[2023-03-15 20:34:26,739] [INFO] DFAST_QC pipeline started.
[2023-03-15 20:34:26,739] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 20:34:26,739] [INFO] DQC Reference Directory: /var/lib/cwl/stg885bbc3e-8577-48af-abd8-d92b905f9e85/dqc_reference
[2023-03-15 20:34:28,460] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 20:34:28,460] [INFO] Task started: Prodigal
[2023-03-15 20:34:28,460] [INFO] Running command: cat /var/lib/cwl/stg65a64c92-a7f3-4c48-8df9-513d9ffe2627/OceanDNA-b9808.fa | prodigal -d OceanDNA-b9808/cds.fna -a OceanDNA-b9808/protein.faa -g 11 -q > /dev/null
[2023-03-15 20:34:47,543] [INFO] Task succeeded: Prodigal
[2023-03-15 20:34:47,543] [INFO] Task started: HMMsearch
[2023-03-15 20:34:47,543] [INFO] Running command: hmmsearch --tblout OceanDNA-b9808/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg885bbc3e-8577-48af-abd8-d92b905f9e85/dqc_reference/reference_markers.hmm OceanDNA-b9808/protein.faa > /dev/null
[2023-03-15 20:34:47,744] [INFO] Task succeeded: HMMsearch
[2023-03-15 20:34:47,744] [INFO] Found 6/6 markers.
[2023-03-15 20:34:47,764] [INFO] Query marker FASTA was written to OceanDNA-b9808/markers.fasta
[2023-03-15 20:34:47,765] [INFO] Task started: Blastn
[2023-03-15 20:34:47,765] [INFO] Running command: blastn -query OceanDNA-b9808/markers.fasta -db /var/lib/cwl/stg885bbc3e-8577-48af-abd8-d92b905f9e85/dqc_reference/reference_markers.fasta -out OceanDNA-b9808/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 20:34:48,387] [INFO] Task succeeded: Blastn
[2023-03-15 20:34:48,388] [INFO] Selected 17 target genomes.
[2023-03-15 20:34:48,388] [INFO] Target genome list was writen to OceanDNA-b9808/target_genomes.txt
[2023-03-15 20:34:48,397] [INFO] Task started: fastANI
[2023-03-15 20:34:48,397] [INFO] Running command: fastANI --query /var/lib/cwl/stg65a64c92-a7f3-4c48-8df9-513d9ffe2627/OceanDNA-b9808.fa --refList OceanDNA-b9808/target_genomes.txt --output OceanDNA-b9808/fastani_result.tsv --threads 1
[2023-03-15 20:34:59,548] [INFO] Task succeeded: fastANI
[2023-03-15 20:34:59,549] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg885bbc3e-8577-48af-abd8-d92b905f9e85/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 20:34:59,549] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg885bbc3e-8577-48af-abd8-d92b905f9e85/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 20:34:59,559] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 20:34:59,559] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 20:34:59,560] [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
Olleya marilimosa	strain=CAM030	GCA_000518485.1	272164	272164	type	True	91.1398	915	1062	95	below_threshold
Olleya namhaensis	strain=DSM 28881	GCA_900114005.1	1144750	1144750	type	True	83.7752	779	1062	95	below_threshold
Olleya aquimaris	strain=DSM 24464	GCA_003259525.1	639310	639310	type	True	80.8867	634	1062	95	below_threshold
Lacinutrix algicola	strain=AKS293	GCA_001418085.1	342954	342954	type	True	79.4543	508	1062	95	below_threshold
Mesoflavibacter zeaxanthinifaciens subsp. sabulilitoris	strain=KCTC 42117	GCA_003008435.1	1520893	393060	type	True	79.2201	521	1062	95	below_threshold
Lacinutrix mariniflava	strain=AKS432	GCA_001418015.1	342955	342955	type	True	79.1926	490	1062	95	below_threshold
Mesoflavibacter zeaxanthinifaciens subsp. sabulilitoris	strain=CECT 8597	GCA_014191595.1	1520893	393060	type	True	79.1806	516	1062	95	below_threshold
Mesoflavibacter zeaxanthinifaciens	strain=DSM 18436	GCA_000422365.1	393060	393060	type	True	78.9545	512	1062	95	below_threshold
Lacinutrix himadriensis	strain=E4-9a	GCA_001418105.1	641549	641549	type	True	78.7797	452	1062	95	below_threshold
Mesoflavibacter profundi	strain=YC1039	GCA_014764305.1	2708110	2708110	type	True	78.7668	524	1062	95	below_threshold
Winogradskyella ludwigii	strain=HL116	GCA_013403985.1	2686076	2686076	type	True	77.773	302	1062	95	below_threshold
Psychroserpens luteolus	strain=XSD401	GCA_021032705.1	2855840	2855840	type	True	77.2973	231	1062	95	below_threshold
Flavivirga rizhaonensis	strain=RZ03	GCA_004791695.1	2559571	2559571	type	True	77.1989	230	1062	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	77.0428	241	1062	95	below_threshold
