[2024-01-24 15:26:33,096] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:26:33,098] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:26:33,098] [INFO] DQC Reference Directory: /var/lib/cwl/stgc86b57d4-0afc-4c00-afde-e6a71f25bbee/dqc_reference
[2024-01-24 15:26:35,759] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:26:35,760] [INFO] Task started: Prodigal
[2024-01-24 15:26:35,760] [INFO] Running command: gunzip -c /var/lib/cwl/stg093de53c-c6a9-4037-af8f-143e03ae0eb7/GCF_004524855.1_ASM452485v1_genomic.fna.gz | prodigal -d GCF_004524855.1_ASM452485v1_genomic.fna/cds.fna -a GCF_004524855.1_ASM452485v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:27:08,540] [INFO] Task succeeded: Prodigal
[2024-01-24 15:27:08,540] [INFO] Task started: HMMsearch
[2024-01-24 15:27:08,541] [INFO] Running command: hmmsearch --tblout GCF_004524855.1_ASM452485v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc86b57d4-0afc-4c00-afde-e6a71f25bbee/dqc_reference/reference_markers.hmm GCF_004524855.1_ASM452485v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:27:08,949] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:27:08,951] [INFO] Found 6/6 markers.
[2024-01-24 15:27:09,028] [INFO] Query marker FASTA was written to GCF_004524855.1_ASM452485v1_genomic.fna/markers.fasta
[2024-01-24 15:27:09,029] [INFO] Task started: Blastn
[2024-01-24 15:27:09,029] [INFO] Running command: blastn -query GCF_004524855.1_ASM452485v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc86b57d4-0afc-4c00-afde-e6a71f25bbee/dqc_reference/reference_markers.fasta -out GCF_004524855.1_ASM452485v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:10,082] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:10,086] [INFO] Selected 11 target genomes.
[2024-01-24 15:27:10,087] [INFO] Target genome list was writen to GCF_004524855.1_ASM452485v1_genomic.fna/target_genomes.txt
[2024-01-24 15:27:10,093] [INFO] Task started: fastANI
[2024-01-24 15:27:10,093] [INFO] Running command: fastANI --query /var/lib/cwl/stg093de53c-c6a9-4037-af8f-143e03ae0eb7/GCF_004524855.1_ASM452485v1_genomic.fna.gz --refList GCF_004524855.1_ASM452485v1_genomic.fna/target_genomes.txt --output GCF_004524855.1_ASM452485v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:27:38,889] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:38,889] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc86b57d4-0afc-4c00-afde-e6a71f25bbee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:27:38,889] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc86b57d4-0afc-4c00-afde-e6a71f25bbee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:27:38,899] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 15:27:38,899] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 15:27:38,900] [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 pallida	strain=7MH5	GCA_004524855.1	2547399	2547399	type	True	100.0	3462	3462	95	inconclusive
Paraburkholderia oxyphila	strain=NBRC 105797	GCA_000685075.1	614212	614212	type	True	95.3146	2510	3462	95	inconclusive
Paraburkholderia silviterrae	strain=4M-K11	GCA_004353915.1	2528715	2528715	type	True	93.4544	2388	3462	95	below_threshold
Paraburkholderia sacchari	strain=LMG 19450	GCA_902833715.1	159450	159450	type	True	88.64	1728	3462	95	below_threshold
Paraburkholderia sacchari	strain=LMG 19450	GCA_000785435.2	159450	159450	type	True	88.6199	1731	3462	95	below_threshold
Paraburkholderia heleia	strain=NBRC 101817	GCA_000739775.1	634127	634127	type	True	85.4033	1544	3462	95	below_threshold
Paraburkholderia guartelaensis	strain=CNPSo 3008	GCA_004353905.1	2546446	2546446	type	True	85.3121	1713	3462	95	below_threshold
Paraburkholderia acidiphila	strain=7Q-K02	GCA_009789655.1	2571747	2571747	type	True	85.2731	1686	3462	95	below_threshold
Burkholderia perseverans	strain=INN12	GCA_022870505.1	2615214	2615214	type	True	81.3136	1167	3462	95	below_threshold
Paraburkholderia podalyriae	strain=WC7.3b	GCA_014397785.1	1938811	1938811	type	True	81.1509	1229	3462	95	below_threshold
Burkholderia anthina	strain=DSM 16086	GCA_016836725.1	179879	179879	suspected-type	True	81.1293	1230	3462	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:27:38,904] [INFO] DFAST Taxonomy check result was written to GCF_004524855.1_ASM452485v1_genomic.fna/tc_result.tsv
