[2023-03-16 21:45:13,524] [INFO] DFAST_QC pipeline started.
[2023-03-16 21:45:13,524] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 21:45:13,525] [INFO] DQC Reference Directory: /var/lib/cwl/stgd6e3d43b-6686-4437-aff9-fd959b7d44ad/dqc_reference
[2023-03-16 21:45:15,326] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 21:45:15,327] [INFO] Task started: Prodigal
[2023-03-16 21:45:15,327] [INFO] Running command: cat /var/lib/cwl/stg408660b9-4161-4931-99c3-446f82ab914e/OceanDNA-b7217.fa | prodigal -d OceanDNA-b7217/cds.fna -a OceanDNA-b7217/protein.faa -g 11 -q > /dev/null
[2023-03-16 21:45:26,883] [INFO] Task succeeded: Prodigal
[2023-03-16 21:45:26,883] [INFO] Task started: HMMsearch
[2023-03-16 21:45:26,884] [INFO] Running command: hmmsearch --tblout OceanDNA-b7217/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd6e3d43b-6686-4437-aff9-fd959b7d44ad/dqc_reference/reference_markers.hmm OceanDNA-b7217/protein.faa > /dev/null
[2023-03-16 21:45:27,097] [INFO] Task succeeded: HMMsearch
[2023-03-16 21:45:27,098] [INFO] Found 6/6 markers.
[2023-03-16 21:45:27,109] [INFO] Query marker FASTA was written to OceanDNA-b7217/markers.fasta
[2023-03-16 21:45:27,109] [INFO] Task started: Blastn
[2023-03-16 21:45:27,109] [INFO] Running command: blastn -query OceanDNA-b7217/markers.fasta -db /var/lib/cwl/stgd6e3d43b-6686-4437-aff9-fd959b7d44ad/dqc_reference/reference_markers.fasta -out OceanDNA-b7217/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 21:45:27,689] [INFO] Task succeeded: Blastn
[2023-03-16 21:45:27,690] [INFO] Selected 29 target genomes.
[2023-03-16 21:45:27,690] [INFO] Target genome list was writen to OceanDNA-b7217/target_genomes.txt
[2023-03-16 21:45:27,705] [INFO] Task started: fastANI
[2023-03-16 21:45:27,705] [INFO] Running command: fastANI --query /var/lib/cwl/stg408660b9-4161-4931-99c3-446f82ab914e/OceanDNA-b7217.fa --refList OceanDNA-b7217/target_genomes.txt --output OceanDNA-b7217/fastani_result.tsv --threads 1
[2023-03-16 21:45:44,633] [INFO] Task succeeded: fastANI
[2023-03-16 21:45:44,633] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd6e3d43b-6686-4437-aff9-fd959b7d44ad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 21:45:44,633] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd6e3d43b-6686-4437-aff9-fd959b7d44ad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 21:45:44,642] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 21:45:44,642] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 21:45:44,643] [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
Patiriisocius marinistellae	strain=KK4	GCA_009014635.1	2494560	2494560	type	True	77.1994	138	565	95	below_threshold
Patiriisocius marinus	strain=NBRC 109484	GCA_008974325.1	1397112	1397112	type	True	77.0686	126	565	95	below_threshold
Cochleicola gelatinilyticus	strain=LPB0005	GCA_001637325.1	1763537	1763537	type	True	76.607	69	565	95	below_threshold
Ulvibacter litoralis	strain=KCTC 12104	GCA_014651275.1	227084	227084	type	True	76.3706	83	565	95	below_threshold
Halomarinibacterium sedimenti	strain=CAU 1614	GCA_019312585.1	2857106	2857106	type	True	76.0118	59	565	95	below_threshold
Lacinutrix himadriensis	strain=E4-9a	GCA_001418105.1	641549	641549	type	True	75.9954	62	565	95	below_threshold
Flavivirga rizhaonensis	strain=RZ03	GCA_004791695.1	2559571	2559571	type	True	75.9719	53	565	95	below_threshold
Algibacter amylolyticus	strain=DSM 29199	GCA_014202225.1	1608400	1608400	type	True	75.9512	61	565	95	below_threshold
Algibacter amylolyticus	strain=RU-4-M-4	GCA_008630605.1	1608400	1608400	type	True	75.9511	61	565	95	below_threshold
Algibacter amylolyticus	strain=RU-4-M-4	GCA_007559325.1	1608400	1608400	type	True	75.9511	61	565	95	below_threshold
Algibacter marinivivus	strain=ZY111	GCA_003143755.1	2100723	2100723	type	True	75.9423	55	565	95	below_threshold
Marixanthomonas ophiurae	strain=KMM 3046	GCA_003413745.1	387659	387659	type	True	75.9249	68	565	95	below_threshold
Aequorivita antarctica	strain=SW49	GCA_007997155.1	153266	153266	type	True	75.7982	60	565	95	below_threshold
Aequorivita sublithincola	strain=DSM 14238	GCA_000265385.1	101385	101385	type	True	75.7427	64	565	95	below_threshold
Tamlana sedimentorum	strain=JCM 19808	GCA_000943565.1	1435349	1435349	type	True	75.7008	55	565	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 21:45:44,643] [INFO] DFAST Taxonomy check result was written to OceanDNA-b7217/tc_result.tsv
