[2024-01-24 13:55:41,182] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:55:41,186] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:55:41,187] [INFO] DQC Reference Directory: /var/lib/cwl/stg9087f221-9fb7-433e-ba93-75ee62fee5c9/dqc_reference
[2024-01-24 13:55:42,534] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:55:42,535] [INFO] Task started: Prodigal
[2024-01-24 13:55:42,535] [INFO] Running command: gunzip -c /var/lib/cwl/stgdde153ba-3c8d-49c9-89be-7e31fdfabc4d/GCF_009455625.1_ASM945562v1_genomic.fna.gz | prodigal -d GCF_009455625.1_ASM945562v1_genomic.fna/cds.fna -a GCF_009455625.1_ASM945562v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:55:58,080] [INFO] Task succeeded: Prodigal
[2024-01-24 13:55:58,081] [INFO] Task started: HMMsearch
[2024-01-24 13:55:58,081] [INFO] Running command: hmmsearch --tblout GCF_009455625.1_ASM945562v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9087f221-9fb7-433e-ba93-75ee62fee5c9/dqc_reference/reference_markers.hmm GCF_009455625.1_ASM945562v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:55:58,373] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:55:58,374] [INFO] Found 6/6 markers.
[2024-01-24 13:55:58,408] [INFO] Query marker FASTA was written to GCF_009455625.1_ASM945562v1_genomic.fna/markers.fasta
[2024-01-24 13:55:58,408] [INFO] Task started: Blastn
[2024-01-24 13:55:58,409] [INFO] Running command: blastn -query GCF_009455625.1_ASM945562v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9087f221-9fb7-433e-ba93-75ee62fee5c9/dqc_reference/reference_markers.fasta -out GCF_009455625.1_ASM945562v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:55:59,222] [INFO] Task succeeded: Blastn
[2024-01-24 13:55:59,225] [INFO] Selected 23 target genomes.
[2024-01-24 13:55:59,226] [INFO] Target genome list was writen to GCF_009455625.1_ASM945562v1_genomic.fna/target_genomes.txt
[2024-01-24 13:55:59,241] [INFO] Task started: fastANI
[2024-01-24 13:55:59,241] [INFO] Running command: fastANI --query /var/lib/cwl/stgdde153ba-3c8d-49c9-89be-7e31fdfabc4d/GCF_009455625.1_ASM945562v1_genomic.fna.gz --refList GCF_009455625.1_ASM945562v1_genomic.fna/target_genomes.txt --output GCF_009455625.1_ASM945562v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:56:28,093] [INFO] Task succeeded: fastANI
[2024-01-24 13:56:28,093] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9087f221-9fb7-433e-ba93-75ee62fee5c9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:56:28,094] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9087f221-9fb7-433e-ba93-75ee62fee5c9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:56:28,115] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:56:28,115] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:56:28,115] [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 bonniea	strain=BbQS859	GCA_009455625.1	2152891	2152891	type	True	100.0	1364	1365	95	conclusive
Paraburkholderia hayleyella	strain=BhQS11	GCA_009455685.1	2152889	2152889	type	True	81.1782	850	1365	95	below_threshold
Paraburkholderia ribeironis	strain=STM 7296	GCA_900019265.2	1247936	1247936	type	True	79.0903	517	1365	95	below_threshold
Paraburkholderia lacunae	strain=S27	GCA_003353175.1	2211104	2211104	type	True	79.0109	560	1365	95	below_threshold
Paraburkholderia terricola	strain=LMG 20594	GCA_902833815.1	169427	169427	type	True	78.9598	571	1365	95	below_threshold
Paraburkholderia graminis	strain=LMG 18924	GCA_902859785.1	60548	60548	type	True	78.9304	519	1365	95	below_threshold
Paraburkholderia phytofirmans	strain=PsJN	GCA_000020125.1	261302	261302	type	True	78.9234	586	1365	95	below_threshold
Paraburkholderia kirstenboschensis	strain=KB15	GCA_001636975.1	1245436	1245436	type	True	78.9226	424	1365	95	below_threshold
Paraburkholderia gardini	strain=LMG 32171	GCA_907164575.1	2823469	2823469	type	True	78.8946	519	1365	95	below_threshold
Paraburkholderia terricola	strain=LMG 20594	GCA_900142195.1	169427	169427	type	True	78.8354	570	1365	95	below_threshold
Paraburkholderia panacisoli	strain=DCY113	GCA_008369935.1	2603818	2603818	type	True	78.816	552	1365	95	below_threshold
Paraburkholderia graminis	strain=C4D1M	GCA_000172415.1	60548	60548	type	True	78.8137	502	1365	95	below_threshold
Paraburkholderia nemoris	strain=LMG 31836	GCA_905221015.1	2793076	2793076	type	True	78.7926	564	1365	95	below_threshold
Paraburkholderia saeva	strain=LMG 31841	GCA_907164555.1	2777537	2777537	type	True	78.7903	516	1365	95	below_threshold
Paraburkholderia hospita	strain=DSM 17164	GCA_002902965.1	169430	169430	type	True	78.7596	543	1365	95	below_threshold
Paraburkholderia domus	strain=LMG 31832	GCA_905220705.1	2793075	2793075	type	True	78.6925	562	1365	95	below_threshold
Paraburkholderia azotifigens	strain=NF 2-5-3	GCA_007995085.1	2057004	2057004	type	True	78.6748	531	1365	95	below_threshold
Paraburkholderia hospita	strain=LMG 20598	GCA_902833685.1	169430	169430	type	True	78.5485	531	1365	95	below_threshold
Paraburkholderia hospita	strain=LMG 20598	GCA_900108355.1	169430	169430	type	True	78.5466	536	1365	95	below_threshold
Paraburkholderia sabiae	strain=LMG 24235	GCA_904848645.1	273251	273251	type	True	78.5441	528	1365	95	below_threshold
Paraburkholderia bannensis	strain=NBRC 103871	GCA_000685015.1	765414	765414	type	True	78.2188	467	1365	95	below_threshold
Caballeronia udeis		GCA_001544555.2	1232866	1232866	type	True	77.4878	402	1365	95	below_threshold
