[2024-01-24 15:10:23,009] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:10:23,011] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:10:23,012] [INFO] DQC Reference Directory: /var/lib/cwl/stgd98cb28e-9038-4626-ba9a-42088a255b5e/dqc_reference
[2024-01-24 15:10:24,476] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:10:24,477] [INFO] Task started: Prodigal
[2024-01-24 15:10:24,477] [INFO] Running command: gunzip -c /var/lib/cwl/stg17d15efc-a47c-4d01-acaf-dac229078edb/GCF_005845365.1_ASM584536v1_genomic.fna.gz | prodigal -d GCF_005845365.1_ASM584536v1_genomic.fna/cds.fna -a GCF_005845365.1_ASM584536v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:10:28,725] [INFO] Task succeeded: Prodigal
[2024-01-24 15:10:28,726] [INFO] Task started: HMMsearch
[2024-01-24 15:10:28,726] [INFO] Running command: hmmsearch --tblout GCF_005845365.1_ASM584536v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd98cb28e-9038-4626-ba9a-42088a255b5e/dqc_reference/reference_markers.hmm GCF_005845365.1_ASM584536v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:10:28,932] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:10:28,933] [INFO] Found 6/6 markers.
[2024-01-24 15:10:28,957] [INFO] Query marker FASTA was written to GCF_005845365.1_ASM584536v1_genomic.fna/markers.fasta
[2024-01-24 15:10:28,957] [INFO] Task started: Blastn
[2024-01-24 15:10:28,957] [INFO] Running command: blastn -query GCF_005845365.1_ASM584536v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd98cb28e-9038-4626-ba9a-42088a255b5e/dqc_reference/reference_markers.fasta -out GCF_005845365.1_ASM584536v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:10:30,417] [INFO] Task succeeded: Blastn
[2024-01-24 15:10:30,421] [INFO] Selected 21 target genomes.
[2024-01-24 15:10:30,421] [INFO] Target genome list was writen to GCF_005845365.1_ASM584536v1_genomic.fna/target_genomes.txt
[2024-01-24 15:10:30,497] [INFO] Task started: fastANI
[2024-01-24 15:10:30,498] [INFO] Running command: fastANI --query /var/lib/cwl/stg17d15efc-a47c-4d01-acaf-dac229078edb/GCF_005845365.1_ASM584536v1_genomic.fna.gz --refList GCF_005845365.1_ASM584536v1_genomic.fna/target_genomes.txt --output GCF_005845365.1_ASM584536v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:10:41,897] [INFO] Task succeeded: fastANI
[2024-01-24 15:10:41,897] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd98cb28e-9038-4626-ba9a-42088a255b5e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:10:41,898] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd98cb28e-9038-4626-ba9a-42088a255b5e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:10:41,903] [INFO] Found 3 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:10:41,903] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:10:41,903] [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
Rhodoluna limnophila	strain=27D-LEPI	GCA_005845365.1	232537	232537	type	True	100.0	466	466	95	conclusive
Rhodoluna lacicola	strain=MWH-Ta8	GCA_000699505.1	529884	529884	type	True	79.492	160	466	95	below_threshold
Candidatus Rhodoluna planktonica	strain=MWH-Dar1	GCA_001854225.1	535712	535712	type	True	78.8239	107	466	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:10:41,905] [INFO] DFAST Taxonomy check result was written to GCF_005845365.1_ASM584536v1_genomic.fna/tc_result.tsv
[2024-01-24 15:10:41,905] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:10:41,905] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:10:41,906] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd98cb28e-9038-4626-ba9a-42088a255b5e/dqc_reference/checkm_data
[2024-01-24 15:10:41,907] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:10:41,923] [INFO] Task started: CheckM
[2024-01-24 15:10:41,924] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005845365.1_ASM584536v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005845365.1_ASM584536v1_genomic.fna/checkm_input GCF_005845365.1_ASM584536v1_genomic.fna/checkm_result
[2024-01-24 15:11:02,490] [INFO] Task succeeded: CheckM
[2024-01-24 15:11:02,491] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:11:02,519] [INFO] ===== Completeness check finished =====
[2024-01-24 15:11:02,519] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:11:02,520] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005845365.1_ASM584536v1_genomic.fna/markers.fasta)
[2024-01-24 15:11:02,520] [INFO] Task started: Blastn
[2024-01-24 15:11:02,520] [INFO] Running command: blastn -query GCF_005845365.1_ASM584536v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd98cb28e-9038-4626-ba9a-42088a255b5e/dqc_reference/reference_markers_gtdb.fasta -out GCF_005845365.1_ASM584536v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:11:03,338] [INFO] Task succeeded: Blastn
[2024-01-24 15:11:03,341] [INFO] Selected 22 target genomes.
[2024-01-24 15:11:03,342] [INFO] Target genome list was writen to GCF_005845365.1_ASM584536v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:11:03,378] [INFO] Task started: fastANI
[2024-01-24 15:11:03,378] [INFO] Running command: fastANI --query /var/lib/cwl/stg17d15efc-a47c-4d01-acaf-dac229078edb/GCF_005845365.1_ASM584536v1_genomic.fna.gz --refList GCF_005845365.1_ASM584536v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005845365.1_ASM584536v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:11:12,554] [INFO] Task succeeded: fastANI
[2024-01-24 15:11:12,564] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:11:12,564] [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_005845365.1	s__Rhodoluna limnophila	100.0	466	466	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rhodoluna	95.0	98.04	97.94	0.96	0.95	3	conclusive
GCF_000699505.1	s__Rhodoluna lacicola	79.492	160	466	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rhodoluna	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903866485.1	s__Rhodoluna sp903866485	79.3937	87	466	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rhodoluna	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009703445.1	s__Rhodoluna sp009703445	79.1092	117	466	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rhodoluna	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001854225.1	s__Rhodoluna planktonica	78.8239	107	466	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rhodoluna	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017984715.1	s__Rhodoluna sp017984715	78.4842	71	466	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rhodoluna	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903935175.1	s__Rhodoluna sp903935175	78.0878	81	466	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rhodoluna	95.0	99.50	99.50	0.86	0.86	2	-
GCA_903909605.1	s__Rhodoluna sp903909605	78.0453	86	466	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rhodoluna	95.0	99.84	99.84	0.93	0.93	2	-
GCA_903893675.1	s__Rhodoluna sp903893675	77.8046	77	466	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rhodoluna	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903820955.1	s__Rhodoluna sp903820955	77.2647	68	466	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rhodoluna	95.0	98.52	98.11	0.83	0.79	6	-
GCA_009703465.1	s__Rhodoluna sp009703465	76.9576	54	466	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rhodoluna	95.0	98.63	98.63	0.78	0.78	2	-
--------------------------------------------------------------------------------
[2024-01-24 15:11:12,566] [INFO] GTDB search result was written to GCF_005845365.1_ASM584536v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:11:12,567] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:11:12,573] [INFO] DFAST_QC result json was written to GCF_005845365.1_ASM584536v1_genomic.fna/dqc_result.json
[2024-01-24 15:11:12,573] [INFO] DFAST_QC completed!
[2024-01-24 15:11:12,573] [INFO] Total running time: 0h0m50s