[2023-03-14 14:26:08,603] [INFO] DFAST_QC pipeline started.
[2023-03-14 14:26:08,603] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 14:26:08,604] [INFO] DQC Reference Directory: /var/lib/cwl/stg02849c0b-15a2-44a5-a3bb-687febabc076/dqc_reference
[2023-03-14 14:26:11,006] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 14:26:11,007] [INFO] Task started: Prodigal
[2023-03-14 14:26:11,007] [INFO] Running command: cat /var/lib/cwl/stga1252ff0-78e8-4233-8293-f9f0e88f88c7/OceanDNA-b30722.fa | prodigal -d OceanDNA-b30722/cds.fna -a OceanDNA-b30722/protein.faa -g 11 -q > /dev/null
[2023-03-14 14:26:23,513] [INFO] Task succeeded: Prodigal
[2023-03-14 14:26:23,513] [INFO] Task started: HMMsearch
[2023-03-14 14:26:23,513] [INFO] Running command: hmmsearch --tblout OceanDNA-b30722/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg02849c0b-15a2-44a5-a3bb-687febabc076/dqc_reference/reference_markers.hmm OceanDNA-b30722/protein.faa > /dev/null
[2023-03-14 14:26:23,652] [INFO] Task succeeded: HMMsearch
[2023-03-14 14:26:23,653] [WARNING] Found 4/6 markers. [/var/lib/cwl/stga1252ff0-78e8-4233-8293-f9f0e88f88c7/OceanDNA-b30722.fa]
[2023-03-14 14:26:23,666] [INFO] Query marker FASTA was written to OceanDNA-b30722/markers.fasta
[2023-03-14 14:26:23,666] [INFO] Task started: Blastn
[2023-03-14 14:26:23,666] [INFO] Running command: blastn -query OceanDNA-b30722/markers.fasta -db /var/lib/cwl/stg02849c0b-15a2-44a5-a3bb-687febabc076/dqc_reference/reference_markers.fasta -out OceanDNA-b30722/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 14:26:24,187] [INFO] Task succeeded: Blastn
[2023-03-14 14:26:24,188] [INFO] Selected 18 target genomes.
[2023-03-14 14:26:24,188] [INFO] Target genome list was writen to OceanDNA-b30722/target_genomes.txt
[2023-03-14 14:26:24,197] [INFO] Task started: fastANI
[2023-03-14 14:26:24,197] [INFO] Running command: fastANI --query /var/lib/cwl/stga1252ff0-78e8-4233-8293-f9f0e88f88c7/OceanDNA-b30722.fa --refList OceanDNA-b30722/target_genomes.txt --output OceanDNA-b30722/fastani_result.tsv --threads 1
[2023-03-14 14:26:35,504] [INFO] Task succeeded: fastANI
[2023-03-14 14:26:35,504] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg02849c0b-15a2-44a5-a3bb-687febabc076/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 14:26:35,504] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg02849c0b-15a2-44a5-a3bb-687febabc076/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 14:26:35,511] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 14:26:35,511] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-14 14:26:35,511] [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
Yoonia maricola	strain=DSM 29128	GCA_002797915.1	420999	420999	type	True	78.1747	145	313	95	below_threshold
Yoonia rosea	strain=DSM 29591	GCA_900156505.1	287098	287098	type	True	78.0939	137	313	95	below_threshold
Yoonia litorea	strain=DSM 29433	GCA_900114675.1	1123755	1123755	type	True	77.4631	85	313	95	below_threshold
Yoonia maritima	strain=DSM 101533	GCA_003003285.1	1435347	1435347	type	True	77.3644	79	313	95	below_threshold
Yoonia tamlensis	strain=DSM 26879	GCA_900115105.1	390270	390270	type	True	77.1623	96	313	95	below_threshold
Yoonia sediminilitoris	strain=DSM 29955	GCA_003058085.1	1286148	1286148	type	True	77.1358	92	313	95	below_threshold
Yoonia sediminilitoris	strain=CECT 8284	GCA_003337495.1	1286148	1286148	type	True	77.1358	92	313	95	below_threshold
Yoonia vestfoldensis	strain=DSM 16212	GCA_000382265.1	245188	245188	type	True	77.1192	97	313	95	below_threshold
Loktanella ponticola	strain=DSM 101064	GCA_014199395.1	1524255	1524255	type	True	76.4567	78	313	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 14:26:35,512] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30722/tc_result.tsv
[2023-03-14 14:26:35,512] [INFO] ===== Taxonomy check completed =====
[2023-03-14 14:26:35,512] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 14:26:35,512] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg02849c0b-15a2-44a5-a3bb-687febabc076/dqc_reference/checkm_data
[2023-03-14 14:26:35,513] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 14:26:35,516] [INFO] Task started: CheckM
[2023-03-14 14:26:35,516] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30722/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30722/checkm_input OceanDNA-b30722/checkm_result
[2023-03-14 14:26:58,475] [INFO] Task succeeded: CheckM
[2023-03-14 14:26:58,475] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 50.69%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 14:26:58,477] [INFO] ===== Completeness check finished =====
[2023-03-14 14:26:58,477] [INFO] ===== Start GTDB Search =====
[2023-03-14 14:26:58,478] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30722/markers.fasta)
[2023-03-14 14:26:58,479] [INFO] Task started: Blastn
[2023-03-14 14:26:58,479] [INFO] Running command: blastn -query OceanDNA-b30722/markers.fasta -db /var/lib/cwl/stg02849c0b-15a2-44a5-a3bb-687febabc076/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30722/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 14:26:59,149] [INFO] Task succeeded: Blastn
[2023-03-14 14:26:59,150] [INFO] Selected 13 target genomes.
[2023-03-14 14:26:59,150] [INFO] Target genome list was writen to OceanDNA-b30722/target_genomes_gtdb.txt
[2023-03-14 14:26:59,167] [INFO] Task started: fastANI
[2023-03-14 14:26:59,167] [INFO] Running command: fastANI --query /var/lib/cwl/stga1252ff0-78e8-4233-8293-f9f0e88f88c7/OceanDNA-b30722.fa --refList OceanDNA-b30722/target_genomes_gtdb.txt --output OceanDNA-b30722/fastani_result_gtdb.tsv --threads 1
[2023-03-14 14:27:06,342] [INFO] Task succeeded: fastANI
[2023-03-14 14:27:06,348] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 14:27:06,348] [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_017854415.1	s__Yoonia sp017854415	96.3941	283	313	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003201935.1	s__Yoonia sp003201935	78.4698	140	313	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002797915.1	s__Yoonia maricola	78.1747	145	313	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001419985.1	s__Yoonia sp001419985	78.1494	159	313	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000169435.1	s__Yoonia sp000169435	78.0354	167	313	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900143545.1	s__Yoonia sp900143545	77.8607	144	313	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003003285.1	s__Yoonia maritima	77.3644	79	313	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115105.1	s__Yoonia tamlensis	77.1623	96	313	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017854565.1	s__Yoonia sp017854565	76.8707	96	313	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 14:27:06,349] [INFO] GTDB search result was written to OceanDNA-b30722/result_gtdb.tsv
[2023-03-14 14:27:06,349] [INFO] ===== GTDB Search completed =====
[2023-03-14 14:27:06,350] [INFO] DFAST_QC result json was written to OceanDNA-b30722/dqc_result.json
[2023-03-14 14:27:06,351] [INFO] DFAST_QC completed!
[2023-03-14 14:27:06,351] [INFO] Total running time: 0h0m58s