[2024-01-24 15:26:53,141] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:26:53,145] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:26:53,145] [INFO] DQC Reference Directory: /var/lib/cwl/stge7a09758-984c-4eb7-a334-f6e808f53f29/dqc_reference
[2024-01-24 15:26:54,390] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:26:54,391] [INFO] Task started: Prodigal
[2024-01-24 15:26:54,391] [INFO] Running command: gunzip -c /var/lib/cwl/stg1f860135-794e-492b-8154-18e6afbf4667/GCF_902459615.1_LMG_31010_genomic.fna.gz | prodigal -d GCF_902459615.1_LMG_31010_genomic.fna/cds.fna -a GCF_902459615.1_LMG_31010_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:27:17,856] [INFO] Task succeeded: Prodigal
[2024-01-24 15:27:17,857] [INFO] Task started: HMMsearch
[2024-01-24 15:27:17,857] [INFO] Running command: hmmsearch --tblout GCF_902459615.1_LMG_31010_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge7a09758-984c-4eb7-a334-f6e808f53f29/dqc_reference/reference_markers.hmm GCF_902459615.1_LMG_31010_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:27:18,247] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:27:18,249] [INFO] Found 6/6 markers.
[2024-01-24 15:27:18,307] [INFO] Query marker FASTA was written to GCF_902459615.1_LMG_31010_genomic.fna/markers.fasta
[2024-01-24 15:27:18,308] [INFO] Task started: Blastn
[2024-01-24 15:27:18,308] [INFO] Running command: blastn -query GCF_902459615.1_LMG_31010_genomic.fna/markers.fasta -db /var/lib/cwl/stge7a09758-984c-4eb7-a334-f6e808f53f29/dqc_reference/reference_markers.fasta -out GCF_902459615.1_LMG_31010_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:19,262] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:19,266] [INFO] Selected 11 target genomes.
[2024-01-24 15:27:19,266] [INFO] Target genome list was writen to GCF_902459615.1_LMG_31010_genomic.fna/target_genomes.txt
[2024-01-24 15:27:19,271] [INFO] Task started: fastANI
[2024-01-24 15:27:19,272] [INFO] Running command: fastANI --query /var/lib/cwl/stg1f860135-794e-492b-8154-18e6afbf4667/GCF_902459615.1_LMG_31010_genomic.fna.gz --refList GCF_902459615.1_LMG_31010_genomic.fna/target_genomes.txt --output GCF_902459615.1_LMG_31010_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:27:35,306] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:35,307] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge7a09758-984c-4eb7-a334-f6e808f53f29/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:27:35,307] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge7a09758-984c-4eb7-a334-f6e808f53f29/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:27:35,317] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:27:35,318] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:27:35,318] [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 commovens	strain=LMG 31010	GCA_902459615.1	2508289	2508289	type	True	100.0	1996	1998	95	conclusive
Pandoraea anapnoica	strain=LMG 31117	GCA_902459765.1	2508301	2508301	type	True	94.1354	1703	1998	95	below_threshold
Pandoraea sputorum	strain=DSM 21091	GCA_000814845.2	93222	93222	type	True	94.1331	1745	1998	95	below_threshold
Pandoraea sputorum	strain=NCTC13161	GCA_900187205.1	93222	93222	type	True	94.1259	1744	1998	95	below_threshold
Pandoraea oxalativorans	strain=DSM 23570	GCA_000972785.3	573737	573737	type	True	93.3504	1621	1998	95	below_threshold
Pandoraea aquatica	strain=LMG 31011	GCA_902459565.1	2508290	2508290	type	True	93.3129	1733	1998	95	below_threshold
Paraburkholderia saeva	strain=LMG 31841	GCA_907164555.1	2777537	2777537	type	True	78.5256	444	1998	95	below_threshold
Burkholderia ubonensis		GCA_902499185.1	101571	101571	type	True	78.4289	557	1998	95	below_threshold
Burkholderia ubonensis	strain=LMG 20358	GCA_902833085.1	101571	101571	type	True	78.4116	567	1998	95	below_threshold
Paraburkholderia nemoris	strain=LMG 31836	GCA_905221015.1	2793076	2793076	type	True	78.3235	498	1998	95	below_threshold
Paraburkholderia haematera	strain=LMG 31837	GCA_905220975.1	2793077	2793077	type	True	78.2519	479	1998	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:27:35,320] [INFO] DFAST Taxonomy check result was written to GCF_902459615.1_LMG_31010_genomic.fna/tc_result.tsv
[2024-01-24 15:27:35,320] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:27:35,320] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:27:35,320] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge7a09758-984c-4eb7-a334-f6e808f53f29/dqc_reference/checkm_data
[2024-01-24 15:27:35,321] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:27:35,380] [INFO] Task started: CheckM
[2024-01-24 15:27:35,380] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_902459615.1_LMG_31010_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_902459615.1_LMG_31010_genomic.fna/checkm_input GCF_902459615.1_LMG_31010_genomic.fna/checkm_result
[2024-01-24 15:28:40,341] [INFO] Task succeeded: CheckM
[2024-01-24 15:28:40,342] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:28:40,360] [INFO] ===== Completeness check finished =====
[2024-01-24 15:28:40,360] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:28:40,360] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_902459615.1_LMG_31010_genomic.fna/markers.fasta)
[2024-01-24 15:28:40,361] [INFO] Task started: Blastn
[2024-01-24 15:28:40,361] [INFO] Running command: blastn -query GCF_902459615.1_LMG_31010_genomic.fna/markers.fasta -db /var/lib/cwl/stge7a09758-984c-4eb7-a334-f6e808f53f29/dqc_reference/reference_markers_gtdb.fasta -out GCF_902459615.1_LMG_31010_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:28:41,990] [INFO] Task succeeded: Blastn
[2024-01-24 15:28:41,993] [INFO] Selected 5 target genomes.
[2024-01-24 15:28:41,993] [INFO] Target genome list was writen to GCF_902459615.1_LMG_31010_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:28:41,997] [INFO] Task started: fastANI
[2024-01-24 15:28:41,997] [INFO] Running command: fastANI --query /var/lib/cwl/stg1f860135-794e-492b-8154-18e6afbf4667/GCF_902459615.1_LMG_31010_genomic.fna.gz --refList GCF_902459615.1_LMG_31010_genomic.fna/target_genomes_gtdb.txt --output GCF_902459615.1_LMG_31010_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:28:49,475] [INFO] Task succeeded: fastANI
[2024-01-24 15:28:49,481] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:28:49,481] [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_902459615.1	s__Pandoraea commovens	100.0	1996	1998	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_000814845.2	s__Pandoraea sputorum	94.1432	1744	1998	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	99.03	97.40	0.96	0.92	5	-
GCF_902459765.1	s__Pandoraea anapnoica	94.1354	1703	1998	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	93.3504	1621	1998	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	93.3129	1733	1998	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 15:28:49,483] [INFO] GTDB search result was written to GCF_902459615.1_LMG_31010_genomic.fna/result_gtdb.tsv
[2024-01-24 15:28:49,483] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:28:49,486] [INFO] DFAST_QC result json was written to GCF_902459615.1_LMG_31010_genomic.fna/dqc_result.json
[2024-01-24 15:28:49,486] [INFO] DFAST_QC completed!
[2024-01-24 15:28:49,486] [INFO] Total running time: 0h1m56s