[2024-01-25 20:06:20,762] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:06:20,763] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:06:20,764] [INFO] DQC Reference Directory: /var/lib/cwl/stg6ba8fa62-3cd4-4375-89b7-c02491a2b5ed/dqc_reference
[2024-01-25 20:06:21,908] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:06:21,909] [INFO] Task started: Prodigal
[2024-01-25 20:06:21,909] [INFO] Running command: gunzip -c /var/lib/cwl/stge2382ac0-19af-4dd4-9746-a739e9b67821/GCF_900113525.1_IMG-taxon_2634166297_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900113525.1_IMG-taxon_2634166297_annotated_assembly_genomic.fna/cds.fna -a GCF_900113525.1_IMG-taxon_2634166297_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:06:35,786] [INFO] Task succeeded: Prodigal
[2024-01-25 20:06:35,786] [INFO] Task started: HMMsearch
[2024-01-25 20:06:35,786] [INFO] Running command: hmmsearch --tblout GCF_900113525.1_IMG-taxon_2634166297_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6ba8fa62-3cd4-4375-89b7-c02491a2b5ed/dqc_reference/reference_markers.hmm GCF_900113525.1_IMG-taxon_2634166297_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:06:36,103] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:06:36,104] [INFO] Found 6/6 markers.
[2024-01-25 20:06:36,143] [INFO] Query marker FASTA was written to GCF_900113525.1_IMG-taxon_2634166297_annotated_assembly_genomic.fna/markers.fasta
[2024-01-25 20:06:36,144] [INFO] Task started: Blastn
[2024-01-25 20:06:36,144] [INFO] Running command: blastn -query GCF_900113525.1_IMG-taxon_2634166297_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg6ba8fa62-3cd4-4375-89b7-c02491a2b5ed/dqc_reference/reference_markers.fasta -out GCF_900113525.1_IMG-taxon_2634166297_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:06:36,737] [INFO] Task succeeded: Blastn
[2024-01-25 20:06:36,740] [INFO] Selected 19 target genomes.
[2024-01-25 20:06:36,740] [INFO] Target genome list was writen to GCF_900113525.1_IMG-taxon_2634166297_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-25 20:06:36,753] [INFO] Task started: fastANI
[2024-01-25 20:06:36,754] [INFO] Running command: fastANI --query /var/lib/cwl/stge2382ac0-19af-4dd4-9746-a739e9b67821/GCF_900113525.1_IMG-taxon_2634166297_annotated_assembly_genomic.fna.gz --refList GCF_900113525.1_IMG-taxon_2634166297_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900113525.1_IMG-taxon_2634166297_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:06:54,868] [INFO] Task succeeded: fastANI
[2024-01-25 20:06:54,868] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6ba8fa62-3cd4-4375-89b7-c02491a2b5ed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:06:54,868] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6ba8fa62-3cd4-4375-89b7-c02491a2b5ed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:06:54,876] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:06:54,876] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:06:54,876] [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
Pedobacter insulae	strain=DSM 18684	GCA_900113525.1	414048	414048	type	True	100.0	1449	1452	95	conclusive
Pedobacter cryotolerans	strain=AR-2-6	GCA_005116475.1	2571270	2571270	type	True	79.2963	370	1452	95	below_threshold
Pedobacter planticolens	strain=LMG 31464	GCA_014172375.1	2679964	2679964	type	True	78.9602	414	1452	95	below_threshold
Pedobacter polaris	strain=RP-3-22	GCA_005116505.1	2571273	2571273	type	True	78.8492	396	1452	95	below_threshold
Pedobacter frigiditerrae	strain=RP-1-13	GCA_004331645.1	2530452	2530452	type	True	78.8459	423	1452	95	below_threshold
Pedobacter steynii	strain=DSM 19110	GCA_900103665.1	430522	430522	type	True	78.0872	156	1452	95	below_threshold
Pedobacter xixiisoli	strain=CGMCC 1.12803	GCA_900215335.1	1476464	1476464	type	True	77.9799	188	1452	95	below_threshold
Pedobacter caeni	strain=DSM 16990	GCA_900129215.1	288992	288992	type	True	77.8159	167	1452	95	below_threshold
Pedobacter nototheniae	strain=36B243	GCA_004335085.1	2488994	2488994	type	True	77.678	181	1452	95	below_threshold
Pedobacter rhizosphaerae	strain=DSM 18610	GCA_900111155.1	390241	390241	type	True	77.4486	163	1452	95	below_threshold