Tenacibaculum aquimarinum	strain=K20-16	GCA_022478115.1	2910675	2910675	type	True	77.0393	185	1062	95	below_threshold
Hyunsoonleella flava	strain=T58	GCA_004310325.1	2527939	2527939	type	True	76.725	197	1062	95	below_threshold
Hyunsoonleella aquatilis	strain=SJ7	GCA_014270105.1	2762758	2762758	type	True	76.5909	95	1062	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 20:34:59,560] [INFO] DFAST Taxonomy check result was written to OceanDNA-b9808/tc_result.tsv
[2023-03-15 20:34:59,560] [INFO] ===== Taxonomy check completed =====
[2023-03-15 20:34:59,560] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 20:34:59,560] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg885bbc3e-8577-48af-abd8-d92b905f9e85/dqc_reference/checkm_data
[2023-03-15 20:34:59,561] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 20:34:59,565] [INFO] Task started: CheckM
[2023-03-15 20:34:59,565] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b9808/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b9808/checkm_input OceanDNA-b9808/checkm_result
[2023-03-15 20:35:47,654] [INFO] Task succeeded: CheckM
[2023-03-15 20:35:47,655] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 20:35:47,657] [INFO] ===== Completeness check finished =====
[2023-03-15 20:35:47,657] [INFO] ===== Start GTDB Search =====
[2023-03-15 20:35:47,657] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b9808/markers.fasta)
[2023-03-15 20:35:47,658] [INFO] Task started: Blastn
[2023-03-15 20:35:47,659] [INFO] Running command: blastn -query OceanDNA-b9808/markers.fasta -db /var/lib/cwl/stg885bbc3e-8577-48af-abd8-d92b905f9e85/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b9808/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 20:35:48,544] [INFO] Task succeeded: Blastn
[2023-03-15 20:35:48,544] [INFO] Selected 8 target genomes.
[2023-03-15 20:35:48,545] [INFO] Target genome list was writen to OceanDNA-b9808/target_genomes_gtdb.txt
[2023-03-15 20:35:48,647] [INFO] Task started: fastANI
[2023-03-15 20:35:48,647] [INFO] Running command: fastANI --query /var/lib/cwl/stg65a64c92-a7f3-4c48-8df9-513d9ffe2627/OceanDNA-b9808.fa --refList OceanDNA-b9808/target_genomes_gtdb.txt --output OceanDNA-b9808/fastani_result_gtdb.tsv --threads 1
[2023-03-15 20:35:55,208] [INFO] Task succeeded: fastANI
[2023-03-15 20:35:55,214] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 20:35:55,214] [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_007827365.1	s__Olleya sp002323495	96.7768	977	1062	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Olleya	95.0	96.78	96.78	0.90	0.90	2	conclusive
GCF_000518485.1	s__Olleya marilimosa	91.1398	915	1062	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Olleya	95.0	97.58	97.25	0.92	0.89	4	-
GCF_900114005.1	s__Olleya namhaensis	83.7752	779	1062	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Olleya	95.0	98.20	98.20	0.94	0.94	2	-
GCF_016785945.1	s__Olleya sediminilitoris	82.7879	720	1062	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Olleya	95.0	98.16	97.66	0.93	0.91	5	-
GCF_004843725.1	s__Olleya sp004843725	82.6623	714	1062	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Olleya	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002831645.1	s__Olleya sp002831645	82.5103	737	1062	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Olleya	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003259525.1	s__Olleya aquimaris	80.9035	632	1062	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Olleya	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001418085.1	s__Lacinutrix algicola	79.4375	511	1062	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lacinutrix	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 20:35:55,215] [INFO] GTDB search result was written to OceanDNA-b9808/result_gtdb.tsv
[2023-03-15 20:35:55,215] [INFO] ===== GTDB Search completed =====
[2023-03-15 20:35:55,216] [INFO] DFAST_QC result json was written to OceanDNA-b9808/dqc_result.json
[2023-03-15 20:35:55,216] [INFO] DFAST_QC completed!
[2023-03-15 20:35:55,216] [INFO] Total running time: 0h1m28s