[2024-01-24 13:32:41,157] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:41,160] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:41,160] [INFO] DQC Reference Directory: /var/lib/cwl/stgda11538e-9bcc-4103-b485-956d85819f88/dqc_reference
[2024-01-24 13:32:42,386] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:42,387] [INFO] Task started: Prodigal
[2024-01-24 13:32:42,387] [INFO] Running command: gunzip -c /var/lib/cwl/stgde35a788-8cf1-4006-b891-98ccb5ab3429/GCF_902459805.1_LMG_20603_genomic.fna.gz | prodigal -d GCF_902459805.1_LMG_20603_genomic.fna/cds.fna -a GCF_902459805.1_LMG_20603_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:33:00,562] [INFO] Task succeeded: Prodigal
[2024-01-24 13:33:00,563] [INFO] Task started: HMMsearch
[2024-01-24 13:33:00,563] [INFO] Running command: hmmsearch --tblout GCF_902459805.1_LMG_20603_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgda11538e-9bcc-4103-b485-956d85819f88/dqc_reference/reference_markers.hmm GCF_902459805.1_LMG_20603_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:33:00,919] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:33:00,920] [INFO] Found 6/6 markers.
[2024-01-24 13:33:00,959] [INFO] Query marker FASTA was written to GCF_902459805.1_LMG_20603_genomic.fna/markers.fasta
[2024-01-24 13:33:00,960] [INFO] Task started: Blastn
[2024-01-24 13:33:00,960] [INFO] Running command: blastn -query GCF_902459805.1_LMG_20603_genomic.fna/markers.fasta -db /var/lib/cwl/stgda11538e-9bcc-4103-b485-956d85819f88/dqc_reference/reference_markers.fasta -out GCF_902459805.1_LMG_20603_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:01,822] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:01,825] [INFO] Selected 12 target genomes.
[2024-01-24 13:33:01,825] [INFO] Target genome list was writen to GCF_902459805.1_LMG_20603_genomic.fna/target_genomes.txt
[2024-01-24 13:33:01,829] [INFO] Task started: fastANI
[2024-01-24 13:33:01,829] [INFO] Running command: fastANI --query /var/lib/cwl/stgde35a788-8cf1-4006-b891-98ccb5ab3429/GCF_902459805.1_LMG_20603_genomic.fna.gz --refList GCF_902459805.1_LMG_20603_genomic.fna/target_genomes.txt --output GCF_902459805.1_LMG_20603_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:33:17,071] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:17,072] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgda11538e-9bcc-4103-b485-956d85819f88/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:33:17,072] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgda11538e-9bcc-4103-b485-956d85819f88/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:33:17,081] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:33:17,081] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:33:17,081] [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 bronchicola	strain=LMG 20603	GCA_902459805.1	2508287	2508287	type	True	100.0	1765	1768	95	conclusive
Pandoraea communis	strain=LMG 31110	GCA_902459745.1	2508297	2508297	type	True	89.6924	1460	1768	95	below_threshold
Pandoraea horticolens	strain=LMG 31112	GCA_902459555.1	2508298	2508298	type	True	89.6619	1432	1768	95	below_threshold
Pandoraea fibrosis	strain=6399	GCA_000807775.2	1891094	1891094	type	True	89.0421	1437	1768	95	below_threshold
Pandoraea apista	strain=LMG16407	GCA_001049515.1	93218	93218	type	True	88.7531	1416	1768	95	below_threshold
Pandoraea apista	strain=DSM 16535	GCA_001465595.2	93218	93218	type	True	88.6875	1457	1768	95	below_threshold
Pandoraea soli	strain=LMG 31014	GCA_902459595.1	2508293	2508293	type	True	86.6803	1206	1768	95	below_threshold
Burkholderia ubonensis		GCA_902499185.1	101571	101571	type	True	78.4817	523	1768	95	below_threshold
Burkholderia ubonensis	strain=LMG 20358	GCA_902833085.1	101571	101571	type	True	78.4428	535	1768	95	below_threshold
Paraburkholderia saeva	strain=LMG 31841	GCA_907164555.1	2777537	2777537	type	True	78.4087	414	1768	95	below_threshold
