[2024-01-24 14:14:20,432] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:14:20,434] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:14:20,434] [INFO] DQC Reference Directory: /var/lib/cwl/stg8a12a0f4-67f7-4edc-910c-839810657995/dqc_reference
[2024-01-24 14:14:21,712] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:14:21,713] [INFO] Task started: Prodigal
[2024-01-24 14:14:21,713] [INFO] Running command: gunzip -c /var/lib/cwl/stg4acb9a2a-a4cc-44e3-bfe9-7d5993711c96/GCF_009455685.1_ASM945568v1_genomic.fna.gz | prodigal -d GCF_009455685.1_ASM945568v1_genomic.fna/cds.fna -a GCF_009455685.1_ASM945568v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:14:36,092] [INFO] Task succeeded: Prodigal
[2024-01-24 14:14:36,093] [INFO] Task started: HMMsearch
[2024-01-24 14:14:36,093] [INFO] Running command: hmmsearch --tblout GCF_009455685.1_ASM945568v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8a12a0f4-67f7-4edc-910c-839810657995/dqc_reference/reference_markers.hmm GCF_009455685.1_ASM945568v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:14:36,375] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:14:36,377] [INFO] Found 6/6 markers.
[2024-01-24 14:14:36,413] [INFO] Query marker FASTA was written to GCF_009455685.1_ASM945568v1_genomic.fna/markers.fasta
[2024-01-24 14:14:36,413] [INFO] Task started: Blastn
[2024-01-24 14:14:36,413] [INFO] Running command: blastn -query GCF_009455685.1_ASM945568v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8a12a0f4-67f7-4edc-910c-839810657995/dqc_reference/reference_markers.fasta -out GCF_009455685.1_ASM945568v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:37,224] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:37,227] [INFO] Selected 24 target genomes.
[2024-01-24 14:14:37,227] [INFO] Target genome list was writen to GCF_009455685.1_ASM945568v1_genomic.fna/target_genomes.txt
[2024-01-24 14:14:37,239] [INFO] Task started: fastANI
[2024-01-24 14:14:37,239] [INFO] Running command: fastANI --query /var/lib/cwl/stg4acb9a2a-a4cc-44e3-bfe9-7d5993711c96/GCF_009455685.1_ASM945568v1_genomic.fna.gz --refList GCF_009455685.1_ASM945568v1_genomic.fna/target_genomes.txt --output GCF_009455685.1_ASM945568v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:15:08,436] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:08,437] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8a12a0f4-67f7-4edc-910c-839810657995/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:15:08,437] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8a12a0f4-67f7-4edc-910c-839810657995/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:15:08,458] [INFO] Found 24 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:15:08,458] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:15:08,459] [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 hayleyella	strain=BhQS11	GCA_009455685.1	2152889	2152889	type	True	100.0	1372	1374	95	conclusive
Paraburkholderia bonniea	strain=BbQS859	GCA_009455625.1	2152891	2152891	type	True	81.1911	847	1374	95	below_threshold
Paraburkholderia lacunae	strain=S27	GCA_003353175.1	2211104	2211104	type	True	79.2473	557	1374	95	below_threshold
Paraburkholderia fynbosensis	strain=LMG 27177	GCA_902859935.1	1200993	1200993	type	True	79.2231	556	1374	95	below_threshold
Paraburkholderia phytofirmans	strain=PsJN	GCA_000020125.1	261302	261302	type	True	79.1225	575	1374	95	below_threshold
Paraburkholderia ginsengiterrae	strain=DCY85	GCA_001645125.1	1462993	1462993	type	True	79.1038	533	1374	95	below_threshold
Paraburkholderia phenazinium	strain=LMG 2247	GCA_900100735.1	60549	60549	type	True	79.0241	559	1374	95	below_threshold
Paraburkholderia saeva	strain=LMG 31841	GCA_907164555.1	2777537	2777537	type	True	79.011	513	1374	95	below_threshold
Paraburkholderia flava	strain=LD6	GCA_004359985.1	2547393	2547393	type	True	78.9842	517	1374	95	below_threshold
Paraburkholderia ribeironis	strain=STM 7296	GCA_900019265.2	1247936	1247936	type	True	78.9699	524	1374	95	below_threshold
Paraburkholderia hospita	strain=DSM 17164	GCA_002902965.1	169430	169430	type	True	78.9627	539	1374	95	below_threshold
Paraburkholderia caribensis	strain=LMG 18531	GCA_902833515.1	75105	75105	type	True	78.9151	515	1374	95	below_threshold
Paraburkholderia monticola	strain=JC2948	GCA_001580545.1	1399968	1399968	type	True	78.8432	531	1374	95	below_threshold
Paraburkholderia azotifigens	strain=NF 2-5-3	GCA_007995085.1	2057004	2057004	type	True	78.7977	540	1374	95	below_threshold
Paraburkholderia hospita	strain=LMG 20598	GCA_902833685.1	169430	169430	type	True	78.7794	536	1374	95	below_threshold
Paraburkholderia sabiae	strain=LMG 24235	GCA_904848645.1	273251	273251	type	True	78.713	498	1374	95	below_threshold
Paraburkholderia hospita	strain=LMG 20598	GCA_900108355.1	169430	169430	type	True	78.6995	530	1374	95	below_threshold
Paraburkholderia kirstenboschensis	strain=KB15	GCA_001636975.1	1245436	1245436	type	True	78.6294	439	1374	95	below_threshold
Paraburkholderia pallida	strain=7MH5	GCA_004524855.1	2547399	2547399	type	True	78.4811	497	1374	95	below_threshold
Burkholderia ubonensis	strain=LMG 20358	GCA_902833085.1	101571	101571	type	True	78.2732	444	1374	95	below_threshold
Burkholderia stagnalis		GCA_902499155.1	1503054	1503054	type	True	78.2515	445	1374	95	below_threshold
Burkholderia stagnalis	strain=LMG 28156	GCA_902830275.1	1503054	1503054	type	True	78.1761	454	1374	95	below_threshold
