[2024-01-25 18:48:35,831] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:48:35,832] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:48:35,832] [INFO] DQC Reference Directory: /var/lib/cwl/stgdcb26b20-656e-43d7-91ad-1266b0d83f5f/dqc_reference
[2024-01-25 18:48:36,985] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:48:36,985] [INFO] Task started: Prodigal
[2024-01-25 18:48:36,986] [INFO] Running command: gunzip -c /var/lib/cwl/stgbf8c577b-a234-4591-b009-e9b79099a5c5/GCF_009362735.1_ASM936273v1_genomic.fna.gz | prodigal -d GCF_009362735.1_ASM936273v1_genomic.fna/cds.fna -a GCF_009362735.1_ASM936273v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:49:04,359] [INFO] Task succeeded: Prodigal
[2024-01-25 18:49:04,360] [INFO] Task started: HMMsearch
[2024-01-25 18:49:04,360] [INFO] Running command: hmmsearch --tblout GCF_009362735.1_ASM936273v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdcb26b20-656e-43d7-91ad-1266b0d83f5f/dqc_reference/reference_markers.hmm GCF_009362735.1_ASM936273v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:49:04,796] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:49:04,797] [INFO] Found 6/6 markers.
[2024-01-25 18:49:04,874] [INFO] Query marker FASTA was written to GCF_009362735.1_ASM936273v1_genomic.fna/markers.fasta
[2024-01-25 18:49:04,874] [INFO] Task started: Blastn
[2024-01-25 18:49:04,874] [INFO] Running command: blastn -query GCF_009362735.1_ASM936273v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdcb26b20-656e-43d7-91ad-1266b0d83f5f/dqc_reference/reference_markers.fasta -out GCF_009362735.1_ASM936273v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:49:05,813] [INFO] Task succeeded: Blastn
[2024-01-25 18:49:05,816] [INFO] Selected 16 target genomes.
[2024-01-25 18:49:05,817] [INFO] Target genome list was writen to GCF_009362735.1_ASM936273v1_genomic.fna/target_genomes.txt
[2024-01-25 18:49:05,832] [INFO] Task started: fastANI
[2024-01-25 18:49:05,833] [INFO] Running command: fastANI --query /var/lib/cwl/stgbf8c577b-a234-4591-b009-e9b79099a5c5/GCF_009362735.1_ASM936273v1_genomic.fna.gz --refList GCF_009362735.1_ASM936273v1_genomic.fna/target_genomes.txt --output GCF_009362735.1_ASM936273v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:49:40,600] [INFO] Task succeeded: fastANI
[2024-01-25 18:49:40,601] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdcb26b20-656e-43d7-91ad-1266b0d83f5f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:49:40,601] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdcb26b20-656e-43d7-91ad-1266b0d83f5f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:49:40,611] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:49:40,611] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:49:40,611] [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 franconis	strain=CNPSo 3157	GCA_009362735.1	2654983	2654983	type	True	100.0	3219	3229	95	conclusive
Paraburkholderia piptadeniae	strain=STM 7183	GCA_900007165.2	1701573	1701573	type	True	94.2634	2382	3229	95	below_threshold
Paraburkholderia diazotrophica	strain=LMG 26031	GCA_900108945.1	667676	667676	type	True	93.8513	2287	3229	95	below_threshold
Paraburkholderia sabiae	strain=LMG 24235	GCA_904848645.1	273251	273251	type	True	87.0664	1941	3229	95	below_threshold
Paraburkholderia azotifigens	strain=NF 2-5-3	GCA_007995085.1	2057004	2057004	type	True	86.8897	1957	3229	95	below_threshold
Paraburkholderia terrae	strain=DSM 17804	GCA_002902925.1	311230	311230	type	True	86.7903	1897	3229	95	below_threshold
Paraburkholderia terrae	strain=NBRC 100964	GCA_000739835.1	311230	311230	type	True	86.786	1850	3229	95	below_threshold
Paraburkholderia hospita	strain=LMG 20598	GCA_902833685.1	169430	169430	type	True	86.7626	1980	3229	95	below_threshold
Paraburkholderia caribensis	strain=LMG 18531	GCA_902833515.1	75105	75105	type	True	86.7319	1783	3229	95	below_threshold
Paraburkholderia hospita	strain=DSM 17164	GCA_002902965.1	169430	169430	type	True	86.726	2027	3229	95	below_threshold
Paraburkholderia caribensis	strain=DSM 13236	GCA_002902945.1	75105	75105	type	True	86.7143	1765	3229	95	below_threshold
Paraburkholderia phymatum	strain=LMG 21445	GCA_902833665.1	148447	148447	type	True	86.2673	1858	3229	95	below_threshold