Paraburkholderia domus	strain=LMG 31832	GCA_905220705.1	2793075	2793075	type	True	78.0802	447	1768	95	below_threshold
Paraburkholderia haematera	strain=LMG 31837	GCA_905220975.1	2793077	2793077	type	True	77.909	449	1768	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:33:17,082] [INFO] DFAST Taxonomy check result was written to GCF_902459805.1_LMG_20603_genomic.fna/tc_result.tsv
[2024-01-24 13:33:17,083] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:33:17,083] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:33:17,083] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgda11538e-9bcc-4103-b485-956d85819f88/dqc_reference/checkm_data
[2024-01-24 13:33:17,084] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:33:17,135] [INFO] Task started: CheckM
[2024-01-24 13:33:17,135] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_902459805.1_LMG_20603_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_902459805.1_LMG_20603_genomic.fna/checkm_input GCF_902459805.1_LMG_20603_genomic.fna/checkm_result
[2024-01-24 13:34:10,554] [INFO] Task succeeded: CheckM
[2024-01-24 13:34:10,555] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:34:10,572] [INFO] ===== Completeness check finished =====
[2024-01-24 13:34:10,572] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:34:10,572] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_902459805.1_LMG_20603_genomic.fna/markers.fasta)
[2024-01-24 13:34:10,572] [INFO] Task started: Blastn
[2024-01-24 13:34:10,572] [INFO] Running command: blastn -query GCF_902459805.1_LMG_20603_genomic.fna/markers.fasta -db /var/lib/cwl/stgda11538e-9bcc-4103-b485-956d85819f88/dqc_reference/reference_markers_gtdb.fasta -out GCF_902459805.1_LMG_20603_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:34:12,219] [INFO] Task succeeded: Blastn
[2024-01-24 13:34:12,221] [INFO] Selected 7 target genomes.
[2024-01-24 13:34:12,222] [INFO] Target genome list was writen to GCF_902459805.1_LMG_20603_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:34:12,226] [INFO] Task started: fastANI
[2024-01-24 13:34:12,226] [INFO] Running command: fastANI --query /var/lib/cwl/stgde35a788-8cf1-4006-b891-98ccb5ab3429/GCF_902459805.1_LMG_20603_genomic.fna.gz --refList GCF_902459805.1_LMG_20603_genomic.fna/target_genomes_gtdb.txt --output GCF_902459805.1_LMG_20603_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:34:22,741] [INFO] Task succeeded: fastANI
[2024-01-24 13:34:22,747] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:34:22,747] [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_902459805.1	s__Pandoraea bronchicola	100.0	1765	1768	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_902459745.1	s__Pandoraea communis	89.6998	1459	1768	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0166	98.36	97.48	0.89	0.87	3	-
GCF_902459555.1	s__Pandoraea horticolens	89.6619	1432	1768	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0166	N/A	N/A	N/A	N/A	1	-
GCF_000807775.2	s__Pandoraea fibrosis	89.0421	1437	1768	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	99.41	98.83	0.97	0.94	3	-
GCF_001465595.2	s__Pandoraea apista	88.6875	1457	1768	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	99.24	99.05	0.93	0.91	21	-
GCF_902459565.1	s__Pandoraea aquatica	85.699	1372	1768	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902459615.1	s__Pandoraea commovens	85.5384	1339	1768	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 13:34:22,749] [INFO] GTDB search result was written to GCF_902459805.1_LMG_20603_genomic.fna/result_gtdb.tsv
[2024-01-24 13:34:22,749] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:34:22,752] [INFO] DFAST_QC result json was written to GCF_902459805.1_LMG_20603_genomic.fna/dqc_result.json
[2024-01-24 13:34:22,752] [INFO] DFAST_QC completed!
[2024-01-24 13:34:22,752] [INFO] Total running time: 0h1m42s