[2023-06-08 16:16:11,138] [INFO] DFAST_QC pipeline started.
[2023-06-08 16:16:11,141] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 16:16:11,141] [INFO] DQC Reference Directory: /var/lib/cwl/stgd3712178-c2cb-4710-93a7-5278dc9ee33e/dqc_reference
[2023-06-08 16:16:12,374] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 16:16:12,375] [INFO] Task started: Prodigal
[2023-06-08 16:16:12,376] [INFO] Running command: gunzip -c /var/lib/cwl/stg509142e0-0cf5-411c-90bd-f5bad462234e/GCA_902614985.1_AG-919-D05_genomic.fna.gz | prodigal -d GCA_902614985.1_AG-919-D05_genomic.fna/cds.fna -a GCA_902614985.1_AG-919-D05_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 16:16:14,250] [INFO] Task succeeded: Prodigal
[2023-06-08 16:16:14,251] [INFO] Task started: HMMsearch
[2023-06-08 16:16:14,251] [INFO] Running command: hmmsearch --tblout GCA_902614985.1_AG-919-D05_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd3712178-c2cb-4710-93a7-5278dc9ee33e/dqc_reference/reference_markers.hmm GCA_902614985.1_AG-919-D05_genomic.fna/protein.faa > /dev/null
[2023-06-08 16:16:14,397] [INFO] Task succeeded: HMMsearch
[2023-06-08 16:16:14,398] [WARNING] Found 1/6 markers. [/var/lib/cwl/stg509142e0-0cf5-411c-90bd-f5bad462234e/GCA_902614985.1_AG-919-D05_genomic.fna.gz]
[2023-06-08 16:16:14,411] [INFO] Query marker FASTA was written to GCA_902614985.1_AG-919-D05_genomic.fna/markers.fasta
[2023-06-08 16:16:14,411] [INFO] Task started: Blastn
[2023-06-08 16:16:14,411] [INFO] Running command: blastn -query GCA_902614985.1_AG-919-D05_genomic.fna/markers.fasta -db /var/lib/cwl/stgd3712178-c2cb-4710-93a7-5278dc9ee33e/dqc_reference/reference_markers.fasta -out GCA_902614985.1_AG-919-D05_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 16:16:14,919] [INFO] Task succeeded: Blastn
[2023-06-08 16:16:14,922] [INFO] Selected 4 target genomes.
[2023-06-08 16:16:14,922] [INFO] Target genome list was writen to GCA_902614985.1_AG-919-D05_genomic.fna/target_genomes.txt
[2023-06-08 16:16:14,924] [INFO] Task started: fastANI
[2023-06-08 16:16:14,924] [INFO] Running command: fastANI --query /var/lib/cwl/stg509142e0-0cf5-411c-90bd-f5bad462234e/GCA_902614985.1_AG-919-D05_genomic.fna.gz --refList GCA_902614985.1_AG-919-D05_genomic.fna/target_genomes.txt --output GCA_902614985.1_AG-919-D05_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 16:16:16,029] [INFO] Task succeeded: fastANI
[2023-06-08 16:16:16,030] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd3712178-c2cb-4710-93a7-5278dc9ee33e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 16:16:16,030] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd3712178-c2cb-4710-93a7-5278dc9ee33e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 16:16:16,036] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 16:16:16,036] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 16:16:16,036] [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 Pelagibacter ubique	strain=HTCC1062	GCA_000012345.1	198252	198252	suspected-type	True	78.4493	100	198	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 16:16:16,039] [INFO] DFAST Taxonomy check result was written to GCA_902614985.1_AG-919-D05_genomic.fna/tc_result.tsv
[2023-06-08 16:16:16,039] [INFO] ===== Taxonomy check completed =====
[2023-06-08 16:16:16,040] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 16:16:16,040] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd3712178-c2cb-4710-93a7-5278dc9ee33e/dqc_reference/checkm_data
[2023-06-08 16:16:16,042] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 16:16:16,052] [INFO] Task started: CheckM
[2023-06-08 16:16:16,052] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902614985.1_AG-919-D05_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902614985.1_AG-919-D05_genomic.fna/checkm_input GCA_902614985.1_AG-919-D05_genomic.fna/checkm_result
[2023-06-08 16:16:29,400] [INFO] Task succeeded: CheckM
[2023-06-08 16:16:29,402] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 37.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 16:16:29,420] [INFO] ===== Completeness check finished =====
[2023-06-08 16:16:29,421] [INFO] ===== Start GTDB Search =====
[2023-06-08 16:16:29,421] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902614985.1_AG-919-D05_genomic.fna/markers.fasta)
[2023-06-08 16:16:29,421] [INFO] Task started: Blastn
[2023-06-08 16:16:29,422] [INFO] Running command: blastn -query GCA_902614985.1_AG-919-D05_genomic.fna/markers.fasta -db /var/lib/cwl/stgd3712178-c2cb-4710-93a7-5278dc9ee33e/dqc_reference/reference_markers_gtdb.fasta -out GCA_902614985.1_AG-919-D05_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 16:16:29,877] [INFO] Task succeeded: Blastn
[2023-06-08 16:16:29,882] [INFO] Selected 5 target genomes.
[2023-06-08 16:16:29,882] [INFO] Target genome list was writen to GCA_902614985.1_AG-919-D05_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 16:16:29,886] [INFO] Task started: fastANI
[2023-06-08 16:16:29,887] [INFO] Running command: fastANI --query /var/lib/cwl/stg509142e0-0cf5-411c-90bd-f5bad462234e/GCA_902614985.1_AG-919-D05_genomic.fna.gz --refList GCA_902614985.1_AG-919-D05_genomic.fna/target_genomes_gtdb.txt --output GCA_902614985.1_AG-919-D05_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 16:16:30,934] [INFO] Task succeeded: fastANI
[2023-06-08 16:16:30,940] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 16:16:30,941] [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_902532645.1	s__Pelagibacter sp902532645	95.7385	97	198	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902557155.1	s__Pelagibacter sp902557155	91.7165	155	198	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902558585.1	s__Pelagibacter sp902558585	91.6567	113	198	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000504225.1	s__Pelagibacter ubique_Q	90.5089	156	198	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	95.93	95.93	0.95	0.95	2	-
GCA_902592935.1	s__Pelagibacter sp902592935	89.2057	104	198	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 16:16:30,943] [INFO] GTDB search result was written to GCA_902614985.1_AG-919-D05_genomic.fna/result_gtdb.tsv
[2023-06-08 16:16:30,943] [INFO] ===== GTDB Search completed =====
[2023-06-08 16:16:30,946] [INFO] DFAST_QC result json was written to GCA_902614985.1_AG-919-D05_genomic.fna/dqc_result.json
[2023-06-08 16:16:30,946] [INFO] DFAST_QC completed!
[2023-06-08 16:16:30,946] [INFO] Total running time: 0h0m20s