[2024-01-24 12:15:18,808] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:15:18,810] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:15:18,810] [INFO] DQC Reference Directory: /var/lib/cwl/stgd92f005e-4341-4fd3-9593-8901456e6125/dqc_reference
[2024-01-24 12:15:20,085] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:15:20,086] [INFO] Task started: Prodigal
[2024-01-24 12:15:20,087] [INFO] Running command: gunzip -c /var/lib/cwl/stg5a3793a5-4c88-424b-b5b8-b8dcb3acd0d6/GCF_902833685.1_ASM90283368v1_genomic.fna.gz | prodigal -d GCF_902833685.1_ASM90283368v1_genomic.fna/cds.fna -a GCF_902833685.1_ASM90283368v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:15:54,907] [INFO] Task succeeded: Prodigal
[2024-01-24 12:15:54,908] [INFO] Task started: HMMsearch
[2024-01-24 12:15:54,908] [INFO] Running command: hmmsearch --tblout GCF_902833685.1_ASM90283368v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd92f005e-4341-4fd3-9593-8901456e6125/dqc_reference/reference_markers.hmm GCF_902833685.1_ASM90283368v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:15:55,324] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:15:55,325] [INFO] Found 6/6 markers.
[2024-01-24 12:15:55,413] [INFO] Query marker FASTA was written to GCF_902833685.1_ASM90283368v1_genomic.fna/markers.fasta
[2024-01-24 12:15:55,414] [INFO] Task started: Blastn
[2024-01-24 12:15:55,414] [INFO] Running command: blastn -query GCF_902833685.1_ASM90283368v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd92f005e-4341-4fd3-9593-8901456e6125/dqc_reference/reference_markers.fasta -out GCF_902833685.1_ASM90283368v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:56,386] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:56,389] [INFO] Selected 10 target genomes.
[2024-01-24 12:15:56,389] [INFO] Target genome list was writen to GCF_902833685.1_ASM90283368v1_genomic.fna/target_genomes.txt
[2024-01-24 12:15:56,394] [INFO] Task started: fastANI
[2024-01-24 12:15:56,394] [INFO] Running command: fastANI --query /var/lib/cwl/stg5a3793a5-4c88-424b-b5b8-b8dcb3acd0d6/GCF_902833685.1_ASM90283368v1_genomic.fna.gz --refList GCF_902833685.1_ASM90283368v1_genomic.fna/target_genomes.txt --output GCF_902833685.1_ASM90283368v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:16:25,975] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:25,976] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd92f005e-4341-4fd3-9593-8901456e6125/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:16:25,977] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd92f005e-4341-4fd3-9593-8901456e6125/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:16:25,993] [INFO] Found 10 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 12:16:25,993] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 12:16:25,993] [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 hospita	strain=LMG 20598	GCA_902833685.1	169430	169430	type	True	100.0	3686	3693	95	inconclusive
Paraburkholderia hospita	strain=LMG 20598	GCA_900108355.1	169430	169430	type	True	99.9721	3606	3693	95	inconclusive
Paraburkholderia hospita	strain=DSM 17164	GCA_002902965.1	169430	169430	type	True	99.7797	3480	3693	95	inconclusive
Paraburkholderia terrae	strain=NBRC 100964	GCA_000739835.1	311230	311230	type	True	95.2298	2627	3693	95	inconclusive
Paraburkholderia terrae	strain=DSM 17804	GCA_002902925.1	311230	311230	type	True	95.198	2724	3693	95	inconclusive
Paraburkholderia azotifigens	strain=NF 2-5-3	GCA_007995085.1	2057004	2057004	type	True	87.9734	2324	3693	95	below_threshold
Paraburkholderia gardini	strain=LMG 32171	GCA_907164575.1	2823469	2823469	type	True	82.393	1249	3693	95	below_threshold
Paraburkholderia podalyriae	strain=WC7.3b	GCA_014397785.1	1938811	1938811	type	True	82.2535	1445	3693	95	below_threshold
Paraburkholderia saeva	strain=LMG 31841	GCA_907164555.1	2777537	2777537	type	True	82.2026	1270	3693	95	below_threshold
Paraburkholderia kirstenboschensis	strain=KB15	GCA_001636975.1	1245436	1245436	type	True	81.499	1190	3693	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:16:25,996] [INFO] DFAST Taxonomy check result was written to GCF_902833685.1_ASM90283368v1_genomic.fna/tc_result.tsv
[2024-01-24 12:16:25,996] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:16:25,996] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:16:25,997] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd92f005e-4341-4fd3-9593-8901456e6125/dqc_reference/checkm_data
[2024-01-24 12:16:25,997] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:16:26,098] [INFO] Task started: CheckM
[2024-01-24 12:16:26,098] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_902833685.1_ASM90283368v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_902833685.1_ASM90283368v1_genomic.fna/checkm_input GCF_902833685.1_ASM90283368v1_genomic.fna/checkm_result
[2024-01-24 12:18:02,644] [INFO] Task succeeded: CheckM
[2024-01-24 12:18:02,645] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:18:02,674] [INFO] ===== Completeness check finished =====
[2024-01-24 12:18:02,674] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:18:02,675] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_902833685.1_ASM90283368v1_genomic.fna/markers.fasta)
[2024-01-24 12:18:02,675] [INFO] Task started: Blastn
[2024-01-24 12:18:02,675] [INFO] Running command: blastn -query GCF_902833685.1_ASM90283368v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd92f005e-4341-4fd3-9593-8901456e6125/dqc_reference/reference_markers_gtdb.fasta -out GCF_902833685.1_ASM90283368v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:18:04,506] [INFO] Task succeeded: Blastn
[2024-01-24 12:18:04,509] [INFO] Selected 6 target genomes.
[2024-01-24 12:18:04,509] [INFO] Target genome list was writen to GCF_902833685.1_ASM90283368v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:18:04,513] [INFO] Task started: fastANI
[2024-01-24 12:18:04,514] [INFO] Running command: fastANI --query /var/lib/cwl/stg5a3793a5-4c88-424b-b5b8-b8dcb3acd0d6/GCF_902833685.1_ASM90283368v1_genomic.fna.gz --refList GCF_902833685.1_ASM90283368v1_genomic.fna/target_genomes_gtdb.txt --output GCF_902833685.1_ASM90283368v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:18:30,179] [INFO] Task succeeded: fastANI
[2024-01-24 12:18:30,190] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:18:30,191] [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_002902965.1	s__Paraburkholderia hospita	99.7747	3481	3693	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.2599	98.45	97.70	0.87	0.82	14	conclusive
GCF_002902925.1	s__Paraburkholderia terrae	95.2128	2722	3693	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.2599	98.84	97.67	0.92	0.83	3	-
GCF_013426915.1	s__Paraburkholderia sp013426915	93.9445	2697	3693	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013426895.1	s__Paraburkholderia sp013426895	92.7922	2536	3693	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002902945.1	s__Paraburkholderia caribensis	92.7698	2363	3693	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	98.86	96.01	0.91	0.80	9	-
GCF_017104715.1	s__Paraburkholderia sp017104715	88.4674	2349	3693	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 12:18:30,192] [INFO] GTDB search result was written to GCF_902833685.1_ASM90283368v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:18:30,193] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:18:30,196] [INFO] DFAST_QC result json was written to GCF_902833685.1_ASM90283368v1_genomic.fna/dqc_result.json
[2024-01-24 12:18:30,196] [INFO] DFAST_QC completed!
[2024-01-24 12:18:30,196] [INFO] Total running time: 0h3m11s