_genomic.fna.gz | prodigal -d GCF_902833665.1_Paraburkholderia_phymatum_LMG_21445_genomic.fna/cds.fna -a GCF_902833665.1_Paraburkholderia_phymatum_LMG_21445_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:37:51,999] [INFO] Task succeeded: Prodigal
[2024-01-24 13:37:51,999] [INFO] Task started: HMMsearch
[2024-01-24 13:37:51,999] [INFO] Running command: hmmsearch --tblout GCF_902833665.1_Paraburkholderia_phymatum_LMG_21445_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1b1a30c2-3035-40b0-ab8a-bd7ff4e4bd02/dqc_reference/reference_markers.hmm GCF_902833665.1_Paraburkholderia_phymatum_LMG_21445_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:37:52,343] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:37:52,344] [INFO] Found 6/6 markers.
[2024-01-24 13:37:52,407] [INFO] Query marker FASTA was written to GCF_902833665.1_Paraburkholderia_phymatum_LMG_21445_genomic.fna/markers.fasta
[2024-01-24 13:37:52,407] [INFO] Task started: Blastn
[2024-01-24 13:37:52,407] [INFO] Running command: blastn -query GCF_902833665.1_Paraburkholderia_phymatum_LMG_21445_genomic.fna/markers.fasta -db /var/lib/cwl/stg1b1a30c2-3035-40b0-ab8a-bd7ff4e4bd02/dqc_reference/reference_markers.fasta -out GCF_902833665.1_Paraburkholderia_phymatum_LMG_21445_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:53,344] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:53,350] [INFO] Selected 11 target genomes.
[2024-01-24 13:37:53,350] [INFO] Target genome list was writen to GCF_902833665.1_Paraburkholderia_phymatum_LMG_21445_genomic.fna/target_genomes.txt
[2024-01-24 13:37:53,357] [INFO] Task started: fastANI
[2024-01-24 13:37:53,357] [INFO] Running command: fastANI --query /var/lib/cwl/stg89636649-0234-4a57-80dd-97ac00d923fc/GCF_902833665.1_Paraburkholderia_phymatum_LMG_21445_genomic.fna.gz --refList GCF_902833665.1_Paraburkholderia_phymatum_LMG_21445_genomic.fna/target_genomes.txt --output GCF_902833665.1_Paraburkholderia_phymatum_LMG_21445_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:38:15,908] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:15,909] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1b1a30c2-3035-40b0-ab8a-bd7ff4e4bd02/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:38:15,909] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1b1a30c2-3035-40b0-ab8a-bd7ff4e4bd02/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:38:15,916] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:38:15,916] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:38:15,917] [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 phymatum	strain=LMG 21445	GCA_902833665.1	148447	148447	type	True	100.0	2832	2836	95	conclusive
Paraburkholderia phymatum	strain=STM815	GCA_000020045.1	148447	148447	type	True	99.9984	2832	2836	95	conclusive
Paraburkholderia sabiae	strain=LMG 24235	GCA_904848645.1	273251	273251	type	True	89.135	2096	2836	95	below_threshold
Paraburkholderia azotifigens	strain=NF 2-5-3	GCA_007995085.1	2057004	2057004	type	True	88.9997	2110	2836	95	below_threshold
Paraburkholderia terrae	strain=NBRC 100964	GCA_000739835.1	311230	311230	type	True	87.0952	1896	2836	95	below_threshold
Paraburkholderia hospita	strain=LMG 20598	GCA_902833685.1	169430	169430	type	True	86.9929	1987	2836	95	below_threshold
Paraburkholderia diazotrophica	strain=LMG 26031	GCA_900108945.1	667676	667676	type	True	86.4521	1831	2836	95	below_threshold
Paraburkholderia gardini	strain=LMG 32171	GCA_907164575.1	2823469	2823469	type	True	81.9693	1135	2836	95	below_threshold
Paraburkholderia podalyriae	strain=WC7.3b	GCA_014397785.1	1938811	1938811	type	True	81.8615	1316	2836	95	below_threshold
Paraburkholderia saeva	strain=LMG 31841	GCA_907164555.1	2777537	2777537	type	True	81.7765	1155	2836	95	below_threshold
Paraburkholderia haematera	strain=LMG 31837	GCA_905220975.1	2793077	2793077	type	True	81.3018	1175	2836	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:38:15,918] [INFO] DFAST Taxonomy check result was written to GCF_902833665.1_Paraburkholderia_phymatum_LMG_21445_genomic.fna/tc_result.tsv