Burkholderia ubonensis		GCA_902499185.1	101571	101571	type	True	78.0955	445	1374	95	below_threshold
Ralstonia pseudosolanacearum	strain=LMG 9673	GCA_919586305.1	1310165	1310165	type	True	76.7925	212	1374	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:15:08,460] [INFO] DFAST Taxonomy check result was written to GCF_009455685.1_ASM945568v1_genomic.fna/tc_result.tsv
[2024-01-24 14:15:08,461] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:15:08,461] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:15:08,461] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8a12a0f4-67f7-4edc-910c-839810657995/dqc_reference/checkm_data
[2024-01-24 14:15:08,462] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:15:08,502] [INFO] Task started: CheckM
[2024-01-24 14:15:08,502] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009455685.1_ASM945568v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009455685.1_ASM945568v1_genomic.fna/checkm_input GCF_009455685.1_ASM945568v1_genomic.fna/checkm_result
[2024-01-24 14:15:49,859] [INFO] Task succeeded: CheckM
[2024-01-24 14:15:49,860] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:15:49,877] [INFO] ===== Completeness check finished =====
[2024-01-24 14:15:49,878] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:15:49,878] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009455685.1_ASM945568v1_genomic.fna/markers.fasta)
[2024-01-24 14:15:49,878] [INFO] Task started: Blastn
[2024-01-24 14:15:49,879] [INFO] Running command: blastn -query GCF_009455685.1_ASM945568v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8a12a0f4-67f7-4edc-910c-839810657995/dqc_reference/reference_markers_gtdb.fasta -out GCF_009455685.1_ASM945568v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:51,186] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:51,189] [INFO] Selected 22 target genomes.
[2024-01-24 14:15:51,190] [INFO] Target genome list was writen to GCF_009455685.1_ASM945568v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:15:51,209] [INFO] Task started: fastANI
[2024-01-24 14:15:51,209] [INFO] Running command: fastANI --query /var/lib/cwl/stg4acb9a2a-a4cc-44e3-bfe9-7d5993711c96/GCF_009455685.1_ASM945568v1_genomic.fna.gz --refList GCF_009455685.1_ASM945568v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009455685.1_ASM945568v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:16:20,810] [INFO] Task succeeded: fastANI
[2024-01-24 14:16:20,829] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:16:20,830] [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_009455685.1	s__Paraburkholderia hayleyella	100.0	1372	1374	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_009455625.1	s__Paraburkholderia bonniea	81.149	845	1374	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142845.1	s__Paraburkholderia phenazinium_A	79.2898	567	1374	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003429005.1	s__Paraburkholderia sp003429005	79.2757	513	1374	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	79.2601	555	1374	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900996235.1	s__Paraburkholderia sp900996235	79.2203	533	1374	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	79.2191	518	1374	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	79.214	578	1374	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	95.77	95.72	0.82	0.81	3	-
GCF_012689525.1	s__Paraburkholderia aromaticivorans_A	79.1949	582	1374	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000739735.1	s__Paraburkholderia ginsengisoli	79.1939	567	1374	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004365055.1	s__Paraburkholderia phenazinium_C	79.1789	505	1374	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	98.83	98.79	0.90	0.89	3	-
GCF_001645125.1	s__Paraburkholderia ginsengiterrae	79.0763	536	1374	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	99.96	99.96	1.00	1.00	2	-
GCF_900100735.1	s__Paraburkholderia phenazinium	79.0273	558	1374	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	99.89	99.88	0.92	0.92	3	-
GCF_900019265.1	s__Paraburkholderia ribeironis	78.9701	524	1374	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	78.9647	538	1374	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.2599	98.45	97.70	0.87	0.82	14	-
GCF_005503145.1	s__Paraburkholderia sp005503145	78.8946	586	1374	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000472545.1	s__Paraburkholderia sp000472545	78.782	518	1374	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017104715.1	s__Paraburkholderia sp017104715	78.6722	532	1374	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	78.4296	416	1374	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004343775.1	s__Burkholderia sp004343775	78.2781	471	1374	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018375725.1	s__Burkholderia sp018375725	78.0695	371	1374	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003854275.1	s__Burkholderia sp003854275	77.9779	449	1374	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	95.08	95.08	0.74	0.74	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:16:20,832] [INFO] GTDB search result was written to GCF_009455685.1_ASM945568v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:16:20,832] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:16:20,837] [INFO] DFAST_QC result json was written to GCF_009455685.1_ASM945568v1_genomic.fna/dqc_result.json
[2024-01-24 14:16:20,838] [INFO] DFAST_QC completed!
[2024-01-24 14:16:20,838] [INFO] Total running time: 0h2m0s