[2024-01-24 13:46:25,305] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:25,306] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:25,306] [INFO] DQC Reference Directory: /var/lib/cwl/stgfc6958a4-0f5b-4f60-bdcc-a5198a1cc1bb/dqc_reference
[2024-01-24 13:46:26,641] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:26,642] [INFO] Task started: Prodigal
[2024-01-24 13:46:26,642] [INFO] Running command: gunzip -c /var/lib/cwl/stge8776f5a-0b97-48fc-bace-fa5492600f8c/GCF_902459765.1_LMG_31117_genomic.fna.gz | prodigal -d GCF_902459765.1_LMG_31117_genomic.fna/cds.fna -a GCF_902459765.1_LMG_31117_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:48,252] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:48,252] [INFO] Task started: HMMsearch
[2024-01-24 13:46:48,252] [INFO] Running command: hmmsearch --tblout GCF_902459765.1_LMG_31117_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfc6958a4-0f5b-4f60-bdcc-a5198a1cc1bb/dqc_reference/reference_markers.hmm GCF_902459765.1_LMG_31117_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:48,582] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:48,583] [INFO] Found 6/6 markers.
[2024-01-24 13:46:48,632] [INFO] Query marker FASTA was written to GCF_902459765.1_LMG_31117_genomic.fna/markers.fasta
[2024-01-24 13:46:48,633] [INFO] Task started: Blastn
[2024-01-24 13:46:48,633] [INFO] Running command: blastn -query GCF_902459765.1_LMG_31117_genomic.fna/markers.fasta -db /var/lib/cwl/stgfc6958a4-0f5b-4f60-bdcc-a5198a1cc1bb/dqc_reference/reference_markers.fasta -out GCF_902459765.1_LMG_31117_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:49,560] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:49,563] [INFO] Selected 11 target genomes.
[2024-01-24 13:46:49,564] [INFO] Target genome list was writen to GCF_902459765.1_LMG_31117_genomic.fna/target_genomes.txt
[2024-01-24 13:46:49,573] [INFO] Task started: fastANI
[2024-01-24 13:46:49,574] [INFO] Running command: fastANI --query /var/lib/cwl/stge8776f5a-0b97-48fc-bace-fa5492600f8c/GCF_902459765.1_LMG_31117_genomic.fna.gz --refList GCF_902459765.1_LMG_31117_genomic.fna/target_genomes.txt --output GCF_902459765.1_LMG_31117_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:47:07,980] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:07,981] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfc6958a4-0f5b-4f60-bdcc-a5198a1cc1bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:47:07,982] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfc6958a4-0f5b-4f60-bdcc-a5198a1cc1bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:47:07,996] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:47:07,996] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:47:07,996] [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 anapnoica	strain=LMG 31117	GCA_902459765.1	2508301	2508301	type	True	100.0	2019	2020	95	conclusive
Pandoraea commovens	strain=LMG 31010	GCA_902459615.1	2508289	2508289	type	True	94.1483	1709	2020	95	below_threshold
Pandoraea sputorum	strain=DSM 21091	GCA_000814845.2	93222	93222	type	True	93.6313	1709	2020	95	below_threshold
Pandoraea sputorum	strain=NCTC13161	GCA_900187205.1	93222	93222	type	True	93.607	1719	2020	95	below_threshold
Pandoraea oxalativorans	strain=DSM 23570	GCA_000972785.3	573737	573737	type	True	93.291	1614	2020	95	below_threshold
Pandoraea aquatica	strain=LMG 31011	GCA_902459565.1	2508290	2508290	type	True	93.0163	1694	2020	95	below_threshold
Paraburkholderia saeva	strain=LMG 31841	GCA_907164555.1	2777537	2777537	type	True	78.5768	437	2020	95	below_threshold
Paraburkholderia gardini	strain=LMG 32171	GCA_907164575.1	2823469	2823469	type	True	78.3612	445	2020	95	below_threshold
Paraburkholderia kirstenboschensis	strain=KB15	GCA_001636975.1	1245436	1245436	type	True	78.2251	388	2020	95	below_threshold
Paraburkholderia podalyriae	strain=WC7.3b	GCA_014397785.1	1938811	1938811	type	True	78.1767	496	2020	95	below_threshold
Paraburkholderia nemoris	strain=LMG 31836	GCA_905221015.1	2793076	2793076	type	True	78.115	502	2020	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:47:07,998] [INFO] DFAST Taxonomy check result was written to GCF_902459765.1_LMG_31117_genomic.fna/tc_result.tsv
[2024-01-24 13:47:07,999] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:47:07,999] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:47:07,999] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfc6958a4-0f5b-4f60-bdcc-a5198a1cc1bb/dqc_reference/checkm_data
[2024-01-24 13:47:08,001] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:47:08,070] [INFO] Task started: CheckM
[2024-01-24 13:47:08,070] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_902459765.1_LMG_31117_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_902459765.1_LMG_31117_genomic.fna/checkm_input GCF_902459765.1_LMG_31117_genomic.fna/checkm_result
[2024-01-24 13:48:07,547] [INFO] Task succeeded: CheckM
[2024-01-24 13:48:07,548] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:48:07,564] [INFO] ===== Completeness check finished =====
[2024-01-24 13:48:07,565] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:48:07,565] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_902459765.1_LMG_31117_genomic.fna/markers.fasta)
[2024-01-24 13:48:07,566] [INFO] Task started: Blastn
[2024-01-24 13:48:07,566] [INFO] Running command: blastn -query GCF_902459765.1_LMG_31117_genomic.fna/markers.fasta -db /var/lib/cwl/stgfc6958a4-0f5b-4f60-bdcc-a5198a1cc1bb/dqc_reference/reference_markers_gtdb.fasta -out GCF_902459765.1_LMG_31117_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:48:09,282] [INFO] Task succeeded: Blastn
[2024-01-24 13:48:09,285] [INFO] Selected 5 target genomes.
[2024-01-24 13:48:09,285] [INFO] Target genome list was writen to GCF_902459765.1_LMG_31117_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:48:09,295] [INFO] Task started: fastANI
[2024-01-24 13:48:09,295] [INFO] Running command: fastANI --query /var/lib/cwl/stge8776f5a-0b97-48fc-bace-fa5492600f8c/GCF_902459765.1_LMG_31117_genomic.fna.gz --refList GCF_902459765.1_LMG_31117_genomic.fna/target_genomes_gtdb.txt --output GCF_902459765.1_LMG_31117_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:48:17,167] [INFO] Task succeeded: fastANI
[2024-01-24 13:48:17,178] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:48:17,179] [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_902459765.1	s__Pandoraea anapnoica	100.0	2018	2020	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_902459615.1	s__Pandoraea commovens	94.1496	1709	2020	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000814845.2	s__Pandoraea sputorum	93.6313	1709	2020	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	99.03	97.40	0.96	0.92	5	-
GCF_000972785.3	s__Pandoraea oxalativorans	93.2984	1613	2020	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	93.0163	1694	2020	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 13:48:17,180] [INFO] GTDB search result was written to GCF_902459765.1_LMG_31117_genomic.fna/result_gtdb.tsv
[2024-01-24 13:48:17,181] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:48:17,183] [INFO] DFAST_QC result json was written to GCF_902459765.1_LMG_31117_genomic.fna/dqc_result.json
[2024-01-24 13:48:17,184] [INFO] DFAST_QC completed!
[2024-01-24 13:48:17,184] [INFO] Total running time: 0h1m52s