[2024-01-24 13:32:55,190] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:55,193] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:55,193] [INFO] DQC Reference Directory: /var/lib/cwl/stgb4dea4d4-e725-4660-b1a5-61f8cfc1a1ed/dqc_reference
[2024-01-24 13:32:56,432] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:56,433] [INFO] Task started: Prodigal
[2024-01-24 13:32:56,433] [INFO] Running command: gunzip -c /var/lib/cwl/stg56ecf5d3-841d-43a3-af5e-34ee1b18f20c/GCF_001465545.3_ASM146554v3_genomic.fna.gz | prodigal -d GCF_001465545.3_ASM146554v3_genomic.fna/cds.fna -a GCF_001465545.3_ASM146554v3_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:33:18,326] [INFO] Task succeeded: Prodigal
[2024-01-24 13:33:18,326] [INFO] Task started: HMMsearch
[2024-01-24 13:33:18,327] [INFO] Running command: hmmsearch --tblout GCF_001465545.3_ASM146554v3_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb4dea4d4-e725-4660-b1a5-61f8cfc1a1ed/dqc_reference/reference_markers.hmm GCF_001465545.3_ASM146554v3_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:33:18,683] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:33:18,685] [INFO] Found 6/6 markers.
[2024-01-24 13:33:18,743] [INFO] Query marker FASTA was written to GCF_001465545.3_ASM146554v3_genomic.fna/markers.fasta
[2024-01-24 13:33:18,743] [INFO] Task started: Blastn
[2024-01-24 13:33:18,743] [INFO] Running command: blastn -query GCF_001465545.3_ASM146554v3_genomic.fna/markers.fasta -db /var/lib/cwl/stgb4dea4d4-e725-4660-b1a5-61f8cfc1a1ed/dqc_reference/reference_markers.fasta -out GCF_001465545.3_ASM146554v3_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:19,875] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:19,897] [INFO] Selected 19 target genomes.
[2024-01-24 13:33:19,897] [INFO] Target genome list was writen to GCF_001465545.3_ASM146554v3_genomic.fna/target_genomes.txt
[2024-01-24 13:33:19,919] [INFO] Task started: fastANI
[2024-01-24 13:33:19,919] [INFO] Running command: fastANI --query /var/lib/cwl/stg56ecf5d3-841d-43a3-af5e-34ee1b18f20c/GCF_001465545.3_ASM146554v3_genomic.fna.gz --refList GCF_001465545.3_ASM146554v3_genomic.fna/target_genomes.txt --output GCF_001465545.3_ASM146554v3_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:33:45,372] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:45,373] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb4dea4d4-e725-4660-b1a5-61f8cfc1a1ed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:33:45,373] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb4dea4d4-e725-4660-b1a5-61f8cfc1a1ed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:33:45,387] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:33:45,388] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:33:45,388] [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 norimbergensis	strain=DSM 11628	GCA_001465545.3	93219	93219	type	True	100.0	2053	2055	95	conclusive
Pandoraea iniqua	strain=LMG 31009	GCA_902459685.1	2508288	2508288	type	True	94.0368	1860	2055	95	below_threshold
Pandoraea pneumonica	strain=LMG 31114	GCA_902459645.1	2508299	2508299	type	True	88.0809	1656	2055	95	below_threshold
Pandoraea fibrosis	strain=6399	GCA_000807775.2	1891094	1891094	type	True	84.3942	1406	2055	95	below_threshold
Pandoraea aquatica	strain=LMG 31011	GCA_902459565.1	2508290	2508290	type	True	84.2507	1449	2055	95	below_threshold
Pandoraea pulmonicola	strain=DSM 16583	GCA_000815105.2	93221	93221	type	True	84.1918	1364	2055	95	below_threshold
Pandoraea capi	strain=LMG 20602	GCA_902459735.1	2508286	2508286	type	True	84.1767	1428	2055	95	below_threshold
Pandoraea pulmonicola	strain=NCTC13159	GCA_900454575.1	93221	93221	type	True	84.1632	1349	2055	95	below_threshold
Pandoraea soli	strain=LMG 31014	GCA_902459595.1	2508293	2508293	type	True	84.0337	1151	2055	95	below_threshold
Pandoraea sputorum	strain=NCTC13161	GCA_900187205.1	93222	93222	type	True	84.0295	1424	2055	95	below_threshold
Pandoraea sputorum	strain=DSM 21091	GCA_000814845.2	93222	93222	type	True	84.0038	1416	2055	95	below_threshold
Pandoraea cepalis	strain=LMG 31106	GCA_902459665.1	2508294	2508294	type	True	83.9266	1177	2055	95	below_threshold
Pandoraea pnomenusa	strain=NCTC13160	GCA_900454355.1	93220	93220	type	True	83.6736	1277	2055	95	below_threshold
Pandoraea pnomenusa	strain=DSM 16536	GCA_000767615.3	93220	93220	type	True	83.6599	1295	2055	95	below_threshold
Paraburkholderia pallida	strain=7MH5	GCA_004524855.1	2547399	2547399	type	True	78.7479	615	2055	95	below_threshold
