[2023-06-30 20:45:15,525] [INFO] DFAST_QC pipeline started.
[2023-06-30 20:45:15,528] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 20:45:15,528] [INFO] DQC Reference Directory: /var/lib/cwl/stg2db9e0e1-4365-45b5-802a-597bb1778c45/dqc_reference
[2023-06-30 20:45:17,806] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 20:45:17,807] [INFO] Task started: Prodigal
[2023-06-30 20:45:17,807] [INFO] Running command: gunzip -c /var/lib/cwl/stg88c8d62d-4cdf-431e-af8c-dc47e177d623/GCA_903834635.1_freshwater_MAG_---_A14_bin-3063_genomic.fna.gz | prodigal -d GCA_903834635.1_freshwater_MAG_---_A14_bin-3063_genomic.fna/cds.fna -a GCA_903834635.1_freshwater_MAG_---_A14_bin-3063_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 20:45:21,696] [INFO] Task succeeded: Prodigal
[2023-06-30 20:45:21,697] [INFO] Task started: HMMsearch
[2023-06-30 20:45:21,697] [INFO] Running command: hmmsearch --tblout GCA_903834635.1_freshwater_MAG_---_A14_bin-3063_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2db9e0e1-4365-45b5-802a-597bb1778c45/dqc_reference/reference_markers.hmm GCA_903834635.1_freshwater_MAG_---_A14_bin-3063_genomic.fna/protein.faa > /dev/null
[2023-06-30 20:45:21,914] [INFO] Task succeeded: HMMsearch
[2023-06-30 20:45:21,915] [INFO] Found 6/6 markers.
[2023-06-30 20:45:21,936] [INFO] Query marker FASTA was written to GCA_903834635.1_freshwater_MAG_---_A14_bin-3063_genomic.fna/markers.fasta
[2023-06-30 20:45:21,936] [INFO] Task started: Blastn
[2023-06-30 20:45:21,936] [INFO] Running command: blastn -query GCA_903834635.1_freshwater_MAG_---_A14_bin-3063_genomic.fna/markers.fasta -db /var/lib/cwl/stg2db9e0e1-4365-45b5-802a-597bb1778c45/dqc_reference/reference_markers.fasta -out GCA_903834635.1_freshwater_MAG_---_A14_bin-3063_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 20:45:22,519] [INFO] Task succeeded: Blastn
[2023-06-30 20:45:22,524] [INFO] Selected 23 target genomes.
[2023-06-30 20:45:22,525] [INFO] Target genome list was writen to GCA_903834635.1_freshwater_MAG_---_A14_bin-3063_genomic.fna/target_genomes.txt
[2023-06-30 20:45:22,528] [INFO] Task started: fastANI
[2023-06-30 20:45:22,528] [INFO] Running command: fastANI --query /var/lib/cwl/stg88c8d62d-4cdf-431e-af8c-dc47e177d623/GCA_903834635.1_freshwater_MAG_---_A14_bin-3063_genomic.fna.gz --refList GCA_903834635.1_freshwater_MAG_---_A14_bin-3063_genomic.fna/target_genomes.txt --output GCA_903834635.1_freshwater_MAG_---_A14_bin-3063_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 20:45:33,293] [INFO] Task succeeded: fastANI
[2023-06-30 20:45:33,294] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2db9e0e1-4365-45b5-802a-597bb1778c45/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 20:45:33,295] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2db9e0e1-4365-45b5-802a-597bb1778c45/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 20:45:33,301] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 20:45:33,301] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 20:45:33,301] [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
Candidatus Rhodoluna planktonica	strain=MWH-Dar1	GCA_001854225.1	535712	535712	type	True	78.0621	58	418	95	below_threshold
Rhodoluna lacicola	strain=MWH-Ta8	GCA_000699505.1	529884	529884	type	True	77.7153	71	418	95	below_threshold
Rhodoluna limnophila	strain=27D-LEPI	GCA_005845365.1	232537	232537	type	True	77.5083	78	418	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 20:45:33,303] [INFO] DFAST Taxonomy check result was written to GCA_903834635.1_freshwater_MAG_---_A14_bin-3063_genomic.fna/tc_result.tsv
[2023-06-30 20:45:33,304] [INFO] ===== Taxonomy check completed =====
[2023-06-30 20:45:33,304] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 20:45:33,304] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2db9e0e1-4365-45b5-802a-597bb1778c45/dqc_reference/checkm_data
[2023-06-30 20:45:33,305] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 20:45:33,327] [INFO] Task started: CheckM
[2023-06-30 20:45:33,327] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903834635.1_freshwater_MAG_---_A14_bin-3063_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903834635.1_freshwater_MAG_---_A14_bin-3063_genomic.fna/checkm_input GCA_903834635.1_freshwater_MAG_---_A14_bin-3063_genomic.fna/checkm_result
