[2023-03-14 14:28:46,782] [INFO] DFAST_QC pipeline started.
[2023-03-14 14:28:46,782] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 14:28:46,782] [INFO] DQC Reference Directory: /var/lib/cwl/stg5fb520dc-c29a-4b21-a9bf-eb49bf150b03/dqc_reference
[2023-03-14 14:28:47,894] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 14:28:47,895] [INFO] Task started: Prodigal
[2023-03-14 14:28:47,895] [INFO] Running command: cat /var/lib/cwl/stgaa9ac541-1d91-404a-b338-137b44c7f001/OceanDNA-b9806.fa | prodigal -d OceanDNA-b9806/cds.fna -a OceanDNA-b9806/protein.faa -g 11 -q > /dev/null
[2023-03-14 14:29:06,809] [INFO] Task succeeded: Prodigal
[2023-03-14 14:29:06,809] [INFO] Task started: HMMsearch
[2023-03-14 14:29:06,809] [INFO] Running command: hmmsearch --tblout OceanDNA-b9806/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5fb520dc-c29a-4b21-a9bf-eb49bf150b03/dqc_reference/reference_markers.hmm OceanDNA-b9806/protein.faa > /dev/null
[2023-03-14 14:29:07,013] [INFO] Task succeeded: HMMsearch
[2023-03-14 14:29:07,014] [INFO] Found 6/6 markers.
[2023-03-14 14:29:07,033] [INFO] Query marker FASTA was written to OceanDNA-b9806/markers.fasta
[2023-03-14 14:29:07,035] [INFO] Task started: Blastn
[2023-03-14 14:29:07,035] [INFO] Running command: blastn -query OceanDNA-b9806/markers.fasta -db /var/lib/cwl/stg5fb520dc-c29a-4b21-a9bf-eb49bf150b03/dqc_reference/reference_markers.fasta -out OceanDNA-b9806/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 14:29:07,706] [INFO] Task succeeded: Blastn
[2023-03-14 14:29:07,707] [INFO] Selected 16 target genomes.
[2023-03-14 14:29:07,707] [INFO] Target genome list was writen to OceanDNA-b9806/target_genomes.txt
[2023-03-14 14:29:07,735] [INFO] Task started: fastANI
[2023-03-14 14:29:07,735] [INFO] Running command: fastANI --query /var/lib/cwl/stgaa9ac541-1d91-404a-b338-137b44c7f001/OceanDNA-b9806.fa --refList OceanDNA-b9806/target_genomes.txt --output OceanDNA-b9806/fastani_result.tsv --threads 1
[2023-03-14 14:29:18,011] [INFO] Task succeeded: fastANI
[2023-03-14 14:29:18,011] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5fb520dc-c29a-4b21-a9bf-eb49bf150b03/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 14:29:18,011] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5fb520dc-c29a-4b21-a9bf-eb49bf150b03/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 14:29:18,021] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2023-03-14 14:29:18,021] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-14 14:29:18,021] [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	98.5321	991	1052	95	conclusive
Olleya namhaensis	strain=DSM 28881	GCA_900114005.1	1144750	1144750	type	True	83.7661	787	1052	95	below_threshold
Olleya aquimaris	strain=DSM 24464	GCA_003259525.1	639310	639310	type	True	81.097	656	1052	95	below_threshold
Mesoflavibacter zeaxanthinifaciens	strain=DSM 18436	GCA_000422365.1	393060	393060	type	True	79.5594	542	1052	95	below_threshold
Mesoflavibacter zeaxanthinifaciens subsp. sabulilitoris	strain=KCTC 42117	GCA_003008435.1	1520893	393060	type	True	79.5211	550	1052	95	below_threshold
Mesoflavibacter zeaxanthinifaciens subsp. sabulilitoris	strain=CECT 8597	GCA_014191595.1	1520893	393060	type	True	79.4714	552	1052	95	below_threshold
Lacinutrix algicola	strain=AKS293	GCA_001418085.1	342954	342954	type	True	79.4261	477	1052	95	below_threshold
Mesoflavibacter profundi	strain=YC1039	GCA_014764305.1	2708110	2708110	type	True	79.1804	547	1052	95	below_threshold
Lacinutrix mariniflava	strain=AKS432	GCA_001418015.1	342955	342955	type	True	78.9144	498	1052	95	below_threshold
Winogradskyella ludwigii	strain=HL116	GCA_013403985.1	2686076	2686076	type	True	78.0755	323	1052	95	below_threshold
Winogradskyella marina	strain=F6397	GCA_015645385.1	2785530	2785530	type	True	77.7996	299	1052	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	77.5276	256	1052	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	77.0558	221	1052	95	below_threshold
