[2023-06-30 22:42:36,980] [INFO] DFAST_QC pipeline started.
[2023-06-30 22:42:36,985] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 22:42:36,986] [INFO] DQC Reference Directory: /var/lib/cwl/stg0d282849-31b1-4cb8-ac10-73df1203e497/dqc_reference
[2023-06-30 22:42:38,457] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 22:42:38,458] [INFO] Task started: Prodigal
[2023-06-30 22:42:38,458] [INFO] Running command: gunzip -c /var/lib/cwl/stg2af38424-6a16-4a6f-92dc-40d1f663fc78/GCA_903862645.1_freshwater_MAG_---_ErkenSummer_bin-3118_genomic.fna.gz | prodigal -d GCA_903862645.1_freshwater_MAG_---_ErkenSummer_bin-3118_genomic.fna/cds.fna -a GCA_903862645.1_freshwater_MAG_---_ErkenSummer_bin-3118_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 22:42:47,200] [INFO] Task succeeded: Prodigal
[2023-06-30 22:42:47,200] [INFO] Task started: HMMsearch
[2023-06-30 22:42:47,200] [INFO] Running command: hmmsearch --tblout GCA_903862645.1_freshwater_MAG_---_ErkenSummer_bin-3118_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0d282849-31b1-4cb8-ac10-73df1203e497/dqc_reference/reference_markers.hmm GCA_903862645.1_freshwater_MAG_---_ErkenSummer_bin-3118_genomic.fna/protein.faa > /dev/null
[2023-06-30 22:42:47,501] [INFO] Task succeeded: HMMsearch
[2023-06-30 22:42:47,502] [INFO] Found 6/6 markers.
[2023-06-30 22:42:47,546] [INFO] Query marker FASTA was written to GCA_903862645.1_freshwater_MAG_---_ErkenSummer_bin-3118_genomic.fna/markers.fasta
[2023-06-30 22:42:47,546] [INFO] Task started: Blastn
[2023-06-30 22:42:47,546] [INFO] Running command: blastn -query GCA_903862645.1_freshwater_MAG_---_ErkenSummer_bin-3118_genomic.fna/markers.fasta -db /var/lib/cwl/stg0d282849-31b1-4cb8-ac10-73df1203e497/dqc_reference/reference_markers.fasta -out GCA_903862645.1_freshwater_MAG_---_ErkenSummer_bin-3118_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 22:42:48,319] [INFO] Task succeeded: Blastn
[2023-06-30 22:42:48,323] [INFO] Selected 34 target genomes.
[2023-06-30 22:42:48,324] [INFO] Target genome list was writen to GCA_903862645.1_freshwater_MAG_---_ErkenSummer_bin-3118_genomic.fna/target_genomes.txt
[2023-06-30 22:42:48,326] [INFO] Task started: fastANI
[2023-06-30 22:42:48,326] [INFO] Running command: fastANI --query /var/lib/cwl/stg2af38424-6a16-4a6f-92dc-40d1f663fc78/GCA_903862645.1_freshwater_MAG_---_ErkenSummer_bin-3118_genomic.fna.gz --refList GCA_903862645.1_freshwater_MAG_---_ErkenSummer_bin-3118_genomic.fna/target_genomes.txt --output GCA_903862645.1_freshwater_MAG_---_ErkenSummer_bin-3118_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 22:43:12,940] [INFO] Task succeeded: fastANI
[2023-06-30 22:43:12,941] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0d282849-31b1-4cb8-ac10-73df1203e497/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 22:43:12,941] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0d282849-31b1-4cb8-ac10-73df1203e497/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 22:43:12,947] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 22:43:12,947] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 22:43:12,947] [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
Pseudohongiella spirulinae	strain=KCTC 32221	GCA_001444425.1	1249552	1249552	type	True	76.371	68	884	95	below_threshold
Pseudohongiella acticola	strain=KCTC 42131	GCA_001758195.1	1524254	1524254	type	True	76.3084	83	884	95	below_threshold
Pseudomonas cavernae	strain=K2W31S-8	GCA_003595175.1	2320867	2320867	type	True	75.8949	57	884	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 22:43:12,951] [INFO] DFAST Taxonomy check result was written to GCA_903862645.1_freshwater_MAG_---_ErkenSummer_bin-3118_genomic.fna/tc_result.tsv
[2023-06-30 22:43:12,953] [INFO] ===== Taxonomy check completed =====
[2023-06-30 22:43:12,953] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 22:43:12,953] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0d282849-31b1-4cb8-ac10-73df1203e497/dqc_reference/checkm_data
