[2023-03-19 02:01:35,156] [INFO] DFAST_QC pipeline started.
[2023-03-19 02:01:35,156] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 02:01:35,156] [INFO] DQC Reference Directory: /var/lib/cwl/stg2299d1f5-7f8a-4c40-aad1-e4abc9fb2f51/dqc_reference
[2023-03-19 02:01:36,255] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 02:01:36,255] [INFO] Task started: Prodigal
[2023-03-19 02:01:36,255] [INFO] Running command: cat /var/lib/cwl/stgf5352841-db23-4302-b67b-35ca53eda2d5/OceanDNA-b30719.fa | prodigal -d OceanDNA-b30719/cds.fna -a OceanDNA-b30719/protein.faa -g 11 -q > /dev/null
[2023-03-19 02:01:49,854] [INFO] Task succeeded: Prodigal
[2023-03-19 02:01:49,854] [INFO] Task started: HMMsearch
[2023-03-19 02:01:49,854] [INFO] Running command: hmmsearch --tblout OceanDNA-b30719/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2299d1f5-7f8a-4c40-aad1-e4abc9fb2f51/dqc_reference/reference_markers.hmm OceanDNA-b30719/protein.faa > /dev/null
[2023-03-19 02:01:49,991] [INFO] Task succeeded: HMMsearch
[2023-03-19 02:01:49,991] [WARNING] Found 2/6 markers. [/var/lib/cwl/stgf5352841-db23-4302-b67b-35ca53eda2d5/OceanDNA-b30719.fa]
[2023-03-19 02:01:50,009] [INFO] Query marker FASTA was written to OceanDNA-b30719/markers.fasta
[2023-03-19 02:01:50,010] [INFO] Task started: Blastn
[2023-03-19 02:01:50,010] [INFO] Running command: blastn -query OceanDNA-b30719/markers.fasta -db /var/lib/cwl/stg2299d1f5-7f8a-4c40-aad1-e4abc9fb2f51/dqc_reference/reference_markers.fasta -out OceanDNA-b30719/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:01:50,505] [INFO] Task succeeded: Blastn
[2023-03-19 02:01:50,507] [INFO] Selected 10 target genomes.
[2023-03-19 02:01:50,508] [INFO] Target genome list was writen to OceanDNA-b30719/target_genomes.txt
[2023-03-19 02:01:50,513] [INFO] Task started: fastANI
[2023-03-19 02:01:50,513] [INFO] Running command: fastANI --query /var/lib/cwl/stgf5352841-db23-4302-b67b-35ca53eda2d5/OceanDNA-b30719.fa --refList OceanDNA-b30719/target_genomes.txt --output OceanDNA-b30719/fastani_result.tsv --threads 1
[2023-03-19 02:01:56,619] [INFO] Task succeeded: fastANI
[2023-03-19 02:01:56,619] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2299d1f5-7f8a-4c40-aad1-e4abc9fb2f51/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 02:01:56,620] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2299d1f5-7f8a-4c40-aad1-e4abc9fb2f51/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 02:01:56,627] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 02:01:56,627] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 02:01:56,627] [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	78.3502	277	694	95	below_threshold
Yoonia vestfoldensis	strain=DSM 16212	GCA_000382265.1	245188	245188	type	True	77.6969	247	694	95	below_threshold
Yoonia tamlensis	strain=DSM 26879	GCA_900115105.1	390270	390270	type	True	77.5569	209	694	95	below_threshold
Yoonia sediminilitoris	strain=DSM 29955	GCA_003058085.1	1286148	1286148	type	True	77.3581	231	694	95	below_threshold
Yoonia sediminilitoris	strain=CECT 8284	GCA_003337495.1	1286148	1286148	type	True	77.3326	233	694	95	below_threshold
Roseovarius pacificus	strain=DSM 29589	GCA_900142665.1	337701	337701	type	True	76.2695	92	694	95	below_threshold
Roseovarius pacificus	strain=CGMCC 1.7083	GCA_014645335.1	337701	337701	type	True	76.2695	92	694	95	below_threshold
Octadecabacter antarcticus	strain=307	GCA_000155675.2	1217908	1217908	type	True	76.1375	92	694	95	below_threshold
Lutimaribacter saemankumensis	strain=DSM 28010	GCA_900100005.1	490829	490829	type	True	75.9666	90	694	95	below_threshold
Thalassobius mangrovi	strain=GS-10	GCA_009857745.1	2692236	2692236	type	True	75.8963	105	694	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 02:01:56,628] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30719/tc_result.tsv
[2023-03-19 02:01:56,628] [INFO] ===== Taxonomy check completed =====
[2023-03-19 02:01:56,628] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 02:01:56,628] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2299d1f5-7f8a-4c40-aad1-e4abc9fb2f51/dqc_reference/checkm_data
[2023-03-19 02:01:56,629] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 02:01:56,643] [INFO] Task started: CheckM
[2023-03-19 02:01:56,644] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30719/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30719/checkm_input OceanDNA-b30719/checkm_result
[2023-03-19 02:02:33,716] [INFO] Task succeeded: CheckM
[2023-03-19 02:02:33,717] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 33.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 02:02:33,722] [INFO] ===== Completeness check finished =====
[2023-03-19 02:02:33,722] [INFO] ===== Start GTDB Search =====
[2023-03-19 02:02:33,723] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30719/markers.fasta)
[2023-03-19 02:02:33,724] [INFO] Task started: Blastn
[2023-03-19 02:02:33,724] [INFO] Running command: blastn -query OceanDNA-b30719/markers.fasta -db /var/lib/cwl/stg2299d1f5-7f8a-4c40-aad1-e4abc9fb2f51/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30719/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:02:34,345] [INFO] Task succeeded: Blastn
[2023-03-19 02:02:34,347] [INFO] Selected 9 target genomes.
[2023-03-19 02:02:34,347] [INFO] Target genome list was writen to OceanDNA-b30719/target_genomes_gtdb.txt
[2023-03-19 02:02:34,413] [INFO] Task started: fastANI
[2023-03-19 02:02:34,413] [INFO] Running command: fastANI --query /var/lib/cwl/stgf5352841-db23-4302-b67b-35ca53eda2d5/OceanDNA-b30719.fa --refList OceanDNA-b30719/target_genomes_gtdb.txt --output OceanDNA-b30719/fastani_result_gtdb.tsv --threads 1
[2023-03-19 02:02:40,865] [INFO] Task succeeded: fastANI
[2023-03-19 02:02:40,871] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 02:02:40,871] [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_003201935.1	s__Yoonia sp003201935	78.8363	327	694	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	78.554	296	694	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	78.3222	279	694	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000152785.1	s__Yoonia vestfoldensis_A	78.2149	233	694	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000382265.1	s__Yoonia vestfoldensis	77.6969	247	694	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	77.5569	209	694	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003058085.1	s__Yoonia sediminilitoris	77.3451	232	694	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900142665.1	s__Roseovarius pacificus	76.2695	92	694	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	97.52	95.05	0.91	0.82	3	-
GCF_900184945.1	s__Maliponia aquimaris	76.0143	91	694	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Maliponia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 02:02:40,873] [INFO] GTDB search result was written to OceanDNA-b30719/result_gtdb.tsv
[2023-03-19 02:02:40,875] [INFO] ===== GTDB Search completed =====
[2023-03-19 02:02:40,878] [INFO] DFAST_QC result json was written to OceanDNA-b30719/dqc_result.json
[2023-03-19 02:02:40,878] [INFO] DFAST_QC completed!
[2023-03-19 02:02:40,878] [INFO] Total running time: 0h1m6s