Aestuariivivens marinum	strain=MT3-5-12	GCA_022662175.1	2913555	2913555	type	True	76.9883	141	1052	95	below_threshold
Hyunsoonleella ulvae	strain=HU1-3	GCA_016827605.1	2799948	2799948	type	True	76.805	198	1052	95	below_threshold
Hyunsoonleella aquatilis	strain=SJ7	GCA_014270105.1	2762758	2762758	type	True	76.6766	101	1052	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 14:29:18,021] [INFO] DFAST Taxonomy check result was written to OceanDNA-b9806/tc_result.tsv
[2023-03-14 14:29:18,022] [INFO] ===== Taxonomy check completed =====
[2023-03-14 14:29:18,022] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 14:29:18,022] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5fb520dc-c29a-4b21-a9bf-eb49bf150b03/dqc_reference/checkm_data
[2023-03-14 14:29:18,022] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 14:29:18,033] [INFO] Task started: CheckM
[2023-03-14 14:29:18,033] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b9806/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b9806/checkm_input OceanDNA-b9806/checkm_result
[2023-03-14 14:30:20,178] [INFO] Task succeeded: CheckM
[2023-03-14 14:30:20,179] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 14:30:20,181] [INFO] ===== Completeness check finished =====
[2023-03-14 14:30:20,181] [INFO] ===== Start GTDB Search =====
[2023-03-14 14:30:20,182] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b9806/markers.fasta)
[2023-03-14 14:30:20,183] [INFO] Task started: Blastn
[2023-03-14 14:30:20,183] [INFO] Running command: blastn -query OceanDNA-b9806/markers.fasta -db /var/lib/cwl/stg5fb520dc-c29a-4b21-a9bf-eb49bf150b03/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b9806/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 14:30:21,390] [INFO] Task succeeded: Blastn
[2023-03-14 14:30:21,391] [INFO] Selected 7 target genomes.
[2023-03-14 14:30:21,391] [INFO] Target genome list was writen to OceanDNA-b9806/target_genomes_gtdb.txt
[2023-03-14 14:30:21,404] [INFO] Task started: fastANI
[2023-03-14 14:30:21,404] [INFO] Running command: fastANI --query /var/lib/cwl/stgaa9ac541-1d91-404a-b338-137b44c7f001/OceanDNA-b9806.fa --refList OceanDNA-b9806/target_genomes_gtdb.txt --output OceanDNA-b9806/fastani_result_gtdb.tsv --threads 1
[2023-03-14 14:30:35,302] [INFO] Task succeeded: fastANI
[2023-03-14 14:30:35,307] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 14:30:35,307] [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_000518485.1	s__Olleya marilimosa	98.5321	991	1052	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Olleya	95.0	97.58	97.25	0.92	0.89	4	conclusive
GCF_007827365.1	s__Olleya sp002323495	91.336	959	1052	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Olleya	95.0	96.78	96.78	0.90	0.90	2	-
GCF_900114005.1	s__Olleya namhaensis	83.7661	787	1052	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	82.9005	751	1052	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Olleya	95.0	98.16	97.66	0.93	0.91	5	-
GCF_002831645.1	s__Olleya sp002831645	82.5469	750	1052	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Olleya	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004843725.1	s__Olleya sp004843725	82.2237	746	1052	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	81.097	656	1052	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Olleya	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 14:30:35,308] [INFO] GTDB search result was written to OceanDNA-b9806/result_gtdb.tsv
[2023-03-14 14:30:35,308] [INFO] ===== GTDB Search completed =====
[2023-03-14 14:30:35,309] [INFO] DFAST_QC result json was written to OceanDNA-b9806/dqc_result.json
[2023-03-14 14:30:35,309] [INFO] DFAST_QC completed!
[2023-03-14 14:30:35,309] [INFO] Total running time: 0h1m49s