[2023-03-16 07:18:26,635] [INFO] DFAST_QC pipeline started.
[2023-03-16 07:18:26,635] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 07:18:26,635] [INFO] DQC Reference Directory: /var/lib/cwl/stgf2eace1d-e005-4c4d-9ec9-a7b3e8459a2d/dqc_reference
[2023-03-16 07:18:27,749] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 07:18:27,749] [INFO] Task started: Prodigal
[2023-03-16 07:18:27,749] [INFO] Running command: cat /var/lib/cwl/stg2525bf42-0cbe-47b1-9bd3-586598267251/OceanDNA-b25781.fa | prodigal -d OceanDNA-b25781/cds.fna -a OceanDNA-b25781/protein.faa -g 11 -q > /dev/null
[2023-03-16 07:18:32,606] [INFO] Task succeeded: Prodigal
[2023-03-16 07:18:32,606] [INFO] Task started: HMMsearch
[2023-03-16 07:18:32,607] [INFO] Running command: hmmsearch --tblout OceanDNA-b25781/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf2eace1d-e005-4c4d-9ec9-a7b3e8459a2d/dqc_reference/reference_markers.hmm OceanDNA-b25781/protein.faa > /dev/null
[2023-03-16 07:18:32,741] [INFO] Task succeeded: HMMsearch
[2023-03-16 07:18:32,742] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg2525bf42-0cbe-47b1-9bd3-586598267251/OceanDNA-b25781.fa]
[2023-03-16 07:18:32,751] [INFO] Query marker FASTA was written to OceanDNA-b25781/markers.fasta
[2023-03-16 07:18:32,751] [INFO] Task started: Blastn
[2023-03-16 07:18:32,751] [INFO] Running command: blastn -query OceanDNA-b25781/markers.fasta -db /var/lib/cwl/stgf2eace1d-e005-4c4d-9ec9-a7b3e8459a2d/dqc_reference/reference_markers.fasta -out OceanDNA-b25781/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:18:33,234] [INFO] Task succeeded: Blastn
[2023-03-16 07:18:33,235] [INFO] Selected 10 target genomes.
[2023-03-16 07:18:33,235] [INFO] Target genome list was writen to OceanDNA-b25781/target_genomes.txt
[2023-03-16 07:18:33,242] [INFO] Task started: fastANI
[2023-03-16 07:18:33,242] [INFO] Running command: fastANI --query /var/lib/cwl/stg2525bf42-0cbe-47b1-9bd3-586598267251/OceanDNA-b25781.fa --refList OceanDNA-b25781/target_genomes.txt --output OceanDNA-b25781/fastani_result.tsv --threads 1
[2023-03-16 07:18:37,190] [INFO] Task succeeded: fastANI
[2023-03-16 07:18:37,190] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf2eace1d-e005-4c4d-9ec9-a7b3e8459a2d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 07:18:37,190] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf2eace1d-e005-4c4d-9ec9-a7b3e8459a2d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 07:18:37,244] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 07:18:37,244] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 07:18:37,244] [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	84.5784	217	246	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 07:18:37,245] [INFO] DFAST Taxonomy check result was written to OceanDNA-b25781/tc_result.tsv
[2023-03-16 07:18:37,245] [INFO] ===== Taxonomy check completed =====
[2023-03-16 07:18:37,245] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 07:18:37,245] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf2eace1d-e005-4c4d-9ec9-a7b3e8459a2d/dqc_reference/checkm_data
[2023-03-16 07:18:37,246] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 07:18:37,312] [INFO] Task started: CheckM
[2023-03-16 07:18:37,312] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b25781/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b25781/checkm_input OceanDNA-b25781/checkm_result
[2023-03-16 07:18:56,644] [INFO] Task succeeded: CheckM
[2023-03-16 07:18:56,645] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 8.33%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-16 07:18:56,647] [INFO] ===== Completeness check finished =====
[2023-03-16 07:18:56,647] [INFO] ===== Start GTDB Search =====
[2023-03-16 07:18:56,647] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b25781/markers.fasta)
[2023-03-16 07:18:56,648] [INFO] Task started: Blastn
[2023-03-16 07:18:56,648] [INFO] Running command: blastn -query OceanDNA-b25781/markers.fasta -db /var/lib/cwl/stgf2eace1d-e005-4c4d-9ec9-a7b3e8459a2d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b25781/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:18:57,347] [INFO] Task succeeded: Blastn
[2023-03-16 07:18:57,348] [INFO] Selected 13 target genomes.
[2023-03-16 07:18:57,348] [INFO] Target genome list was writen to OceanDNA-b25781/target_genomes_gtdb.txt
[2023-03-16 07:18:57,363] [INFO] Task started: fastANI
[2023-03-16 07:18:57,363] [INFO] Running command: fastANI --query /var/lib/cwl/stg2525bf42-0cbe-47b1-9bd3-586598267251/OceanDNA-b25781.fa --refList OceanDNA-b25781/target_genomes_gtdb.txt --output OceanDNA-b25781/fastani_result_gtdb.tsv --threads 1
[2023-03-16 07:18:59,730] [INFO] Task succeeded: fastANI
[2023-03-16 07:18:59,738] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 07:18:59,739] [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_013204495.1	s__Pelagibacter sp013204495	96.3902	187	246	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000012345.1	s__Pelagibacter ubique	84.5784	217	246	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	97.94	97.32	0.95	0.89	15	-
GCA_905618905.1	s__Pelagibacter sp905618905	84.0862	133	246	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012276695.1	s__Pelagibacter giovannonii	83.7278	216	246	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905612385.1	s__Pelagibacter sp905612385	83.5899	85	246	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905612495.1	s__Pelagibacter sp905612495	83.5318	131	246	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905616395.1	s__Pelagibacter sp905616395	83.3737	189	246	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	95.02	95.02	0.70	0.70	2	-
GCA_905612465.1	s__Pelagibacter sp905612465	83.1633	103	246	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905612375.1	s__Pelagibacter sp905612375	83.0816	115	246	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905612525.1	s__Pelagibacter sp905612525	82.6955	118	246	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905618805.1	s__Pelagibacter sp905618805	82.5003	117	246	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902552705.1	s__Pelagibacter sp902552705	79.7212	109	246	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905616435.1	s__Pelagibacter sp905616435	79.345	71	246	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 07:18:59,739] [INFO] GTDB search result was written to OceanDNA-b25781/result_gtdb.tsv
[2023-03-16 07:18:59,739] [INFO] ===== GTDB Search completed =====
[2023-03-16 07:18:59,740] [INFO] DFAST_QC result json was written to OceanDNA-b25781/dqc_result.json
[2023-03-16 07:18:59,740] [INFO] DFAST_QC completed!
[2023-03-16 07:18:59,740] [INFO] Total running time: 0h0m33s