[2024-01-24 13:38:15,918] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:38:15,918] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:38:15,918] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1b1a30c2-3035-40b0-ab8a-bd7ff4e4bd02/dqc_reference/checkm_data
[2024-01-24 13:38:15,919] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:38:15,998] [INFO] Task started: CheckM
[2024-01-24 13:38:15,998] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_902833665.1_Paraburkholderia_phymatum_LMG_21445_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_902833665.1_Paraburkholderia_phymatum_LMG_21445_genomic.fna/checkm_input GCF_902833665.1_Paraburkholderia_phymatum_LMG_21445_genomic.fna/checkm_result
[2024-01-24 13:39:28,225] [INFO] Task succeeded: CheckM
[2024-01-24 13:39:28,226] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:39:28,244] [INFO] ===== Completeness check finished =====
[2024-01-24 13:39:28,244] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:39:28,244] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_902833665.1_Paraburkholderia_phymatum_LMG_21445_genomic.fna/markers.fasta)
[2024-01-24 13:39:28,245] [INFO] Task started: Blastn
[2024-01-24 13:39:28,245] [INFO] Running command: blastn -query GCF_902833665.1_Paraburkholderia_phymatum_LMG_21445_genomic.fna/markers.fasta -db /var/lib/cwl/stg1b1a30c2-3035-40b0-ab8a-bd7ff4e4bd02/dqc_reference/reference_markers_gtdb.fasta -out GCF_902833665.1_Paraburkholderia_phymatum_LMG_21445_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:39:30,029] [INFO] Task succeeded: Blastn
[2024-01-24 13:39:30,032] [INFO] Selected 9 target genomes.
[2024-01-24 13:39:30,032] [INFO] Target genome list was writen to GCF_902833665.1_Paraburkholderia_phymatum_LMG_21445_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:39:30,050] [INFO] Task started: fastANI
[2024-01-24 13:39:30,050] [INFO] Running command: fastANI --query /var/lib/cwl/stg89636649-0234-4a57-80dd-97ac00d923fc/GCF_902833665.1_Paraburkholderia_phymatum_LMG_21445_genomic.fna.gz --refList GCF_902833665.1_Paraburkholderia_phymatum_LMG_21445_genomic.fna/target_genomes_gtdb.txt --output GCF_902833665.1_Paraburkholderia_phymatum_LMG_21445_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:39:52,276] [INFO] Task succeeded: fastANI
[2024-01-24 13:39:52,283] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:39:52,283] [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_000020045.1	s__Paraburkholderia phymatum	99.9984	2832	2836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_017104565.1	s__Paraburkholderia sp017104565	91.3828	2028	2836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_904848645.1	s__Paraburkholderia sabiae	89.142	2095	2836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007995085.1	s__Paraburkholderia azotifigens	89.0209	2106	2836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	98.91	98.91	0.86	0.86	2	-
GCF_002902925.1	s__Paraburkholderia terrae	87.0524	1958	2836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.2599	98.84	97.67	0.92	0.83	3	-
GCF_002902965.1	s__Paraburkholderia hospita	87.0451	2000	2836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.2599	98.45	97.70	0.87	0.82	14	-
GCF_017104715.1	s__Paraburkholderia sp017104715	86.7095	1893	2836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900108945.1	s__Paraburkholderia diazotrophica	86.4783	1827	2836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003121405.1	s__Paraburkholderia sp003121405	86.2345	1747	2836	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 13:39:52,284] [INFO] GTDB search result was written to GCF_902833665.1_Paraburkholderia_phymatum_LMG_21445_genomic.fna/result_gtdb.tsv
[2024-01-24 13:39:52,285] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:39:52,287] [INFO] DFAST_QC result json was written to GCF_902833665.1_Paraburkholderia_phymatum_LMG_21445_genomic.fna/dqc_result.json
[2024-01-24 13:39:52,287] [INFO] DFAST_QC completed!
[2024-01-24 13:39:52,288] [INFO] Total running time: 0h2m26s