[2024-01-24 13:13:12,451] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:13:12,453] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:13:12,453] [INFO] DQC Reference Directory: /var/lib/cwl/stg0e219558-d19a-4e94-9ea4-894d0ce6231e/dqc_reference
[2024-01-24 13:13:13,979] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:13:13,980] [INFO] Task started: Prodigal
[2024-01-24 13:13:13,980] [INFO] Running command: gunzip -c /var/lib/cwl/stga9342714-d22a-4800-9bf1-cd5a580cab54/GCF_902459685.1_LMG_31009_genomic.fna.gz | prodigal -d GCF_902459685.1_LMG_31009_genomic.fna/cds.fna -a GCF_902459685.1_LMG_31009_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:40,058] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:40,059] [INFO] Task started: HMMsearch
[2024-01-24 13:13:40,059] [INFO] Running command: hmmsearch --tblout GCF_902459685.1_LMG_31009_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0e219558-d19a-4e94-9ea4-894d0ce6231e/dqc_reference/reference_markers.hmm GCF_902459685.1_LMG_31009_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:40,427] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:40,429] [INFO] Found 6/6 markers.
[2024-01-24 13:13:40,489] [INFO] Query marker FASTA was written to GCF_902459685.1_LMG_31009_genomic.fna/markers.fasta
[2024-01-24 13:13:40,489] [INFO] Task started: Blastn
[2024-01-24 13:13:40,489] [INFO] Running command: blastn -query GCF_902459685.1_LMG_31009_genomic.fna/markers.fasta -db /var/lib/cwl/stg0e219558-d19a-4e94-9ea4-894d0ce6231e/dqc_reference/reference_markers.fasta -out GCF_902459685.1_LMG_31009_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:41,368] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:41,371] [INFO] Selected 23 target genomes.
[2024-01-24 13:13:41,372] [INFO] Target genome list was writen to GCF_902459685.1_LMG_31009_genomic.fna/target_genomes.txt
[2024-01-24 13:13:41,414] [INFO] Task started: fastANI
[2024-01-24 13:13:41,414] [INFO] Running command: fastANI --query /var/lib/cwl/stga9342714-d22a-4800-9bf1-cd5a580cab54/GCF_902459685.1_LMG_31009_genomic.fna.gz --refList GCF_902459685.1_LMG_31009_genomic.fna/target_genomes.txt --output GCF_902459685.1_LMG_31009_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:14:09,013] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:09,013] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0e219558-d19a-4e94-9ea4-894d0ce6231e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:14:09,013] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0e219558-d19a-4e94-9ea4-894d0ce6231e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:14:09,031] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:14:09,031] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:14:09,032] [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 iniqua	strain=LMG 31009	GCA_902459685.1	2508288	2508288	type	True	100.0	2104	2104	95	conclusive
Pandoraea norimbergensis	strain=DSM 11628	GCA_001465545.3	93219	93219	type	True	94.0259	1868	2104	95	below_threshold
Pandoraea pneumonica	strain=LMG 31114	GCA_902459645.1	2508299	2508299	type	True	88.1985	1638	2104	95	below_threshold
Pandoraea fibrosis	strain=6399	GCA_000807775.2	1891094	1891094	type	True	84.4642	1406	2104	95	below_threshold
Pandoraea aquatica	strain=LMG 31011	GCA_902459565.1	2508290	2508290	type	True	84.4008	1435	2104	95	below_threshold
Pandoraea capi	strain=LMG 20602	GCA_902459735.1	2508286	2508286	type	True	84.3465	1423	2104	95	below_threshold
Pandoraea pulmonicola	strain=DSM 16583	GCA_000815105.2	93221	93221	type	True	84.2431	1377	2104	95	below_threshold
Pandoraea pulmonicola	strain=NCTC13159	GCA_900454575.1	93221	93221	type	True	84.2388	1378	2104	95	below_threshold
Pandoraea oxalativorans	strain=DSM 23570	GCA_000972785.3	573737	573737	type	True	84.1916	1382	2104	95	below_threshold
Pandoraea cepalis	strain=LMG 31106	GCA_902459665.1	2508294	2508294	type	True	84.1789	1169	2104	95	below_threshold
Pandoraea soli	strain=LMG 31014	GCA_902459595.1	2508293	2508293	type	True	84.1443	1161	2104	95	below_threshold
Pandoraea pnomenusa	strain=NCTC13160	GCA_900454355.1	93220	93220	type	True	83.8659	1285	2104	95	below_threshold
Pandoraea pnomenusa	strain=DSM 16536	GCA_000767615.3	93220	93220	type	True	83.828	1292	2104	95	below_threshold
Paraburkholderia gardini	strain=LMG 32171	GCA_907164575.1	2823469	2823469	type	True	78.5762	450	2104	95	below_threshold
Paraburkholderia saeva	strain=LMG 31841	GCA_907164555.1	2777537	2777537	type	True	78.499	472	2104	95	below_threshold
Paraburkholderia haematera	strain=LMG 31837	GCA_905220975.1	2793077	2793077	type	True	78.3468	490	2104	95	below_threshold
Paraburkholderia podalyriae	strain=WC7.3b	GCA_014397785.1	1938811	1938811	type	True	78.3117	524	2104	95	below_threshold
Paraburkholderia kirstenboschensis	strain=KB15	GCA_001636975.1	1245436	1245436	type	True	78.2163	404	2104	95	below_threshold
