[2024-01-24 13:58:11,169] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:58:11,171] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:58:11,172] [INFO] DQC Reference Directory: /var/lib/cwl/stgb3a8a4eb-2c30-441c-827e-330e32f959d1/dqc_reference
[2024-01-24 13:58:12,483] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:58:12,486] [INFO] Task started: Prodigal
[2024-01-24 13:58:12,486] [INFO] Running command: gunzip -c /var/lib/cwl/stga3e96a8d-3a23-48bd-8246-0a57da12b01e/GCF_000739835.1_ASM73983v1_genomic.fna.gz | prodigal -d GCF_000739835.1_ASM73983v1_genomic.fna/cds.fna -a GCF_000739835.1_ASM73983v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:45,642] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:45,643] [INFO] Task started: HMMsearch
[2024-01-24 13:58:45,643] [INFO] Running command: hmmsearch --tblout GCF_000739835.1_ASM73983v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb3a8a4eb-2c30-441c-827e-330e32f959d1/dqc_reference/reference_markers.hmm GCF_000739835.1_ASM73983v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:46,156] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:46,157] [INFO] Found 6/6 markers.
[2024-01-24 13:58:46,235] [INFO] Query marker FASTA was written to GCF_000739835.1_ASM73983v1_genomic.fna/markers.fasta
[2024-01-24 13:58:46,236] [INFO] Task started: Blastn
[2024-01-24 13:58:46,236] [INFO] Running command: blastn -query GCF_000739835.1_ASM73983v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb3a8a4eb-2c30-441c-827e-330e32f959d1/dqc_reference/reference_markers.fasta -out GCF_000739835.1_ASM73983v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:47,181] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:47,184] [INFO] Selected 10 target genomes.
[2024-01-24 13:58:47,185] [INFO] Target genome list was writen to GCF_000739835.1_ASM73983v1_genomic.fna/target_genomes.txt
[2024-01-24 13:58:47,195] [INFO] Task started: fastANI
[2024-01-24 13:58:47,196] [INFO] Running command: fastANI --query /var/lib/cwl/stga3e96a8d-3a23-48bd-8246-0a57da12b01e/GCF_000739835.1_ASM73983v1_genomic.fna.gz --refList GCF_000739835.1_ASM73983v1_genomic.fna/target_genomes.txt --output GCF_000739835.1_ASM73983v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:59:14,853] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:14,854] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb3a8a4eb-2c30-441c-827e-330e32f959d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:59:14,855] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb3a8a4eb-2c30-441c-827e-330e32f959d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:59:14,868] [INFO] Found 10 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 13:59:14,869] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:59:14,869] [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 terrae	strain=NBRC 100964	GCA_000739835.1	311230	311230	type	True	100.0	3175	3190	95	inconclusive
Paraburkholderia terrae	strain=DSM 17804	GCA_002902925.1	311230	311230	type	True	99.9993	3188	3190	95	inconclusive
Paraburkholderia hospita	strain=LMG 20598	GCA_902833685.1	169430	169430	type	True	95.2651	2631	3190	95	inconclusive
Paraburkholderia hospita	strain=LMG 20598	GCA_900108355.1	169430	169430	type	True	95.249	2622	3190	95	inconclusive
Paraburkholderia hospita	strain=DSM 17164	GCA_002902965.1	169430	169430	type	True	95.2467	2646	3190	95	inconclusive
Paraburkholderia azotifigens	strain=NF 2-5-3	GCA_007995085.1	2057004	2057004	type	True	87.9787	2204	3190	95	below_threshold
Paraburkholderia flava	strain=LD6	GCA_004359985.1	2547393	2547393	type	True	82.6064	1294	3190	95	below_threshold
Paraburkholderia gardini	strain=LMG 32171	GCA_907164575.1	2823469	2823469	type	True	82.5685	1209	3190	95	below_threshold
Paraburkholderia podalyriae	strain=WC7.3b	GCA_014397785.1	1938811	1938811	type	True	82.2561	1355	3190	95	below_threshold
Paraburkholderia saeva	strain=LMG 31841	GCA_907164555.1	2777537	2777537	type	True	82.2355	1256	3190	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:59:14,871] [INFO] DFAST Taxonomy check result was written to GCF_000739835.1_ASM73983v1_genomic.fna/tc_result.tsv
[2024-01-24 13:59:14,872] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:59:14,872] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:59:14,873] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb3a8a4eb-2c30-441c-827e-330e32f959d1/dqc_reference/checkm_data
[2024-01-24 13:59:14,874] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:59:14,967] [INFO] Task started: CheckM
[2024-01-24 13:59:14,968] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000739835.1_ASM73983v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000739835.1_ASM73983v1_genomic.fna/checkm_input GCF_000739835.1_ASM73983v1_genomic.fna/checkm_result
[2024-01-24 14:00:46,048] [INFO] Task succeeded: CheckM
[2024-01-24 14:00:46,049] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:00:46,074] [INFO] ===== Completeness check finished =====
[2024-01-24 14:00:46,074] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:00:46,075] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000739835.1_ASM73983v1_genomic.fna/markers.fasta)
[2024-01-24 14:00:46,075] [INFO] Task started: Blastn
[2024-01-24 14:00:46,075] [INFO] Running command: blastn -query GCF_000739835.1_ASM73983v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb3a8a4eb-2c30-441c-827e-330e32f959d1/dqc_reference/reference_markers_gtdb.fasta -out GCF_000739835.1_ASM73983v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:00:47,851] [INFO] Task succeeded: Blastn
[2024-01-24 14:00:47,854] [INFO] Selected 6 target genomes.
[2024-01-24 14:00:47,855] [INFO] Target genome list was writen to GCF_000739835.1_ASM73983v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:00:47,859] [INFO] Task started: fastANI
[2024-01-24 14:00:47,859] [INFO] Running command: fastANI --query /var/lib/cwl/stga3e96a8d-3a23-48bd-8246-0a57da12b01e/GCF_000739835.1_ASM73983v1_genomic.fna.gz --refList GCF_000739835.1_ASM73983v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000739835.1_ASM73983v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:01:09,868] [INFO] Task succeeded: fastANI
[2024-01-24 14:01:09,880] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:01:09,881] [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_002902925.1	s__Paraburkholderia terrae	99.9993	3188	3190	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.2599	98.84	97.67	0.92	0.83	3	conclusive
GCF_002902965.1	s__Paraburkholderia hospita	95.2582	2644	3190	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.2599	98.45	97.70	0.87	0.82	14	-
GCF_013426915.1	s__Paraburkholderia sp013426915	94.4329	2472	3190	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	92.9988	2420	3190	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	92.8949	2269	3190	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	88.6428	2256	3190	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 14:01:09,882] [INFO] GTDB search result was written to GCF_000739835.1_ASM73983v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:01:09,883] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:01:09,888] [INFO] DFAST_QC result json was written to GCF_000739835.1_ASM73983v1_genomic.fna/dqc_result.json
[2024-01-24 14:01:09,888] [INFO] DFAST_QC completed!
[2024-01-24 14:01:09,888] [INFO] Total running time: 0h2m59s