[2024-01-25 19:59:50,455] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:59:50,458] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:59:50,458] [INFO] DQC Reference Directory: /var/lib/cwl/stgf0a15178-53f3-4ce1-a58e-2196d00c9d08/dqc_reference
[2024-01-25 19:59:51,593] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:59:51,594] [INFO] Task started: Prodigal
[2024-01-25 19:59:51,594] [INFO] Running command: gunzip -c /var/lib/cwl/stgbb496b0f-a33e-4a36-b024-708a4d0edffb/GCF_900007165.1_BN2476-7183_genomic.fna.gz | prodigal -d GCF_900007165.1_BN2476-7183_genomic.fna/cds.fna -a GCF_900007165.1_BN2476-7183_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:00:17,584] [INFO] Task succeeded: Prodigal
[2024-01-25 20:00:17,584] [INFO] Task started: HMMsearch
[2024-01-25 20:00:17,584] [INFO] Running command: hmmsearch --tblout GCF_900007165.1_BN2476-7183_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf0a15178-53f3-4ce1-a58e-2196d00c9d08/dqc_reference/reference_markers.hmm GCF_900007165.1_BN2476-7183_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:00:17,931] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:00:17,932] [INFO] Found 6/6 markers.
[2024-01-25 20:00:18,004] [INFO] Query marker FASTA was written to GCF_900007165.1_BN2476-7183_genomic.fna/markers.fasta
[2024-01-25 20:00:18,004] [INFO] Task started: Blastn
[2024-01-25 20:00:18,004] [INFO] Running command: blastn -query GCF_900007165.1_BN2476-7183_genomic.fna/markers.fasta -db /var/lib/cwl/stgf0a15178-53f3-4ce1-a58e-2196d00c9d08/dqc_reference/reference_markers.fasta -out GCF_900007165.1_BN2476-7183_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:00:18,956] [INFO] Task succeeded: Blastn
[2024-01-25 20:00:18,958] [INFO] Selected 13 target genomes.
[2024-01-25 20:00:18,959] [INFO] Target genome list was writen to GCF_900007165.1_BN2476-7183_genomic.fna/target_genomes.txt
[2024-01-25 20:00:18,962] [INFO] Task started: fastANI
[2024-01-25 20:00:18,962] [INFO] Running command: fastANI --query /var/lib/cwl/stgbb496b0f-a33e-4a36-b024-708a4d0edffb/GCF_900007165.1_BN2476-7183_genomic.fna.gz --refList GCF_900007165.1_BN2476-7183_genomic.fna/target_genomes.txt --output GCF_900007165.1_BN2476-7183_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:00:46,492] [INFO] Task succeeded: fastANI
[2024-01-25 20:00:46,493] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf0a15178-53f3-4ce1-a58e-2196d00c9d08/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:00:46,493] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf0a15178-53f3-4ce1-a58e-2196d00c9d08/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:00:46,502] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:00:46,502] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:00:46,502] [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 piptadeniae	strain=STM 7183	GCA_900007165.2	1701573	1701573	type	True	100.0	3118	3124	95	conclusive
Paraburkholderia franconis	strain=CNPSo 3157	GCA_009362735.1	2654983	2654983	type	True	94.2865	2400	3124	95	below_threshold
Paraburkholderia diazotrophica	strain=LMG 26031	GCA_900108945.1	667676	667676	type	True	93.2761	2126	3124	95	below_threshold
Paraburkholderia sabiae	strain=LMG 24235	GCA_904848645.1	273251	273251	type	True	87.0331	1887	3124	95	below_threshold
Paraburkholderia terrae	strain=NBRC 100964	GCA_000739835.1	311230	311230	type	True	86.9274	1794	3124	95	below_threshold
Paraburkholderia azotifigens	strain=NF 2-5-3	GCA_007995085.1	2057004	2057004	type	True	86.8785	1875	3124	95	below_threshold
Paraburkholderia terrae	strain=DSM 17804	GCA_002902925.1	311230	311230	type	True	86.8776	1854	3124	95	below_threshold
Paraburkholderia hospita	strain=LMG 20598	GCA_902833685.1	169430	169430	type	True	86.7967	1895	3124	95	below_threshold
Paraburkholderia hospita	strain=DSM 17164	GCA_002902965.1	169430	169430	type	True	86.7763	1910	3124	95	below_threshold
Paraburkholderia flava	strain=LD6	GCA_004359985.1	2547393	2547393	type	True	83.2152	1220	3124	95	below_threshold
