[2023-03-18 01:41:20,939] [INFO] DFAST_QC pipeline started.
[2023-03-18 01:41:20,939] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 01:41:20,939] [INFO] DQC Reference Directory: /var/lib/cwl/stgc5ae18ee-15a3-451c-9e00-35d5e274dd63/dqc_reference
[2023-03-18 01:41:22,074] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 01:41:22,075] [INFO] Task started: Prodigal
[2023-03-18 01:41:22,075] [INFO] Running command: cat /var/lib/cwl/stgd57a565c-52be-4815-8491-a4b045c65677/OceanDNA-b25764.fa | prodigal -d OceanDNA-b25764/cds.fna -a OceanDNA-b25764/protein.faa -g 11 -q > /dev/null
[2023-03-18 01:41:26,353] [INFO] Task succeeded: Prodigal
[2023-03-18 01:41:26,354] [INFO] Task started: HMMsearch
[2023-03-18 01:41:26,354] [INFO] Running command: hmmsearch --tblout OceanDNA-b25764/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc5ae18ee-15a3-451c-9e00-35d5e274dd63/dqc_reference/reference_markers.hmm OceanDNA-b25764/protein.faa > /dev/null
[2023-03-18 01:41:26,509] [INFO] Task succeeded: HMMsearch
[2023-03-18 01:41:26,509] [INFO] Found 6/6 markers.
[2023-03-18 01:41:26,516] [INFO] Query marker FASTA was written to OceanDNA-b25764/markers.fasta
[2023-03-18 01:41:26,517] [INFO] Task started: Blastn
[2023-03-18 01:41:26,517] [INFO] Running command: blastn -query OceanDNA-b25764/markers.fasta -db /var/lib/cwl/stgc5ae18ee-15a3-451c-9e00-35d5e274dd63/dqc_reference/reference_markers.fasta -out OceanDNA-b25764/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:41:27,046] [INFO] Task succeeded: Blastn
[2023-03-18 01:41:27,047] [INFO] Selected 16 target genomes.
[2023-03-18 01:41:27,047] [INFO] Target genome list was writen to OceanDNA-b25764/target_genomes.txt
[2023-03-18 01:41:27,058] [INFO] Task started: fastANI
[2023-03-18 01:41:27,058] [INFO] Running command: fastANI --query /var/lib/cwl/stgd57a565c-52be-4815-8491-a4b045c65677/OceanDNA-b25764.fa --refList OceanDNA-b25764/target_genomes.txt --output OceanDNA-b25764/fastani_result.tsv --threads 1
[2023-03-18 01:41:32,052] [INFO] Task succeeded: fastANI
[2023-03-18 01:41:32,052] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc5ae18ee-15a3-451c-9e00-35d5e274dd63/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 01:41:32,053] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc5ae18ee-15a3-451c-9e00-35d5e274dd63/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 01:41:32,056] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 01:41:32,056] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 01:41:32,056] [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	80.2183	163	209	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 01:41:32,056] [INFO] DFAST Taxonomy check result was written to OceanDNA-b25764/tc_result.tsv
[2023-03-18 01:41:32,056] [INFO] ===== Taxonomy check completed =====
[2023-03-18 01:41:32,056] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 01:41:32,056] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc5ae18ee-15a3-451c-9e00-35d5e274dd63/dqc_reference/checkm_data
[2023-03-18 01:41:32,057] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 01:41:32,059] [INFO] Task started: CheckM
[2023-03-18 01:41:32,059] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b25764/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b25764/checkm_input OceanDNA-b25764/checkm_result
[2023-03-18 01:41:48,630] [INFO] Task succeeded: CheckM
[2023-03-18 01:41:48,630] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.49%
Contamintation: 2.08%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 01:41:48,632] [INFO] ===== Completeness check finished =====
[2023-03-18 01:41:48,632] [INFO] ===== Start GTDB Search =====
[2023-03-18 01:41:48,632] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b25764/markers.fasta)
[2023-03-18 01:41:48,633] [INFO] Task started: Blastn
[2023-03-18 01:41:48,633] [INFO] Running command: blastn -query OceanDNA-b25764/markers.fasta -db /var/lib/cwl/stgc5ae18ee-15a3-451c-9e00-35d5e274dd63/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b25764/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:41:49,511] [INFO] Task succeeded: Blastn
[2023-03-18 01:41:49,512] [INFO] Selected 22 target genomes.
[2023-03-18 01:41:49,512] [INFO] Target genome list was writen to OceanDNA-b25764/target_genomes_gtdb.txt
[2023-03-18 01:41:49,530] [INFO] Task started: fastANI
[2023-03-18 01:41:49,530] [INFO] Running command: fastANI --query /var/lib/cwl/stgd57a565c-52be-4815-8491-a4b045c65677/OceanDNA-b25764.fa --refList OceanDNA-b25764/target_genomes_gtdb.txt --output OceanDNA-b25764/fastani_result_gtdb.tsv --threads 1
[2023-03-18 01:41:53,541] [INFO] Task succeeded: fastANI
[2023-03-18 01:41:53,554] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 01:41:53,554] [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_905478565.1	s__Pelagibacter sp905478565	98.723	129	209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	98.97	98.88	0.54	0.54	3	conclusive
GCA_905616395.1	s__Pelagibacter sp905616395	80.302	135	209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	95.02	95.02	0.70	0.70	2	-
GCF_000012345.1	s__Pelagibacter ubique	80.2183	163	209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	97.94	97.32	0.95	0.89	15	-
GCA_014653975.1	s__Pelagibacter sp014653975	80.2139	111	209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905618905.1	s__Pelagibacter sp905618905	80.1377	91	209	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	80.094	104	209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905618895.1	s__Pelagibacter sp905618895	80.0393	96	209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905612335.1	s__Pelagibacter sp905612335	80.0197	78	209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905612465.1	s__Pelagibacter sp905612465	80.0137	84	209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905612365.1	s__Pelagibacter sp905612365	79.8414	78	209	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	79.755	96	209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902573385.1	s__Pelagibacter sp902573385	79.5684	88	209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905612435.1	s__Pelagibacter sp905612435	79.5392	106	209	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	79.5239	100	209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902560015.1	s__Pelagibacter sp902560015	78.6784	99	209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902515485.1	s__Pelagibacter sp902515485	78.6098	59	209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000701385.1	s__Pelagibacter ubique_M	78.5215	124	209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902517175.1	s__Pelagibacter sp902517175	78.0909	69	209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902543535.1	s__Pelagibacter sp902543535	77.8698	79	209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902564785.1	s__Pelagibacter sp902564785	77.6967	67	209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	99.24	99.24	0.74	0.74	2	-
GCA_902515185.1	s__Pelagibacter sp902515185	77.4923	64	209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 01:41:53,554] [INFO] GTDB search result was written to OceanDNA-b25764/result_gtdb.tsv
[2023-03-18 01:41:53,554] [INFO] ===== GTDB Search completed =====
[2023-03-18 01:41:53,556] [INFO] DFAST_QC result json was written to OceanDNA-b25764/dqc_result.json
[2023-03-18 01:41:53,556] [INFO] DFAST_QC completed!
[2023-03-18 01:41:53,556] [INFO] Total running time: 0h0m33s