Paraburkholderia nemoris	strain=LMG 31836	GCA_905221015.1	2793076	2793076	type	True	78.4329	506	2055	95	below_threshold
Paraburkholderia gardini	strain=LMG 32171	GCA_907164575.1	2823469	2823469	type	True	78.2986	461	2055	95	below_threshold
Paraburkholderia podalyriae	strain=WC7.3b	GCA_014397785.1	1938811	1938811	type	True	78.2883	534	2055	95	below_threshold
Paraburkholderia saeva	strain=LMG 31841	GCA_907164555.1	2777537	2777537	type	True	78.2688	474	2055	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:33:45,390] [INFO] DFAST Taxonomy check result was written to GCF_001465545.3_ASM146554v3_genomic.fna/tc_result.tsv
[2024-01-24 13:33:45,390] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:33:45,390] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:33:45,390] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb4dea4d4-e725-4660-b1a5-61f8cfc1a1ed/dqc_reference/checkm_data
[2024-01-24 13:33:45,391] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:33:45,452] [INFO] Task started: CheckM
[2024-01-24 13:33:45,453] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001465545.3_ASM146554v3_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001465545.3_ASM146554v3_genomic.fna/checkm_input GCF_001465545.3_ASM146554v3_genomic.fna/checkm_result
[2024-01-24 13:34:56,292] [INFO] Task succeeded: CheckM
[2024-01-24 13:34:56,293] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:34:56,317] [INFO] ===== Completeness check finished =====
[2024-01-24 13:34:56,317] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:34:56,317] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001465545.3_ASM146554v3_genomic.fna/markers.fasta)
[2024-01-24 13:34:56,318] [INFO] Task started: Blastn
[2024-01-24 13:34:56,318] [INFO] Running command: blastn -query GCF_001465545.3_ASM146554v3_genomic.fna/markers.fasta -db /var/lib/cwl/stgb4dea4d4-e725-4660-b1a5-61f8cfc1a1ed/dqc_reference/reference_markers_gtdb.fasta -out GCF_001465545.3_ASM146554v3_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:34:58,239] [INFO] Task succeeded: Blastn
[2024-01-24 13:34:58,242] [INFO] Selected 11 target genomes.
[2024-01-24 13:34:58,242] [INFO] Target genome list was writen to GCF_001465545.3_ASM146554v3_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:34:58,252] [INFO] Task started: fastANI
[2024-01-24 13:34:58,253] [INFO] Running command: fastANI --query /var/lib/cwl/stg56ecf5d3-841d-43a3-af5e-34ee1b18f20c/GCF_001465545.3_ASM146554v3_genomic.fna.gz --refList GCF_001465545.3_ASM146554v3_genomic.fna/target_genomes_gtdb.txt --output GCF_001465545.3_ASM146554v3_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:35:13,682] [INFO] Task succeeded: fastANI
[2024-01-24 13:35:13,727] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:35:13,727] [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_001465545.3	s__Pandoraea norimbergensis	100.0	2051	2055	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002179965.1	s__Pandoraea sp002179965	94.9547	1881	2055	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	98.74	98.74	0.95	0.95	2	-
GCF_902459685.1	s__Pandoraea iniqua	94.0368	1860	2055	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	97.87	97.87	0.92	0.92	2	-
GCF_902459645.1	s__Pandoraea pneumonica	88.0767	1657	2055	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	84.3877	1406	2055	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	99.41	98.83	0.97	0.94	3	-
GCF_902459565.1	s__Pandoraea aquatica	84.2442	1449	2055	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000815105.2	s__Pandoraea pulmonicola	84.1907	1364	2055	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000814845.2	s__Pandoraea sputorum	84.0038	1416	2055	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	99.03	97.40	0.96	0.92	5	-
GCF_902459585.1	s__Pandoraea nosoerga	83.9634	1249	2055	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	99.66	99.29	0.94	0.91	4	-
GCF_902459665.1	s__Pandoraea cepalis	83.9352	1176	2055	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	83.6506	1294	2055	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	99.00	95.12	0.95	0.92	14	-
--------------------------------------------------------------------------------
[2024-01-24 13:35:13,729] [INFO] GTDB search result was written to GCF_001465545.3_ASM146554v3_genomic.fna/result_gtdb.tsv
[2024-01-24 13:35:13,732] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:35:13,736] [INFO] DFAST_QC result json was written to GCF_001465545.3_ASM146554v3_genomic.fna/dqc_result.json
[2024-01-24 13:35:13,736] [INFO] DFAST_QC completed!
[2024-01-24 13:35:13,736] [INFO] Total running time: 0h2m19s