Paraburkholderia podalyriae	strain=WC7.3b	GCA_014397785.1	1938811	1938811	type	True	82.7296	1388	3124	95	below_threshold
Paraburkholderia gardini	strain=LMG 32171	GCA_907164575.1	2823469	2823469	type	True	82.7264	1189	3124	95	below_threshold
Paraburkholderia saeva	strain=LMG 31841	GCA_907164555.1	2777537	2777537	type	True	82.4438	1191	3124	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:00:46,503] [INFO] DFAST Taxonomy check result was written to GCF_900007165.1_BN2476-7183_genomic.fna/tc_result.tsv
[2024-01-25 20:00:46,504] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:00:46,504] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:00:46,504] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf0a15178-53f3-4ce1-a58e-2196d00c9d08/dqc_reference/checkm_data
[2024-01-25 20:00:46,505] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:00:46,594] [INFO] Task started: CheckM
[2024-01-25 20:00:46,594] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900007165.1_BN2476-7183_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900007165.1_BN2476-7183_genomic.fna/checkm_input GCF_900007165.1_BN2476-7183_genomic.fna/checkm_result
[2024-01-25 20:02:00,736] [INFO] Task succeeded: CheckM
[2024-01-25 20:02:00,737] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:02:00,759] [INFO] ===== Completeness check finished =====
[2024-01-25 20:02:00,759] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:02:00,760] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900007165.1_BN2476-7183_genomic.fna/markers.fasta)
[2024-01-25 20:02:00,760] [INFO] Task started: Blastn
[2024-01-25 20:02:00,760] [INFO] Running command: blastn -query GCF_900007165.1_BN2476-7183_genomic.fna/markers.fasta -db /var/lib/cwl/stgf0a15178-53f3-4ce1-a58e-2196d00c9d08/dqc_reference/reference_markers_gtdb.fasta -out GCF_900007165.1_BN2476-7183_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:02:02,688] [INFO] Task succeeded: Blastn
[2024-01-25 20:02:02,691] [INFO] Selected 8 target genomes.
[2024-01-25 20:02:02,691] [INFO] Target genome list was writen to GCF_900007165.1_BN2476-7183_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:02:02,698] [INFO] Task started: fastANI
[2024-01-25 20:02:02,699] [INFO] Running command: fastANI --query /var/lib/cwl/stgbb496b0f-a33e-4a36-b024-708a4d0edffb/GCF_900007165.1_BN2476-7183_genomic.fna.gz --refList GCF_900007165.1_BN2476-7183_genomic.fna/target_genomes_gtdb.txt --output GCF_900007165.1_BN2476-7183_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:02:23,090] [INFO] Task succeeded: fastANI
[2024-01-25 20:02:23,096] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:02:23,097] [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_900007165.1	s__Paraburkholderia piptadeniae	100.0	3118	3124	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_009362735.1	s__Paraburkholderia franconis	94.2728	2401	3124	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	93.2876	2124	3124	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	87.3009	1826	3124	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	87.033	1886	3124	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	87.0327	1777	3124	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	86.8816	1875	3124	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	86.7801	1909	3124	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.2599	98.45	97.70	0.87	0.82	14	-
--------------------------------------------------------------------------------
[2024-01-25 20:02:23,098] [INFO] GTDB search result was written to GCF_900007165.1_BN2476-7183_genomic.fna/result_gtdb.tsv
[2024-01-25 20:02:23,099] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:02:23,102] [INFO] DFAST_QC result json was written to GCF_900007165.1_BN2476-7183_genomic.fna/dqc_result.json
[2024-01-25 20:02:23,102] [INFO] DFAST_QC completed!
[2024-01-25 20:02:23,102] [INFO] Total running time: 0h2m33s