[2023-06-30 20:45:52,599] [INFO] Task succeeded: CheckM
[2023-06-30 20:45:52,600] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 14.87%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2023-06-30 20:45:52,624] [INFO] ===== Completeness check finished =====
[2023-06-30 20:45:52,624] [INFO] ===== Start GTDB Search =====
[2023-06-30 20:45:52,624] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903834635.1_freshwater_MAG_---_A14_bin-3063_genomic.fna/markers.fasta)
[2023-06-30 20:45:52,625] [INFO] Task started: Blastn
[2023-06-30 20:45:52,625] [INFO] Running command: blastn -query GCA_903834635.1_freshwater_MAG_---_A14_bin-3063_genomic.fna/markers.fasta -db /var/lib/cwl/stg2db9e0e1-4365-45b5-802a-597bb1778c45/dqc_reference/reference_markers_gtdb.fasta -out GCA_903834635.1_freshwater_MAG_---_A14_bin-3063_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 20:45:53,376] [INFO] Task succeeded: Blastn
[2023-06-30 20:45:53,381] [INFO] Selected 21 target genomes.
[2023-06-30 20:45:53,381] [INFO] Target genome list was writen to GCA_903834635.1_freshwater_MAG_---_A14_bin-3063_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 20:45:53,390] [INFO] Task started: fastANI
[2023-06-30 20:45:53,391] [INFO] Running command: fastANI --query /var/lib/cwl/stg88c8d62d-4cdf-431e-af8c-dc47e177d623/GCA_903834635.1_freshwater_MAG_---_A14_bin-3063_genomic.fna.gz --refList GCA_903834635.1_freshwater_MAG_---_A14_bin-3063_genomic.fna/target_genomes_gtdb.txt --output GCA_903834635.1_freshwater_MAG_---_A14_bin-3063_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 20:45:59,954] [INFO] Task succeeded: fastANI
[2023-06-30 20:45:59,971] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 20:45:59,972] [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
GCA_903834635.1	s__Rhodoluna sp903834635	100.0	414	418	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rhodoluna	95.0	99.34	99.27	0.91	0.89	3	conclusive
GCA_903935175.1	s__Rhodoluna sp903935175	78.7696	124	418	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rhodoluna	95.0	99.50	99.50	0.86	0.86	2	-
GCA_903880095.1	s__Rhodoluna sp903880095	78.3675	101	418	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	78.1666	88	418	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rhodoluna	95.0	98.52	98.11	0.83	0.79	6	-
GCA_009703845.1	s__Rhodoluna sp009703845	77.866	79	418	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rhodoluna	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903893675.1	s__Rhodoluna sp903893675	77.6632	76	418	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rhodoluna	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903909605.1	s__Rhodoluna sp903909605	77.6187	80	418	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rhodoluna	95.0	99.84	99.84	0.93	0.93	2	-
GCA_009698805.1	s__Rhodoluna sp009698805	77.5829	94	418	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rhodoluna	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005845365.1	s__Rhodoluna limnophila	77.5083	78	418	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rhodoluna	95.0	98.04	97.94	0.96	0.95	3	-
GCA_009703445.1	s__Rhodoluna sp009703445	77.416	62	418	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rhodoluna	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017983965.1	s__Rhodoluna sp017983965	77.3918	66	418	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rhodoluna	95.0	99.54	99.54	0.80	0.80	2	-
GCA_903887175.1	s__Rhodoluna sp903887175	77.0627	73	418	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rhodoluna	95.0	99.56	99.56	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2023-06-30 20:45:59,974] [INFO] GTDB search result was written to GCA_903834635.1_freshwater_MAG_---_A14_bin-3063_genomic.fna/result_gtdb.tsv
[2023-06-30 20:45:59,975] [INFO] ===== GTDB Search completed =====
[2023-06-30 20:45:59,980] [INFO] DFAST_QC result json was written to GCA_903834635.1_freshwater_MAG_---_A14_bin-3063_genomic.fna/dqc_result.json
[2023-06-30 20:45:59,980] [INFO] DFAST_QC completed!
[2023-06-30 20:45:59,980] [INFO] Total running time: 0h0m44s