[2024-01-25 19:54:35,774] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:54:35,781] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:54:35,781] [INFO] DQC Reference Directory: /var/lib/cwl/stg304be9ce-6d4c-4347-970b-ff224352eb15/dqc_reference
[2024-01-25 19:54:36,877] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:54:36,878] [INFO] Task started: Prodigal
[2024-01-25 19:54:36,878] [INFO] Running command: gunzip -c /var/lib/cwl/stgd711562b-a48b-463a-8511-5fdac192c708/GCF_900187205.1_52191_D01_genomic.fna.gz | prodigal -d GCF_900187205.1_52191_D01_genomic.fna/cds.fna -a GCF_900187205.1_52191_D01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:54:57,001] [INFO] Task succeeded: Prodigal
[2024-01-25 19:54:57,002] [INFO] Task started: HMMsearch
[2024-01-25 19:54:57,002] [INFO] Running command: hmmsearch --tblout GCF_900187205.1_52191_D01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg304be9ce-6d4c-4347-970b-ff224352eb15/dqc_reference/reference_markers.hmm GCF_900187205.1_52191_D01_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:54:57,287] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:54:57,289] [INFO] Found 6/6 markers.
[2024-01-25 19:54:57,335] [INFO] Query marker FASTA was written to GCF_900187205.1_52191_D01_genomic.fna/markers.fasta
[2024-01-25 19:54:57,335] [INFO] Task started: Blastn
[2024-01-25 19:54:57,336] [INFO] Running command: blastn -query GCF_900187205.1_52191_D01_genomic.fna/markers.fasta -db /var/lib/cwl/stg304be9ce-6d4c-4347-970b-ff224352eb15/dqc_reference/reference_markers.fasta -out GCF_900187205.1_52191_D01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:54:58,209] [INFO] Task succeeded: Blastn
[2024-01-25 19:54:58,211] [INFO] Selected 11 target genomes.
[2024-01-25 19:54:58,212] [INFO] Target genome list was writen to GCF_900187205.1_52191_D01_genomic.fna/target_genomes.txt
[2024-01-25 19:54:58,221] [INFO] Task started: fastANI
[2024-01-25 19:54:58,221] [INFO] Running command: fastANI --query /var/lib/cwl/stgd711562b-a48b-463a-8511-5fdac192c708/GCF_900187205.1_52191_D01_genomic.fna.gz --refList GCF_900187205.1_52191_D01_genomic.fna/target_genomes.txt --output GCF_900187205.1_52191_D01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:55:14,631] [INFO] Task succeeded: fastANI
[2024-01-25 19:55:14,631] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg304be9ce-6d4c-4347-970b-ff224352eb15/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:55:14,632] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg304be9ce-6d4c-4347-970b-ff224352eb15/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:55:14,640] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:55:14,640] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:55:14,640] [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 sputorum	strain=NCTC13161	GCA_900187205.1	93222	93222	type	True	100.0	1914	1914	95	conclusive
Pandoraea sputorum	strain=DSM 21091	GCA_000814845.2	93222	93222	type	True	99.9981	1913	1914	95	conclusive
Pandoraea commovens	strain=LMG 31010	GCA_902459615.1	2508289	2508289	type	True	94.1398	1745	1914	95	below_threshold
Pandoraea anapnoica	strain=LMG 31117	GCA_902459765.1	2508301	2508301	type	True	93.5704	1728	1914	95	below_threshold
Pandoraea oxalativorans	strain=DSM 23570	GCA_000972785.3	573737	573737	type	True	93.0735	1630	1914	95	below_threshold
Pandoraea aquatica	strain=LMG 31011	GCA_902459565.1	2508290	2508290	type	True	92.7658	1695	1914	95	below_threshold
Burkholderia ubonensis	strain=LMG 20358	GCA_902833085.1	101571	101571	type	True	78.4954	559	1914	95	below_threshold
Burkholderia ubonensis		GCA_902499185.1	101571	101571	type	True	78.4703	548	1914	95	below_threshold
Paraburkholderia podalyriae	strain=WC7.3b	GCA_014397785.1	1938811	1938811	type	True	78.3173	507	1914	95	below_threshold
Paraburkholderia haematera	strain=LMG 31837	GCA_905220975.1	2793077	2793077	type	True	78.3095	447	1914	95	below_threshold
Paraburkholderia nemoris	strain=LMG 31836	GCA_905221015.1	2793076	2793076	type	True	78.2354	494	1914	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:55:14,644] [INFO] DFAST Taxonomy check result was written to GCF_900187205.1_52191_D01_genomic.fna/tc_result.tsv
[2024-01-25 19:55:14,644] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:55:14,644] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:55:14,644] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg304be9ce-6d4c-4347-970b-ff224352eb15/dqc_reference/checkm_data
[2024-01-25 19:55:14,645] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:55:14,702] [INFO] Task started: CheckM
[2024-01-25 19:55:14,702] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900187205.1_52191_D01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900187205.1_52191_D01_genomic.fna/checkm_input GCF_900187205.1_52191_D01_genomic.fna/checkm_result
[2024-01-25 19:56:15,826] [INFO] Task succeeded: CheckM
[2024-01-25 19:56:15,828] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:56:15,849] [INFO] ===== Completeness check finished =====
[2024-01-25 19:56:15,850] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:56:15,851] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900187205.1_52191_D01_genomic.fna/markers.fasta)
[2024-01-25 19:56:15,851] [INFO] Task started: Blastn
[2024-01-25 19:56:15,851] [INFO] Running command: blastn -query GCF_900187205.1_52191_D01_genomic.fna/markers.fasta -db /var/lib/cwl/stg304be9ce-6d4c-4347-970b-ff224352eb15/dqc_reference/reference_markers_gtdb.fasta -out GCF_900187205.1_52191_D01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:56:17,508] [INFO] Task succeeded: Blastn
[2024-01-25 19:56:17,511] [INFO] Selected 5 target genomes.
[2024-01-25 19:56:17,511] [INFO] Target genome list was writen to GCF_900187205.1_52191_D01_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:56:17,518] [INFO] Task started: fastANI
[2024-01-25 19:56:17,519] [INFO] Running command: fastANI --query /var/lib/cwl/stgd711562b-a48b-463a-8511-5fdac192c708/GCF_900187205.1_52191_D01_genomic.fna.gz --refList GCF_900187205.1_52191_D01_genomic.fna/target_genomes_gtdb.txt --output GCF_900187205.1_52191_D01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:56:25,329] [INFO] Task succeeded: fastANI
[2024-01-25 19:56:25,334] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:56:25,334] [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_000814845.2	s__Pandoraea sputorum	99.9981	1913	1914	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	99.03	97.40	0.96	0.92	5	conclusive
GCF_902459615.1	s__Pandoraea commovens	94.1398	1745	1914	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902459765.1	s__Pandoraea anapnoica	93.5732	1728	1914	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000972785.3	s__Pandoraea oxalativorans	93.0727	1628	1914	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902459565.1	s__Pandoraea aquatica	92.7658	1695	1914	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:56:25,335] [INFO] GTDB search result was written to GCF_900187205.1_52191_D01_genomic.fna/result_gtdb.tsv
[2024-01-25 19:56:25,336] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:56:25,339] [INFO] DFAST_QC result json was written to GCF_900187205.1_52191_D01_genomic.fna/dqc_result.json
[2024-01-25 19:56:25,339] [INFO] DFAST_QC completed!
[2024-01-25 19:56:25,339] [INFO] Total running time: 0h1m50s