Paraburkholderia flava	strain=LD6	GCA_004359985.1	2547393	2547393	type	True	82.9929	1262	3229	95	below_threshold
Paraburkholderia gardini	strain=LMG 32171	GCA_907164575.1	2823469	2823469	type	True	82.8128	1194	3229	95	below_threshold
Paraburkholderia podalyriae	strain=WC7.3b	GCA_014397785.1	1938811	1938811	type	True	82.6548	1434	3229	95	below_threshold
Paraburkholderia saeva	strain=LMG 31841	GCA_907164555.1	2777537	2777537	type	True	82.498	1201	3229	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:49:40,613] [INFO] DFAST Taxonomy check result was written to GCF_009362735.1_ASM936273v1_genomic.fna/tc_result.tsv
[2024-01-25 18:49:40,613] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:49:40,613] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:49:40,613] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdcb26b20-656e-43d7-91ad-1266b0d83f5f/dqc_reference/checkm_data
[2024-01-25 18:49:40,614] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:49:40,703] [INFO] Task started: CheckM
[2024-01-25 18:49:40,704] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009362735.1_ASM936273v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009362735.1_ASM936273v1_genomic.fna/checkm_input GCF_009362735.1_ASM936273v1_genomic.fna/checkm_result
[2024-01-25 18:51:04,182] [INFO] Task succeeded: CheckM
[2024-01-25 18:51:04,183] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:51:04,207] [INFO] ===== Completeness check finished =====
[2024-01-25 18:51:04,207] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:51:04,208] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009362735.1_ASM936273v1_genomic.fna/markers.fasta)
[2024-01-25 18:51:04,208] [INFO] Task started: Blastn
[2024-01-25 18:51:04,208] [INFO] Running command: blastn -query GCF_009362735.1_ASM936273v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdcb26b20-656e-43d7-91ad-1266b0d83f5f/dqc_reference/reference_markers_gtdb.fasta -out GCF_009362735.1_ASM936273v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:51:06,149] [INFO] Task succeeded: Blastn
[2024-01-25 18:51:06,151] [INFO] Selected 9 target genomes.
[2024-01-25 18:51:06,152] [INFO] Target genome list was writen to GCF_009362735.1_ASM936273v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:51:06,159] [INFO] Task started: fastANI
[2024-01-25 18:51:06,159] [INFO] Running command: fastANI --query /var/lib/cwl/stgbf8c577b-a234-4591-b009-e9b79099a5c5/GCF_009362735.1_ASM936273v1_genomic.fna.gz --refList GCF_009362735.1_ASM936273v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009362735.1_ASM936273v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:51:31,102] [INFO] Task succeeded: fastANI
[2024-01-25 18:51:31,110] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:51:31,110] [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_009362735.1	s__Paraburkholderia franconis	100.0	3219	3229	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_900007165.1	s__Paraburkholderia piptadeniae	94.2499	2384	3229	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900108945.1	s__Paraburkholderia diazotrophica	93.8384	2289	3229	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017814945.1	s__Paraburkholderia sp017814945	87.2325	1954	3229	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_904848645.1	s__Paraburkholderia sabiae	87.0494	1944	3229	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	86.9178	1853	3229	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007995085.1	s__Paraburkholderia azotifigens	86.8602	1964	3229	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	98.91	98.91	0.86	0.86	2	-
GCF_002902965.1	s__Paraburkholderia hospita	86.7505	2024	3229	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	86.5234	2080	3229	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 18:51:31,111] [INFO] GTDB search result was written to GCF_009362735.1_ASM936273v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:51:31,112] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:51:31,114] [INFO] DFAST_QC result json was written to GCF_009362735.1_ASM936273v1_genomic.fna/dqc_result.json
[2024-01-25 18:51:31,115] [INFO] DFAST_QC completed!
[2024-01-25 18:51:31,115] [INFO] Total running time: 0h2m55s