[2024-01-24 13:37:05,127] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:37:05,129] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:37:05,130] [INFO] DQC Reference Directory: /var/lib/cwl/stgd579c979-654b-4290-b191-f959d070c1c5/dqc_reference
[2024-01-24 13:37:06,547] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:37:06,548] [INFO] Task started: Prodigal
[2024-01-24 13:37:06,548] [INFO] Running command: gunzip -c /var/lib/cwl/stge10dae20-e191-476f-8181-52e131d21ebc/GCF_902833865.1_ASM90283386v1_genomic.fna.gz | prodigal -d GCF_902833865.1_ASM90283386v1_genomic.fna/cds.fna -a GCF_902833865.1_ASM90283386v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:37:32,860] [INFO] Task succeeded: Prodigal
[2024-01-24 13:37:32,861] [INFO] Task started: HMMsearch
[2024-01-24 13:37:32,861] [INFO] Running command: hmmsearch --tblout GCF_902833865.1_ASM90283386v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd579c979-654b-4290-b191-f959d070c1c5/dqc_reference/reference_markers.hmm GCF_902833865.1_ASM90283386v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:37:33,262] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:37:33,263] [INFO] Found 6/6 markers.
[2024-01-24 13:37:33,325] [INFO] Query marker FASTA was written to GCF_902833865.1_ASM90283386v1_genomic.fna/markers.fasta
[2024-01-24 13:37:33,325] [INFO] Task started: Blastn
[2024-01-24 13:37:33,326] [INFO] Running command: blastn -query GCF_902833865.1_ASM90283386v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd579c979-654b-4290-b191-f959d070c1c5/dqc_reference/reference_markers.fasta -out GCF_902833865.1_ASM90283386v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:34,330] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:34,333] [INFO] Selected 13 target genomes.
[2024-01-24 13:37:34,333] [INFO] Target genome list was writen to GCF_902833865.1_ASM90283386v1_genomic.fna/target_genomes.txt
[2024-01-24 13:37:34,350] [INFO] Task started: fastANI
[2024-01-24 13:37:34,351] [INFO] Running command: fastANI --query /var/lib/cwl/stge10dae20-e191-476f-8181-52e131d21ebc/GCF_902833865.1_ASM90283386v1_genomic.fna.gz --refList GCF_902833865.1_ASM90283386v1_genomic.fna/target_genomes.txt --output GCF_902833865.1_ASM90283386v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:38:03,406] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:03,406] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd579c979-654b-4290-b191-f959d070c1c5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:38:03,406] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd579c979-654b-4290-b191-f959d070c1c5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:38:03,423] [INFO] Found 13 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:38:03,424] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:38:03,424] [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 tropica	strain=LMG 22274	GCA_902833865.1	92647	92647	type	True	100.0	2841	2846	95	conclusive
Paraburkholderia tropica	strain=Ppe8	GCA_002071575.1	92647	92647	type	True	99.9923	2835	2846	95	conclusive
Paraburkholderia tropica	strain=LMG 22274	GCA_900109265.1	92647	92647	type	True	99.9891	2824	2846	95	conclusive
Paraburkholderia eburnea	strain=JCM 18070	GCA_002917095.1	1189126	1189126	type	True	86.6768	1645	2846	95	below_threshold
Paraburkholderia bannensis	strain=NBRC 103871	GCA_000685015.1	765414	765414	type	True	86.2935	1818	2846	95	below_threshold
Paraburkholderia oxyphila	strain=NBRC 105797	GCA_000685075.1	614212	614212	type	True	86.0543	1625	2846	95	below_threshold
Paraburkholderia silviterrae	strain=4M-K11	GCA_004353915.1	2528715	2528715	type	True	86.0107	1583	2846	95	below_threshold
Paraburkholderia pallida	strain=7MH5	GCA_004524855.1	2547399	2547399	type	True	86.0056	1665	2846	95	below_threshold
Paraburkholderia acidisoli	strain=DHF22	GCA_009789675.1	2571748	2571748	type	True	85.5531	1747	2846	95	below_threshold
Paraburkholderia guartelaensis	strain=CNPSo 3008	GCA_004353905.1	2546446	2546446	type	True	85.0505	1686	2846	95	below_threshold
Paraburkholderia podalyriae	strain=WC7.3b	GCA_014397785.1	1938811	1938811	type	True	81.6853	1230	2846	95	below_threshold
Paraburkholderia azotifigens	strain=NF 2-5-3	GCA_007995085.1	2057004	2057004	type	True	81.5463	1344	2846	95	below_threshold
Paraburkholderia saeva	strain=LMG 31841	GCA_907164555.1	2777537	2777537	type	True	81.4044	1042	2846	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:38:03,433] [INFO] DFAST Taxonomy check result was written to GCF_902833865.1_ASM90283386v1_genomic.fna/tc_result.tsv
