[2024-01-24 10:57:50,263] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:50,266] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:50,266] [INFO] DQC Reference Directory: /var/lib/cwl/stgf33de96d-95ff-4318-9aa4-e32a1e5faeed/dqc_reference
[2024-01-24 10:57:52,642] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:52,643] [INFO] Task started: Prodigal
[2024-01-24 10:57:52,644] [INFO] Running command: gunzip -c /var/lib/cwl/stg4f76e73d-002b-4106-bb46-9f5f02578b8b/GCF_902459665.1_LMG_31106_genomic.fna.gz | prodigal -d GCF_902459665.1_LMG_31106_genomic.fna/cds.fna -a GCF_902459665.1_LMG_31106_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:58:10,082] [INFO] Task succeeded: Prodigal
[2024-01-24 10:58:10,082] [INFO] Task started: HMMsearch
[2024-01-24 10:58:10,083] [INFO] Running command: hmmsearch --tblout GCF_902459665.1_LMG_31106_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf33de96d-95ff-4318-9aa4-e32a1e5faeed/dqc_reference/reference_markers.hmm GCF_902459665.1_LMG_31106_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:58:10,370] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:58:10,372] [INFO] Found 6/6 markers.
[2024-01-24 10:58:10,419] [INFO] Query marker FASTA was written to GCF_902459665.1_LMG_31106_genomic.fna/markers.fasta
[2024-01-24 10:58:10,419] [INFO] Task started: Blastn
[2024-01-24 10:58:10,419] [INFO] Running command: blastn -query GCF_902459665.1_LMG_31106_genomic.fna/markers.fasta -db /var/lib/cwl/stgf33de96d-95ff-4318-9aa4-e32a1e5faeed/dqc_reference/reference_markers.fasta -out GCF_902459665.1_LMG_31106_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:11,365] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:11,370] [INFO] Selected 13 target genomes.
[2024-01-24 10:58:11,370] [INFO] Target genome list was writen to GCF_902459665.1_LMG_31106_genomic.fna/target_genomes.txt
[2024-01-24 10:58:11,376] [INFO] Task started: fastANI
[2024-01-24 10:58:11,377] [INFO] Running command: fastANI --query /var/lib/cwl/stg4f76e73d-002b-4106-bb46-9f5f02578b8b/GCF_902459665.1_LMG_31106_genomic.fna.gz --refList GCF_902459665.1_LMG_31106_genomic.fna/target_genomes.txt --output GCF_902459665.1_LMG_31106_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:58:28,542] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:28,543] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf33de96d-95ff-4318-9aa4-e32a1e5faeed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:58:28,543] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf33de96d-95ff-4318-9aa4-e32a1e5faeed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:58:28,557] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 10:58:28,557] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 10:58:28,557] [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
Pandoraea cepalis	strain=LMG 31106	GCA_902459665.1	2508294	2508294	type	True	100.0	1732	1733	95	inconclusive
Pandoraea soli	strain=LMG 31014	GCA_902459595.1	2508293	2508293	type	True	95.8013	1466	1733	95	inconclusive
Pandoraea eparura	strain=LMG 31012	GCA_902459725.1	2508291	2508291	type	True	91.2531	1395	1733	95	below_threshold
Pandoraea terrigena	strain=LMG 31013	GCA_902459705.1	2508292	2508292	type	True	90.5683	1397	1733	95	below_threshold
Pandoraea bronchicola	strain=LMG 20603	GCA_902459805.1	2508287	2508287	type	True	86.684	1219	1733	95	below_threshold
Pandoraea communis	strain=LMG 31110	GCA_902459745.1	2508297	2508297	type	True	86.3531	1272	1733	95	below_threshold
Pandoraea capi	strain=LMG 20602	GCA_902459735.1	2508286	2508286	type	True	84.9849	1201	1733	95	below_threshold
Pandoraea pnomenusa	strain=NCTC13160	GCA_900454355.1	93220	93220	type	True	84.9339	1215	1733	95	below_threshold
Paraburkholderia pallida	strain=7MH5	GCA_004524855.1	2547399	2547399	type	True	78.6663	574	1733	95	below_threshold
Paraburkholderia gardini	strain=LMG 32171	GCA_907164575.1	2823469	2823469	type	True	78.4588	460	1733	95	below_threshold
Paraburkholderia podalyriae	strain=WC7.3b	GCA_014397785.1	1938811	1938811	type	True	78.3222	513	1733	95	below_threshold