Duganella phyllosphaerae	strain=T54	GCA_001758785.1	762836	762836	type	True	76.1484	137	1365	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:56:28,117] [INFO] DFAST Taxonomy check result was written to GCF_009455625.1_ASM945562v1_genomic.fna/tc_result.tsv
[2024-01-24 13:56:28,118] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:56:28,118] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:56:28,118] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9087f221-9fb7-433e-ba93-75ee62fee5c9/dqc_reference/checkm_data
[2024-01-24 13:56:28,119] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:56:28,159] [INFO] Task started: CheckM
[2024-01-24 13:56:28,159] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009455625.1_ASM945562v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009455625.1_ASM945562v1_genomic.fna/checkm_input GCF_009455625.1_ASM945562v1_genomic.fna/checkm_result
[2024-01-24 13:57:13,324] [INFO] Task succeeded: CheckM
[2024-01-24 13:57:13,325] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:57:13,358] [INFO] ===== Completeness check finished =====
[2024-01-24 13:57:13,359] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:57:13,359] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009455625.1_ASM945562v1_genomic.fna/markers.fasta)
[2024-01-24 13:57:13,359] [INFO] Task started: Blastn
[2024-01-24 13:57:13,359] [INFO] Running command: blastn -query GCF_009455625.1_ASM945562v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9087f221-9fb7-433e-ba93-75ee62fee5c9/dqc_reference/reference_markers_gtdb.fasta -out GCF_009455625.1_ASM945562v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:14,709] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:14,713] [INFO] Selected 21 target genomes.
[2024-01-24 13:57:14,713] [INFO] Target genome list was writen to GCF_009455625.1_ASM945562v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:57:14,739] [INFO] Task started: fastANI
[2024-01-24 13:57:14,739] [INFO] Running command: fastANI --query /var/lib/cwl/stgdde153ba-3c8d-49c9-89be-7e31fdfabc4d/GCF_009455625.1_ASM945562v1_genomic.fna.gz --refList GCF_009455625.1_ASM945562v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009455625.1_ASM945562v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:57:43,623] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:43,642] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:57:43,642] [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_009455625.1	s__Paraburkholderia bonniea	100.0	1364	1365	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009455685.1	s__Paraburkholderia hayleyella	81.1108	850	1365	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003368325.1	s__Paraburkholderia caffeinilytica	79.0845	561	1365	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	100.00	100.00	1.00	1.00	3	-
GCF_000739735.1	s__Paraburkholderia ginsengisoli	79.0568	551	1365	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900996235.1	s__Paraburkholderia sp900996235	79.0495	546	1365	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902859915.1	s__Paraburkholderia ultramafica	79.0429	564	1365	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003353175.1	s__Paraburkholderia lacunae	79.011	560	1365	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900141745.1	s__Paraburkholderia phenazinium_B	78.9934	517	1365	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000020125.1	s__Paraburkholderia phytofirmans	78.9461	586	1365	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	95.77	95.72	0.82	0.81	3	-
GCF_003610295.1	s__Paraburkholderia sp003610295	78.8839	559	1365	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005503145.1	s__Paraburkholderia sp005503145	78.8745	555	1365	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003269035.1	s__Paraburkholderia bryophila	78.848	575	1365	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	98.31	96.63	0.94	0.89	3	-
GCF_900142195.1	s__Paraburkholderia terricola	78.847	568	1365	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	99.26	98.60	0.95	0.92	6	-
GCF_900996225.1	s__Paraburkholderia sp900996225	78.8389	553	1365	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002902965.1	s__Paraburkholderia hospita	78.7998	543	1365	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.2599	98.45	97.70	0.87	0.82	14	-
GCF_012275575.1	s__Paraburkholderia sp012275575	78.7878	516	1365	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017104565.1	s__Paraburkholderia sp017104565	78.5439	522	1365	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000472445.1	s__Paraburkholderia sp000472445	78.4973	523	1365	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000687455.2	s__Burkholderia sp000687455	78.1637	395	1365	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011493005.1	s__Caballeronia sp011493005	77.905	394	1365	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia	95.0	99.62	99.62	0.93	0.93	2	-
GCF_002220365.1	s__Caballeronia sordidicola_C	77.6401	373	1365	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:57:43,644] [INFO] GTDB search result was written to GCF_009455625.1_ASM945562v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:57:43,645] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:57:43,649] [INFO] DFAST_QC result json was written to GCF_009455625.1_ASM945562v1_genomic.fna/dqc_result.json
[2024-01-24 13:57:43,650] [INFO] DFAST_QC completed!
[2024-01-24 13:57:43,650] [INFO] Total running time: 0h2m2s