[2023-03-19 00:53:19,705] [INFO] DFAST_QC pipeline started.
[2023-03-19 00:53:19,705] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 00:53:19,705] [INFO] DQC Reference Directory: /var/lib/cwl/stg545e1da5-b2fe-420b-89ad-846fb5ffa4f3/dqc_reference
[2023-03-19 00:53:20,795] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 00:53:20,796] [INFO] Task started: Prodigal
[2023-03-19 00:53:20,796] [INFO] Running command: cat /var/lib/cwl/stge044b25f-3c5e-40a8-835f-b03f378d2202/OceanDNA-b26783.fa | prodigal -d OceanDNA-b26783/cds.fna -a OceanDNA-b26783/protein.faa -g 11 -q > /dev/null
[2023-03-19 00:53:29,653] [INFO] Task succeeded: Prodigal
[2023-03-19 00:53:29,654] [INFO] Task started: HMMsearch
[2023-03-19 00:53:29,654] [INFO] Running command: hmmsearch --tblout OceanDNA-b26783/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg545e1da5-b2fe-420b-89ad-846fb5ffa4f3/dqc_reference/reference_markers.hmm OceanDNA-b26783/protein.faa > /dev/null
[2023-03-19 00:53:29,794] [INFO] Task succeeded: HMMsearch
[2023-03-19 00:53:29,795] [WARNING] Found 3/6 markers. [/var/lib/cwl/stge044b25f-3c5e-40a8-835f-b03f378d2202/OceanDNA-b26783.fa]
[2023-03-19 00:53:29,809] [INFO] Query marker FASTA was written to OceanDNA-b26783/markers.fasta
[2023-03-19 00:53:29,810] [INFO] Task started: Blastn
[2023-03-19 00:53:29,810] [INFO] Running command: blastn -query OceanDNA-b26783/markers.fasta -db /var/lib/cwl/stg545e1da5-b2fe-420b-89ad-846fb5ffa4f3/dqc_reference/reference_markers.fasta -out OceanDNA-b26783/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:53:30,262] [INFO] Task succeeded: Blastn
[2023-03-19 00:53:30,263] [INFO] Selected 16 target genomes.
[2023-03-19 00:53:30,264] [INFO] Target genome list was writen to OceanDNA-b26783/target_genomes.txt
[2023-03-19 00:53:30,273] [INFO] Task started: fastANI
[2023-03-19 00:53:30,273] [INFO] Running command: fastANI --query /var/lib/cwl/stge044b25f-3c5e-40a8-835f-b03f378d2202/OceanDNA-b26783.fa --refList OceanDNA-b26783/target_genomes.txt --output OceanDNA-b26783/fastani_result.tsv --threads 1
[2023-03-19 00:53:43,462] [INFO] Task succeeded: fastANI
[2023-03-19 00:53:43,462] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg545e1da5-b2fe-420b-89ad-846fb5ffa4f3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 00:53:43,462] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg545e1da5-b2fe-420b-89ad-846fb5ffa4f3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 00:53:43,465] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 00:53:43,466] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 00:53:43,466] [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
Mesorhizobium composti	strain=CC-YTH430	GCA_004801285.1	2675109	2675109	type	True	75.9439	50	432	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 00:53:43,466] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26783/tc_result.tsv
[2023-03-19 00:53:43,466] [INFO] ===== Taxonomy check completed =====
[2023-03-19 00:53:43,466] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 00:53:43,467] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg545e1da5-b2fe-420b-89ad-846fb5ffa4f3/dqc_reference/checkm_data
[2023-03-19 00:53:43,467] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 00:53:43,536] [INFO] Task started: CheckM
[2023-03-19 00:53:43,537] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26783/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26783/checkm_input OceanDNA-b26783/checkm_result
[2023-03-19 00:54:09,809] [INFO] Task succeeded: CheckM
[2023-03-19 00:54:09,810] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 49.48%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 00:54:09,812] [INFO] ===== Completeness check finished =====
[2023-03-19 00:54:09,812] [INFO] ===== Start GTDB Search =====
[2023-03-19 00:54:09,812] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26783/markers.fasta)
[2023-03-19 00:54:09,814] [INFO] Task started: Blastn
[2023-03-19 00:54:09,814] [INFO] Running command: blastn -query OceanDNA-b26783/markers.fasta -db /var/lib/cwl/stg545e1da5-b2fe-420b-89ad-846fb5ffa4f3/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26783/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:54:10,267] [INFO] Task succeeded: Blastn
[2023-03-19 00:54:10,268] [INFO] Selected 19 target genomes.
[2023-03-19 00:54:10,268] [INFO] Target genome list was writen to OceanDNA-b26783/target_genomes_gtdb.txt
[2023-03-19 00:54:10,279] [INFO] Task started: fastANI
[2023-03-19 00:54:10,279] [INFO] Running command: fastANI --query /var/lib/cwl/stge044b25f-3c5e-40a8-835f-b03f378d2202/OceanDNA-b26783.fa --refList OceanDNA-b26783/target_genomes_gtdb.txt --output OceanDNA-b26783/fastani_result_gtdb.tsv --threads 1
[2023-03-19 00:54:26,143] [INFO] Task succeeded: fastANI
[2023-03-19 00:54:26,147] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 00:54:26,147] [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_004801285.1	s__Mesorhizobium composti	75.9439	50	432	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	96.99	96.99	0.90	0.90	2	-
GCF_001014615.2	s__Aquamicrobium_A sp001014615	75.7979	57	432	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aquamicrobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004331955.1	s__Roseitalea porphyridii	75.6309	64	432	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Roseitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003012745.1	s__Mesorhizobium_D ephedrae	75.6249	60	432	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium_D	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 00:54:26,147] [INFO] GTDB search result was written to OceanDNA-b26783/result_gtdb.tsv
[2023-03-19 00:54:26,147] [INFO] ===== GTDB Search completed =====
[2023-03-19 00:54:26,148] [INFO] DFAST_QC result json was written to OceanDNA-b26783/dqc_result.json
[2023-03-19 00:54:26,149] [INFO] DFAST_QC completed!
[2023-03-19 00:54:26,149] [INFO] Total running time: 0h1m6s