[2024-01-25 19:56:50,415] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:56:50,416] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:56:50,417] [INFO] DQC Reference Directory: /var/lib/cwl/stgfab9da94-ccb3-487c-938b-d5b72461295e/dqc_reference
[2024-01-25 19:56:51,553] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:56:51,554] [INFO] Task started: Prodigal
[2024-01-25 19:56:51,554] [INFO] Running command: gunzip -c /var/lib/cwl/stg5ddcdaae-e2f0-4156-ae99-04e8d3cc1e90/GCF_002902925.1_ASM290292v1_genomic.fna.gz | prodigal -d GCF_002902925.1_ASM290292v1_genomic.fna/cds.fna -a GCF_002902925.1_ASM290292v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:57:21,602] [INFO] Task succeeded: Prodigal
[2024-01-25 19:57:21,602] [INFO] Task started: HMMsearch
[2024-01-25 19:57:21,602] [INFO] Running command: hmmsearch --tblout GCF_002902925.1_ASM290292v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfab9da94-ccb3-487c-938b-d5b72461295e/dqc_reference/reference_markers.hmm GCF_002902925.1_ASM290292v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:57:22,095] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:57:22,096] [INFO] Found 6/6 markers.
[2024-01-25 19:57:22,182] [INFO] Query marker FASTA was written to GCF_002902925.1_ASM290292v1_genomic.fna/markers.fasta
[2024-01-25 19:57:22,182] [INFO] Task started: Blastn
[2024-01-25 19:57:22,182] [INFO] Running command: blastn -query GCF_002902925.1_ASM290292v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfab9da94-ccb3-487c-938b-d5b72461295e/dqc_reference/reference_markers.fasta -out GCF_002902925.1_ASM290292v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:57:23,049] [INFO] Task succeeded: Blastn
[2024-01-25 19:57:23,051] [INFO] Selected 10 target genomes.
[2024-01-25 19:57:23,052] [INFO] Target genome list was writen to GCF_002902925.1_ASM290292v1_genomic.fna/target_genomes.txt
[2024-01-25 19:57:23,055] [INFO] Task started: fastANI
[2024-01-25 19:57:23,055] [INFO] Running command: fastANI --query /var/lib/cwl/stg5ddcdaae-e2f0-4156-ae99-04e8d3cc1e90/GCF_002902925.1_ASM290292v1_genomic.fna.gz --refList GCF_002902925.1_ASM290292v1_genomic.fna/target_genomes.txt --output GCF_002902925.1_ASM290292v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:57:55,030] [INFO] Task succeeded: fastANI
[2024-01-25 19:57:55,030] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfab9da94-ccb3-487c-938b-d5b72461295e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:57:55,031] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfab9da94-ccb3-487c-938b-d5b72461295e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:57:55,038] [INFO] Found 10 fastANI hits (5 hits with ANI > threshold)
[2024-01-25 19:57:55,038] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-25 19:57:55,038] [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=DSM 17804	GCA_002902925.1	311230	311230	type	True	100.0	3353	3353	95	inconclusive
Paraburkholderia terrae	strain=NBRC 100964	GCA_000739835.1	311230	311230	type	True	99.9381	3171	3353	95	inconclusive
Paraburkholderia hospita	strain=DSM 17164	GCA_002902965.1	169430	169430	type	True	95.2662	2756	3353	95	inconclusive
Paraburkholderia hospita	strain=LMG 20598	GCA_902833685.1	169430	169430	type	True	95.2636	2714	3353	95	inconclusive
Paraburkholderia hospita	strain=LMG 20598	GCA_900108355.1	169430	169430	type	True	95.2567	2698	3353	95	inconclusive
Paraburkholderia azotifigens	strain=NF 2-5-3	GCA_007995085.1	2057004	2057004	type	True	87.9549	2272	3353	95	below_threshold
Paraburkholderia flava	strain=LD6	GCA_004359985.1	2547393	2547393	type	True	82.6297	1340	3353	95	below_threshold
Paraburkholderia gardini	strain=LMG 32171	GCA_907164575.1	2823469	2823469	type	True	82.4679	1257	3353	95	below_threshold
Paraburkholderia podalyriae	strain=WC7.3b	GCA_014397785.1	1938811	1938811	type	True	82.238	1405	3353	95	below_threshold
Paraburkholderia saeva	strain=LMG 31841	GCA_907164555.1	2777537	2777537	type	True	82.2357	1280	3353	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:57:55,039] [INFO] DFAST Taxonomy check result was written to GCF_002902925.1_ASM290292v1_genomic.fna/tc_result.tsv
[2024-01-25 19:57:55,040] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:57:55,040] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:57:55,040] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfab9da94-ccb3-487c-938b-d5b72461295e/dqc_reference/checkm_data
[2024-01-25 19:57:55,041] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:57:55,132] [INFO] Task started: CheckM
[2024-01-25 19:57:55,132] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002902925.1_ASM290292v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002902925.1_ASM290292v1_genomic.fna/checkm_input GCF_002902925.1_ASM290292v1_genomic.fna/checkm_result
[2024-01-25 19:59:24,935] [INFO] Task succeeded: CheckM
[2024-01-25 19:59:24,936] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:59:24,963] [INFO] ===== Completeness check finished =====
[2024-01-25 19:59:24,963] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:59:24,964] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002902925.1_ASM290292v1_genomic.fna/markers.fasta)
[2024-01-25 19:59:24,964] [INFO] Task started: Blastn
[2024-01-25 19:59:24,964] [INFO] Running command: blastn -query GCF_002902925.1_ASM290292v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfab9da94-ccb3-487c-938b-d5b72461295e/dqc_reference/reference_markers_gtdb.fasta -out GCF_002902925.1_ASM290292v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:59:26,649] [INFO] Task succeeded: Blastn
[2024-01-25 19:59:26,652] [INFO] Selected 6 target genomes.
[2024-01-25 19:59:26,652] [INFO] Target genome list was writen to GCF_002902925.1_ASM290292v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:59:26,661] [INFO] Task started: fastANI
[2024-01-25 19:59:26,661] [INFO] Running command: fastANI --query /var/lib/cwl/stg5ddcdaae-e2f0-4156-ae99-04e8d3cc1e90/GCF_002902925.1_ASM290292v1_genomic.fna.gz --refList GCF_002902925.1_ASM290292v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002902925.1_ASM290292v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:59:56,841] [INFO] Task succeeded: fastANI
[2024-01-25 19:59:56,846] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:59:56,846] [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	100.0	3353	3353	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	95.2594	2756	3353	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	94.3793	2581	3353	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	92.9033	2545	3353	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	92.7731	2382	3353	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	88.5829	2317	3353	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:59:56,847] [INFO] GTDB search result was written to GCF_002902925.1_ASM290292v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:59:56,848] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:59:56,850] [INFO] DFAST_QC result json was written to GCF_002902925.1_ASM290292v1_genomic.fna/dqc_result.json
[2024-01-25 19:59:56,851] [INFO] DFAST_QC completed!
[2024-01-25 19:59:56,851] [INFO] Total running time: 0h3m6s