[2023-06-30 22:43:12,955] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 22:43:12,994] [INFO] Task started: CheckM
[2023-06-30 22:43:12,994] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903862645.1_freshwater_MAG_---_ErkenSummer_bin-3118_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903862645.1_freshwater_MAG_---_ErkenSummer_bin-3118_genomic.fna/checkm_input GCA_903862645.1_freshwater_MAG_---_ErkenSummer_bin-3118_genomic.fna/checkm_result
[2023-06-30 22:43:43,886] [INFO] Task succeeded: CheckM
[2023-06-30 22:43:43,887] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 22:43:43,910] [INFO] ===== Completeness check finished =====
[2023-06-30 22:43:43,910] [INFO] ===== Start GTDB Search =====
[2023-06-30 22:43:43,911] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903862645.1_freshwater_MAG_---_ErkenSummer_bin-3118_genomic.fna/markers.fasta)
[2023-06-30 22:43:43,911] [INFO] Task started: Blastn
[2023-06-30 22:43:43,911] [INFO] Running command: blastn -query GCA_903862645.1_freshwater_MAG_---_ErkenSummer_bin-3118_genomic.fna/markers.fasta -db /var/lib/cwl/stg0d282849-31b1-4cb8-ac10-73df1203e497/dqc_reference/reference_markers_gtdb.fasta -out GCA_903862645.1_freshwater_MAG_---_ErkenSummer_bin-3118_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 22:43:44,938] [INFO] Task succeeded: Blastn
[2023-06-30 22:43:44,943] [INFO] Selected 17 target genomes.
[2023-06-30 22:43:44,943] [INFO] Target genome list was writen to GCA_903862645.1_freshwater_MAG_---_ErkenSummer_bin-3118_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 22:43:44,992] [INFO] Task started: fastANI
[2023-06-30 22:43:44,992] [INFO] Running command: fastANI --query /var/lib/cwl/stg2af38424-6a16-4a6f-92dc-40d1f663fc78/GCA_903862645.1_freshwater_MAG_---_ErkenSummer_bin-3118_genomic.fna.gz --refList GCA_903862645.1_freshwater_MAG_---_ErkenSummer_bin-3118_genomic.fna/target_genomes_gtdb.txt --output GCA_903862645.1_freshwater_MAG_---_ErkenSummer_bin-3118_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 22:43:56,824] [INFO] Task succeeded: fastANI
[2023-06-30 22:43:56,832] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 22:43:56,832] [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_903862645.1	s__UBA5078 sp903862645	100.0	880	884	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA5078	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_903876785.1	s__UBA5078 sp903876785	84.7435	510	884	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA5078	95.0	99.18	99.13	0.80	0.78	4	-
GCA_001802565.1	s__UBA5078 sp001802565	78.5522	346	884	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA5078	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903889815.1	s__UBA5078 sp903889815	77.9192	227	884	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA5078	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002416505.1	s__UBA5078 sp002416505	77.082	187	884	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA5078	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011050365.1	s__Pseudohongiella sp011050365	76.5356	84	884	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__Pseudohongiella	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002706685.1	s__Pseudohongiella sp002706685	76.3887	69	884	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__Pseudohongiella	95.0	99.93	99.90	0.98	0.96	5	-
GCA_002354805.1	s__Pseudohongiella sp002354805	76.0839	70	884	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__Pseudohongiella	95.0	99.49	99.10	0.99	0.98	3	-
--------------------------------------------------------------------------------
[2023-06-30 22:43:56,834] [INFO] GTDB search result was written to GCA_903862645.1_freshwater_MAG_---_ErkenSummer_bin-3118_genomic.fna/result_gtdb.tsv
[2023-06-30 22:43:56,835] [INFO] ===== GTDB Search completed =====
[2023-06-30 22:43:56,837] [INFO] DFAST_QC result json was written to GCA_903862645.1_freshwater_MAG_---_ErkenSummer_bin-3118_genomic.fna/dqc_result.json
[2023-06-30 22:43:56,838] [INFO] DFAST_QC completed!
[2023-06-30 22:43:56,838] [INFO] Total running time: 0h1m20s