[2023-03-16 21:45:44,643] [INFO] ===== Taxonomy check completed =====
[2023-03-16 21:45:44,643] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 21:45:44,643] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd6e3d43b-6686-4437-aff9-fd959b7d44ad/dqc_reference/checkm_data
[2023-03-16 21:45:44,644] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 21:45:44,647] [INFO] Task started: CheckM
[2023-03-16 21:45:44,647] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b7217/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b7217/checkm_input OceanDNA-b7217/checkm_result
[2023-03-16 21:46:17,266] [INFO] Task succeeded: CheckM
[2023-03-16 21:46:17,267] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 67.01%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 21:46:17,268] [INFO] ===== Completeness check finished =====
[2023-03-16 21:46:17,269] [INFO] ===== Start GTDB Search =====
[2023-03-16 21:46:17,269] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b7217/markers.fasta)
[2023-03-16 21:46:17,269] [INFO] Task started: Blastn
[2023-03-16 21:46:17,269] [INFO] Running command: blastn -query OceanDNA-b7217/markers.fasta -db /var/lib/cwl/stgd6e3d43b-6686-4437-aff9-fd959b7d44ad/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b7217/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 21:46:18,096] [INFO] Task succeeded: Blastn
[2023-03-16 21:46:18,097] [INFO] Selected 14 target genomes.
[2023-03-16 21:46:18,097] [INFO] Target genome list was writen to OceanDNA-b7217/target_genomes_gtdb.txt
[2023-03-16 21:46:18,141] [INFO] Task started: fastANI
[2023-03-16 21:46:18,142] [INFO] Running command: fastANI --query /var/lib/cwl/stg408660b9-4161-4931-99c3-446f82ab914e/OceanDNA-b7217.fa --refList OceanDNA-b7217/target_genomes_gtdb.txt --output OceanDNA-b7217/fastani_result_gtdb.tsv --threads 1
[2023-03-16 21:46:25,129] [INFO] Task succeeded: fastANI
[2023-03-16 21:46:25,137] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 21:46:25,137] [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_003450155.1	s__Patiriisocius sp003450155	87.3188	435	565	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Patiriisocius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905182755.1	s__Patiriisocius sp905182755	85.7782	446	565	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Patiriisocius	95.0	96.66	96.28	0.84	0.84	6	-
GCA_018656255.1	s__Patiriisocius sp018656255	84.9866	351	565	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Patiriisocius	95.0	97.76	97.76	0.76	0.76	2	-
GCF_009014635.1	s__Patiriisocius marinistellae	77.1994	138	565	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Patiriisocius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008974325.1	s__Patiriisocius marinus	77.0491	127	565	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Patiriisocius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001637325.1	s__Cochleicola gelatinilyticus	76.607	69	565	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cochleicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000170815.1	s__Patiriisocius sp000170815	76.4919	114	565	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Patiriisocius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001418105.1	s__Oceanihabitans himadriensis	75.9954	62	565	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Oceanihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003443635.1	s__AU392 sp003443635	75.9	59	565	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__AU392	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003663945.1	s__Lacinutrix venerupis	75.8709	67	565	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lacinutrix	95.0	98.08	98.08	0.92	0.92	2	-
GCF_000265385.1	s__Aequorivita sublithincola	75.7427	64	565	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 21:46:25,137] [INFO] GTDB search result was written to OceanDNA-b7217/result_gtdb.tsv
[2023-03-16 21:46:25,137] [INFO] ===== GTDB Search completed =====
[2023-03-16 21:46:25,139] [INFO] DFAST_QC result json was written to OceanDNA-b7217/dqc_result.json
[2023-03-16 21:46:25,139] [INFO] DFAST_QC completed!
[2023-03-16 21:46:25,139] [INFO] Total running time: 0h1m12s