[2024-01-24 15:27:38,904] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:27:38,904] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:27:38,904] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc86b57d4-0afc-4c00-afde-e6a71f25bbee/dqc_reference/checkm_data
[2024-01-24 15:27:38,906] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:27:39,007] [INFO] Task started: CheckM
[2024-01-24 15:27:39,007] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004524855.1_ASM452485v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004524855.1_ASM452485v1_genomic.fna/checkm_input GCF_004524855.1_ASM452485v1_genomic.fna/checkm_result
[2024-01-24 15:29:14,038] [INFO] Task succeeded: CheckM
[2024-01-24 15:29:14,040] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:29:14,068] [INFO] ===== Completeness check finished =====
[2024-01-24 15:29:14,068] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:29:14,070] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004524855.1_ASM452485v1_genomic.fna/markers.fasta)
[2024-01-24 15:29:14,070] [INFO] Task started: Blastn
[2024-01-24 15:29:14,070] [INFO] Running command: blastn -query GCF_004524855.1_ASM452485v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc86b57d4-0afc-4c00-afde-e6a71f25bbee/dqc_reference/reference_markers_gtdb.fasta -out GCF_004524855.1_ASM452485v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:29:16,142] [INFO] Task succeeded: Blastn
[2024-01-24 15:29:16,146] [INFO] Selected 11 target genomes.
[2024-01-24 15:29:16,146] [INFO] Target genome list was writen to GCF_004524855.1_ASM452485v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:29:16,155] [INFO] Task started: fastANI
[2024-01-24 15:29:16,155] [INFO] Running command: fastANI --query /var/lib/cwl/stg093de53c-c6a9-4037-af8f-143e03ae0eb7/GCF_004524855.1_ASM452485v1_genomic.fna.gz --refList GCF_004524855.1_ASM452485v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004524855.1_ASM452485v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:29:40,649] [INFO] Task succeeded: fastANI
[2024-01-24 15:29:40,669] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:29:40,669] [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_000685075.1	s__Paraburkholderia oxyphila	95.3037	2512	3462	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	95.32	95.32	0.74	0.74	2	conclusive
GCF_004353915.1	s__Paraburkholderia sp004353915	93.4517	2389	3462	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902859945.1	s__Paraburkholderia caffeinitolerans	88.8379	1808	3462	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	99.86	99.86	0.95	0.95	2	-
GCF_000785435.2	s__Paraburkholderia sacchari	88.6419	1729	3462	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	98.05	96.11	0.93	0.86	3	-
GCF_002917095.1	s__Paraburkholderia eburnea	86.0778	1578	3462	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	99.11	98.22	0.96	0.92	3	-
GCF_003096715.1	s__Paraburkholderia silvatlantica	85.5343	1541	3462	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.5542	99.65	99.23	0.96	0.92	5	-
GCF_000739775.1	s__Paraburkholderia heleia	85.4167	1542	3462	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.5542	N/A	N/A	N/A	N/A	1	-
GCF_003268775.1	s__Paraburkholderia unamae	85.3176	1709	3462	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	98.69	98.69	0.91	0.91	2	-
GCF_004353905.1	s__Paraburkholderia guartelaensis	85.3008	1714	3462	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009789655.1	s__Paraburkholderia acidiphila	85.2614	1682	3462	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000685035.1	s__Paraburkholderia ferrariae	84.8307	1479	3462	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 15:29:40,671] [INFO] GTDB search result was written to GCF_004524855.1_ASM452485v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:29:40,672] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:29:40,675] [INFO] DFAST_QC result json was written to GCF_004524855.1_ASM452485v1_genomic.fna/dqc_result.json
[2024-01-24 15:29:40,675] [INFO] DFAST_QC completed!
[2024-01-24 15:29:40,675] [INFO] Total running time: 0h3m8s