Paraburkholderia saeva	strain=LMG 31841	GCA_907164555.1	2777537	2777537	type	True	78.261	442	1733	95	below_threshold
Paraburkholderia azotifigens	strain=NF 2-5-3	GCA_007995085.1	2057004	2057004	type	True	78.1908	527	1733	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:58:28,559] [INFO] DFAST Taxonomy check result was written to GCF_902459665.1_LMG_31106_genomic.fna/tc_result.tsv
[2024-01-24 10:58:28,559] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:58:28,559] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:58:28,560] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf33de96d-95ff-4318-9aa4-e32a1e5faeed/dqc_reference/checkm_data
[2024-01-24 10:58:28,560] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:58:28,610] [INFO] Task started: CheckM
[2024-01-24 10:58:28,610] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_902459665.1_LMG_31106_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_902459665.1_LMG_31106_genomic.fna/checkm_input GCF_902459665.1_LMG_31106_genomic.fna/checkm_result
[2024-01-24 10:59:22,050] [INFO] Task succeeded: CheckM
[2024-01-24 10:59:22,052] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:59:22,074] [INFO] ===== Completeness check finished =====
[2024-01-24 10:59:22,074] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:59:22,075] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_902459665.1_LMG_31106_genomic.fna/markers.fasta)
[2024-01-24 10:59:22,075] [INFO] Task started: Blastn
[2024-01-24 10:59:22,075] [INFO] Running command: blastn -query GCF_902459665.1_LMG_31106_genomic.fna/markers.fasta -db /var/lib/cwl/stgf33de96d-95ff-4318-9aa4-e32a1e5faeed/dqc_reference/reference_markers_gtdb.fasta -out GCF_902459665.1_LMG_31106_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:59:23,821] [INFO] Task succeeded: Blastn
[2024-01-24 10:59:23,825] [INFO] Selected 9 target genomes.
[2024-01-24 10:59:23,826] [INFO] Target genome list was writen to GCF_902459665.1_LMG_31106_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:59:23,833] [INFO] Task started: fastANI
[2024-01-24 10:59:23,833] [INFO] Running command: fastANI --query /var/lib/cwl/stg4f76e73d-002b-4106-bb46-9f5f02578b8b/GCF_902459665.1_LMG_31106_genomic.fna.gz --refList GCF_902459665.1_LMG_31106_genomic.fna/target_genomes_gtdb.txt --output GCF_902459665.1_LMG_31106_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:59:35,237] [INFO] Task succeeded: fastANI
[2024-01-24 10:59:35,253] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:59:35,253] [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_902459665.1	s__Pandoraea cepalis	100.0	1732	1733	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	97.00	95.81	0.88	0.85	6	conclusive
GCF_902459725.1	s__Pandoraea eparura	91.2605	1394	1733	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902459705.1	s__Pandoraea terrigena	90.5622	1398	1733	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902459805.1	s__Pandoraea bronchicola	86.684	1219	1733	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902459745.1	s__Pandoraea communis	86.3623	1271	1733	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0166	98.36	97.48	0.89	0.87	3	-
GCF_000807775.2	s__Pandoraea fibrosis	85.9956	1240	1733	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	99.41	98.83	0.97	0.94	3	-
GCF_902459735.1	s__Pandoraea capi	85.0004	1199	1733	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	96.45	96.45	0.90	0.90	2	-
GCF_000767615.3	s__Pandoraea pnomenusa	84.9438	1216	1733	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	99.00	95.12	0.95	0.92	14	-
GCF_902459615.1	s__Pandoraea commovens	84.9411	1209	1733	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:59:35,255] [INFO] GTDB search result was written to GCF_902459665.1_LMG_31106_genomic.fna/result_gtdb.tsv
[2024-01-24 10:59:35,255] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:59:35,258] [INFO] DFAST_QC result json was written to GCF_902459665.1_LMG_31106_genomic.fna/dqc_result.json
[2024-01-24 10:59:35,258] [INFO] DFAST_QC completed!
[2024-01-24 10:59:35,258] [INFO] Total running time: 0h1m45s