[2024-01-24 13:38:03,434] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:38:03,434] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:38:03,435] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd579c979-654b-4290-b191-f959d070c1c5/dqc_reference/checkm_data
[2024-01-24 13:38:03,436] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:38:03,527] [INFO] Task started: CheckM
[2024-01-24 13:38:03,527] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_902833865.1_ASM90283386v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_902833865.1_ASM90283386v1_genomic.fna/checkm_input GCF_902833865.1_ASM90283386v1_genomic.fna/checkm_result
[2024-01-24 13:39:18,484] [INFO] Task succeeded: CheckM
[2024-01-24 13:39:18,486] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:39:18,512] [INFO] ===== Completeness check finished =====
[2024-01-24 13:39:18,513] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:39:18,513] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_902833865.1_ASM90283386v1_genomic.fna/markers.fasta)
[2024-01-24 13:39:18,514] [INFO] Task started: Blastn
[2024-01-24 13:39:18,514] [INFO] Running command: blastn -query GCF_902833865.1_ASM90283386v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd579c979-654b-4290-b191-f959d070c1c5/dqc_reference/reference_markers_gtdb.fasta -out GCF_902833865.1_ASM90283386v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:39:20,641] [INFO] Task succeeded: Blastn
[2024-01-24 13:39:20,646] [INFO] Selected 13 target genomes.
[2024-01-24 13:39:20,646] [INFO] Target genome list was writen to GCF_902833865.1_ASM90283386v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:39:20,661] [INFO] Task started: fastANI
[2024-01-24 13:39:20,662] [INFO] Running command: fastANI --query /var/lib/cwl/stge10dae20-e191-476f-8181-52e131d21ebc/GCF_902833865.1_ASM90283386v1_genomic.fna.gz --refList GCF_902833865.1_ASM90283386v1_genomic.fna/target_genomes_gtdb.txt --output GCF_902833865.1_ASM90283386v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:39:48,095] [INFO] Task succeeded: fastANI
[2024-01-24 13:39:48,107] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:39:48,107] [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_900109265.1	s__Paraburkholderia tropica	99.9891	2824	2846	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	99.07	95.97	0.93	0.85	14	conclusive
GCF_002917095.1	s__Paraburkholderia eburnea	86.6853	1643	2846	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	99.11	98.22	0.96	0.92	3	-
GCF_017104965.1	s__Paraburkholderia sp017104965	86.6561	1819	2846	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000685015.1	s__Paraburkholderia bannensis	86.3285	1813	2846	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011753055.1	s__Paraburkholderia sp011753055	86.1517	1772	2846	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000685075.1	s__Paraburkholderia oxyphila	86.095	1620	2846	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	95.32	95.32	0.74	0.74	2	-
GCF_014200455.1	s__Paraburkholderia bannensis_A	85.9762	1747	2846	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	99.99	99.99	0.99	0.99	2	-
GCF_004353915.1	s__Paraburkholderia sp004353915	85.9533	1591	2846	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009789675.1	s__Paraburkholderia acidisoli	85.5401	1749	2846	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003268775.1	s__Paraburkholderia unamae	85.516	1726	2846	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	85.0913	1679	2846	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000739775.1	s__Paraburkholderia heleia	85.0091	1573	2846	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.5542	N/A	N/A	N/A	N/A	1	-
GCF_000739815.1	s__Paraburkholderia mimosarum	84.8352	1462	2846	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	99.63	98.93	0.95	0.86	4	-
--------------------------------------------------------------------------------
[2024-01-24 13:39:48,109] [INFO] GTDB search result was written to GCF_902833865.1_ASM90283386v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:39:48,110] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:39:48,113] [INFO] DFAST_QC result json was written to GCF_902833865.1_ASM90283386v1_genomic.fna/dqc_result.json
[2024-01-24 13:39:48,113] [INFO] DFAST_QC completed!
[2024-01-24 13:39:48,113] [INFO] Total running time: 0h2m43s