Sphaerotilus hippei	strain=DSM 566	GCA_003201595.1	744406	744406	type	True	76.7899	218	2104	95	below_threshold
Nocardioides panaciterrulae	strain=DSM 21350	GCA_013409645.1	661492	661492	type	True	75.0888	53	2104	95	below_threshold
Nocardioides exalbidus	strain=DSM 22017	GCA_900105585.1	402596	402596	type	True	74.947	66	2104	95	below_threshold
Nocardioides szechwanensis	strain=NBRC 108562	GCA_007992395.1	1005944	1005944	type	True	74.8484	60	2104	95	below_threshold
Nocardioides szechwanensis	strain=CGMCC 1.11147	GCA_900103935.1	1005944	1005944	type	True	74.7153	60	2104	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:14:09,033] [INFO] DFAST Taxonomy check result was written to GCF_902459685.1_LMG_31009_genomic.fna/tc_result.tsv
[2024-01-24 13:14:09,033] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:14:09,034] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:14:09,034] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0e219558-d19a-4e94-9ea4-894d0ce6231e/dqc_reference/checkm_data
[2024-01-24 13:14:09,035] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:14:09,100] [INFO] Task started: CheckM
[2024-01-24 13:14:09,100] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_902459685.1_LMG_31009_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_902459685.1_LMG_31009_genomic.fna/checkm_input GCF_902459685.1_LMG_31009_genomic.fna/checkm_result
[2024-01-24 13:15:22,104] [INFO] Task succeeded: CheckM
[2024-01-24 13:15:22,105] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:15:22,126] [INFO] ===== Completeness check finished =====
[2024-01-24 13:15:22,126] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:15:22,126] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_902459685.1_LMG_31009_genomic.fna/markers.fasta)
[2024-01-24 13:15:22,127] [INFO] Task started: Blastn
[2024-01-24 13:15:22,127] [INFO] Running command: blastn -query GCF_902459685.1_LMG_31009_genomic.fna/markers.fasta -db /var/lib/cwl/stg0e219558-d19a-4e94-9ea4-894d0ce6231e/dqc_reference/reference_markers_gtdb.fasta -out GCF_902459685.1_LMG_31009_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:15:23,495] [INFO] Task succeeded: Blastn
[2024-01-24 13:15:23,499] [INFO] Selected 13 target genomes.
[2024-01-24 13:15:23,499] [INFO] Target genome list was writen to GCF_902459685.1_LMG_31009_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:15:23,515] [INFO] Task started: fastANI
[2024-01-24 13:15:23,515] [INFO] Running command: fastANI --query /var/lib/cwl/stga9342714-d22a-4800-9bf1-cd5a580cab54/GCF_902459685.1_LMG_31009_genomic.fna.gz --refList GCF_902459685.1_LMG_31009_genomic.fna/target_genomes_gtdb.txt --output GCF_902459685.1_LMG_31009_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:15:38,727] [INFO] Task succeeded: fastANI
[2024-01-24 13:15:38,743] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:15:38,744] [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_902459685.1	s__Pandoraea iniqua	100.0	2104	2104	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	97.87	97.87	0.92	0.92	2	conclusive
GCF_002179965.1	s__Pandoraea sp002179965	94.5458	1892	2104	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	98.74	98.74	0.95	0.95	2	-
GCF_001465545.3	s__Pandoraea norimbergensis	94.0259	1868	2104	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902459645.1	s__Pandoraea pneumonica	88.1985	1638	2104	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000807775.2	s__Pandoraea fibrosis	84.4666	1405	2104	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	84.3359	1424	2104	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	96.45	96.45	0.90	0.90	2	-
GCF_000815105.2	s__Pandoraea pulmonicola	84.2349	1379	2104	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	100.00	100.00	1.00	1.00	2	-
GCF_902459665.1	s__Pandoraea cepalis	84.1712	1170	2104	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	97.00	95.81	0.88	0.85	6	-
GCF_000767615.3	s__Pandoraea pnomenusa	83.8362	1290	2104	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	99.00	95.12	0.95	0.92	14	-
GCF_008119665.1	s__Pigmentiphaga aceris	76.9055	257	2104	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pigmentiphaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017307855.1	s__JAGOCV01 sp017307855	76.4985	240	2104	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__JAGOCV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017848855.1	s__Rhodanobacter denitrificans_B	75.8927	119	2104	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:15:38,745] [INFO] GTDB search result was written to GCF_902459685.1_LMG_31009_genomic.fna/result_gtdb.tsv
[2024-01-24 13:15:38,746] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:15:38,749] [INFO] DFAST_QC result json was written to GCF_902459685.1_LMG_31009_genomic.fna/dqc_result.json
[2024-01-24 13:15:38,750] [INFO] DFAST_QC completed!
[2024-01-24 13:15:38,750] [INFO] Total running time: 0h2m26s