[2023-03-15 20:34:28,406] [INFO] DFAST_QC pipeline started.
[2023-03-15 20:34:28,406] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 20:34:28,406] [INFO] DQC Reference Directory: /var/lib/cwl/stg973c167e-d29a-4df1-8c17-854a3280825f/dqc_reference
[2023-03-15 20:34:29,508] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 20:34:29,508] [INFO] Task started: Prodigal
[2023-03-15 20:34:29,509] [INFO] Running command: cat /var/lib/cwl/stg37ab362d-9610-407c-84e3-63cb8c19fdc6/OceanDNA-b30060.fa | prodigal -d OceanDNA-b30060/cds.fna -a OceanDNA-b30060/protein.faa -g 11 -q > /dev/null
[2023-03-15 20:34:35,878] [INFO] Task succeeded: Prodigal
[2023-03-15 20:34:35,878] [INFO] Task started: HMMsearch
[2023-03-15 20:34:35,878] [INFO] Running command: hmmsearch --tblout OceanDNA-b30060/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg973c167e-d29a-4df1-8c17-854a3280825f/dqc_reference/reference_markers.hmm OceanDNA-b30060/protein.faa > /dev/null
[2023-03-15 20:34:36,025] [INFO] Task succeeded: HMMsearch
[2023-03-15 20:34:36,026] [WARNING] Found 1/6 markers. [/var/lib/cwl/stg37ab362d-9610-407c-84e3-63cb8c19fdc6/OceanDNA-b30060.fa]
[2023-03-15 20:34:36,040] [INFO] Query marker FASTA was written to OceanDNA-b30060/markers.fasta
[2023-03-15 20:34:36,040] [INFO] Task started: Blastn
[2023-03-15 20:34:36,040] [INFO] Running command: blastn -query OceanDNA-b30060/markers.fasta -db /var/lib/cwl/stg973c167e-d29a-4df1-8c17-854a3280825f/dqc_reference/reference_markers.fasta -out OceanDNA-b30060/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 20:34:36,508] [INFO] Task succeeded: Blastn
[2023-03-15 20:34:36,508] [INFO] Selected 13 target genomes.
[2023-03-15 20:34:36,509] [INFO] Target genome list was writen to OceanDNA-b30060/target_genomes.txt
[2023-03-15 20:34:36,516] [INFO] Task started: fastANI
[2023-03-15 20:34:36,516] [INFO] Running command: fastANI --query /var/lib/cwl/stg37ab362d-9610-407c-84e3-63cb8c19fdc6/OceanDNA-b30060.fa --refList OceanDNA-b30060/target_genomes.txt --output OceanDNA-b30060/fastani_result.tsv --threads 1
[2023-03-15 20:34:44,124] [INFO] Task succeeded: fastANI
[2023-03-15 20:34:44,124] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg973c167e-d29a-4df1-8c17-854a3280825f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 20:34:44,124] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg973c167e-d29a-4df1-8c17-854a3280825f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 20:34:44,132] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 20:34:44,132] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 20:34:44,132] [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
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	78.6209	91	151	95	below_threshold
Nioella ostreopsis	strain=Z7-4	GCA_004000255.1	2448479	2448479	type	True	77.9261	60	151	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	77.8058	54	151	95	below_threshold
Ruegeria pomeroyi	strain=DSS-3	GCA_000011965.2	89184	89184	suspected-type	True	77.7732	52	151	95	below_threshold
Rhodovulum strictum	strain=DSM 11289	GCA_009649175.1	58314	58314	type	True	77.701	64	151	95	below_threshold
Nioella sediminis	strain=JS7-11	GCA_001879695.1	1912092	1912092	type	True	77.5159	60	151	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	77.5006	59	151	95	below_threshold
Nioella nitratireducens	strain=SSW136	GCA_001879715.1	1287720	1287720	type	True	77.4155	62	151	95	below_threshold
Cribrihabitans marinus	strain=CGMCC 1.13219	GCA_014640375.1	1227549	1227549	type	True	77.3921	52	151	95	below_threshold
Cribrihabitans marinus	strain=DSM 29340	GCA_900109035.1	1227549	1227549	type	True	77.3373	53	151	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 20:34:44,132] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30060/tc_result.tsv
[2023-03-15 20:34:44,132] [INFO] ===== Taxonomy check completed =====
[2023-03-15 20:34:44,132] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 20:34:44,132] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg973c167e-d29a-4df1-8c17-854a3280825f/dqc_reference/checkm_data
[2023-03-15 20:34:44,133] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 20:34:44,136] [INFO] Task started: CheckM
[2023-03-15 20:34:44,136] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30060/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30060/checkm_input OceanDNA-b30060/checkm_result
[2023-03-15 20:35:05,675] [INFO] Task succeeded: CheckM
[2023-03-15 20:35:05,675] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 61.45%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 20:35:05,677] [INFO] ===== Completeness check finished =====
[2023-03-15 20:35:05,677] [INFO] ===== Start GTDB Search =====
[2023-03-15 20:35:05,677] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30060/markers.fasta)
[2023-03-15 20:35:05,677] [INFO] Task started: Blastn
[2023-03-15 20:35:05,677] [INFO] Running command: blastn -query OceanDNA-b30060/markers.fasta -db /var/lib/cwl/stg973c167e-d29a-4df1-8c17-854a3280825f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30060/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 20:35:06,256] [INFO] Task succeeded: Blastn
[2023-03-15 20:35:06,257] [INFO] Selected 6 target genomes.
[2023-03-15 20:35:06,257] [INFO] Target genome list was writen to OceanDNA-b30060/target_genomes_gtdb.txt
[2023-03-15 20:35:06,376] [INFO] Task started: fastANI
[2023-03-15 20:35:06,376] [INFO] Running command: fastANI --query /var/lib/cwl/stg37ab362d-9610-407c-84e3-63cb8c19fdc6/OceanDNA-b30060.fa --refList OceanDNA-b30060/target_genomes_gtdb.txt --output OceanDNA-b30060/fastani_result_gtdb.tsv --threads 1
[2023-03-15 20:35:09,732] [INFO] Task succeeded: fastANI
[2023-03-15 20:35:09,737] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 20:35:09,737] [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_018402035.1	s__Roseicyclus sp018402035	89.9569	139	151	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015689735.1	s__Roseicyclus sp015689735	84.9384	136	151	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018401965.1	s__Roseicyclus sp018401965	80.8118	103	151	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003148775.1	s__Roseicyclus mahoneyensis	80.5361	116	151	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015689745.1	s__Roseicyclus sp015689745	79.9184	107	151	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012395815.1	s__Roseicyclus sp012395815	79.7377	114	151	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 20:35:09,737] [INFO] GTDB search result was written to OceanDNA-b30060/result_gtdb.tsv
[2023-03-15 20:35:09,737] [INFO] ===== GTDB Search completed =====
[2023-03-15 20:35:09,738] [INFO] DFAST_QC result json was written to OceanDNA-b30060/dqc_result.json
[2023-03-15 20:35:09,739] [INFO] DFAST_QC completed!
[2023-03-15 20:35:09,739] [INFO] Total running time: 0h0m41s