Pedobacter ghigonis	strain=Marseille-Q2390	GCA_903166585.1	2730403	2730403	type	True	77.3587	186	1452	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:06:54,877] [INFO] DFAST Taxonomy check result was written to GCF_900113525.1_IMG-taxon_2634166297_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-25 20:06:54,878] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:06:54,878] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:06:54,878] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6ba8fa62-3cd4-4375-89b7-c02491a2b5ed/dqc_reference/checkm_data
[2024-01-25 20:06:54,879] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:06:54,921] [INFO] Task started: CheckM
[2024-01-25 20:06:54,921] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900113525.1_IMG-taxon_2634166297_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900113525.1_IMG-taxon_2634166297_annotated_assembly_genomic.fna/checkm_input GCF_900113525.1_IMG-taxon_2634166297_annotated_assembly_genomic.fna/checkm_result
[2024-01-25 20:07:35,801] [INFO] Task succeeded: CheckM
[2024-01-25 20:07:35,802] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:07:35,826] [INFO] ===== Completeness check finished =====
[2024-01-25 20:07:35,826] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:07:35,826] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900113525.1_IMG-taxon_2634166297_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-25 20:07:35,827] [INFO] Task started: Blastn
[2024-01-25 20:07:35,827] [INFO] Running command: blastn -query GCF_900113525.1_IMG-taxon_2634166297_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg6ba8fa62-3cd4-4375-89b7-c02491a2b5ed/dqc_reference/reference_markers_gtdb.fasta -out GCF_900113525.1_IMG-taxon_2634166297_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:07:36,673] [INFO] Task succeeded: Blastn
[2024-01-25 20:07:36,677] [INFO] Selected 14 target genomes.
[2024-01-25 20:07:36,677] [INFO] Target genome list was writen to GCF_900113525.1_IMG-taxon_2634166297_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:07:36,690] [INFO] Task started: fastANI
[2024-01-25 20:07:36,690] [INFO] Running command: fastANI --query /var/lib/cwl/stge2382ac0-19af-4dd4-9746-a739e9b67821/GCF_900113525.1_IMG-taxon_2634166297_annotated_assembly_genomic.fna.gz --refList GCF_900113525.1_IMG-taxon_2634166297_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900113525.1_IMG-taxon_2634166297_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:07:50,317] [INFO] Task succeeded: fastANI
[2024-01-25 20:07:50,325] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:07:50,325] [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_900113525.1	s__Pedobacter insulae	100.0	1450	1452	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_014377775.1	s__Pedobacter sp014377775	79.3189	400	1452	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005116475.1	s__Pedobacter sp005116475	79.309	369	1452	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014172375.1	s__Pedobacter planticolens	78.9633	415	1452	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001412215.1	s__Pedobacter sp001412215	78.9077	389	1452	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004331645.1	s__Pedobacter sp004331645	78.8595	424	1452	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005116505.1	s__Pedobacter sp005116505	78.8527	397	1452	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013204825.1	s__Pedobacter boryungensis	78.7934	393	1452	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003054115.1	s__Pedobacter sp003054115	78.0014	186	1452	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016429155.1	s__Pedobacter sp016429155	77.9827	215	1452	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001636695.1	s__Pedobacter panaciterrae_A	77.8586	180	1452	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004335085.1	s__Pedobacter nototheniae	77.6909	183	1452	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	98.28	98.28	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2024-01-25 20:07:50,329] [INFO] GTDB search result was written to GCF_900113525.1_IMG-taxon_2634166297_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-25 20:07:50,329] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:07:50,332] [INFO] DFAST_QC result json was written to GCF_900113525.1_IMG-taxon_2634166297_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-25 20:07:50,332] [INFO] DFAST_QC completed!
[2024-01-25 20:07:50,332] [INFO] Total running time: 0h1m30s