[2023-03-16 23:35:13,127] [INFO] DFAST_QC pipeline started.
[2023-03-16 23:35:13,127] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 23:35:13,127] [INFO] DQC Reference Directory: /var/lib/cwl/stgc12a26f0-5e9a-435f-bdcf-ef8e3a3140b8/dqc_reference
[2023-03-16 23:35:14,214] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 23:35:14,214] [INFO] Task started: Prodigal
[2023-03-16 23:35:14,215] [INFO] Running command: cat /var/lib/cwl/stg942eb126-d204-482e-ae6d-cdb43303d34b/OceanDNA-b22917.fa | prodigal -d OceanDNA-b22917/cds.fna -a OceanDNA-b22917/protein.faa -g 11 -q > /dev/null
[2023-03-16 23:35:55,100] [INFO] Task succeeded: Prodigal
[2023-03-16 23:35:55,100] [INFO] Task started: HMMsearch
[2023-03-16 23:35:55,100] [INFO] Running command: hmmsearch --tblout OceanDNA-b22917/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc12a26f0-5e9a-435f-bdcf-ef8e3a3140b8/dqc_reference/reference_markers.hmm OceanDNA-b22917/protein.faa > /dev/null
[2023-03-16 23:35:55,372] [INFO] Task succeeded: HMMsearch
[2023-03-16 23:35:55,373] [INFO] Found 6/6 markers.
[2023-03-16 23:35:55,409] [INFO] Query marker FASTA was written to OceanDNA-b22917/markers.fasta
[2023-03-16 23:35:55,410] [INFO] Task started: Blastn
[2023-03-16 23:35:55,410] [INFO] Running command: blastn -query OceanDNA-b22917/markers.fasta -db /var/lib/cwl/stgc12a26f0-5e9a-435f-bdcf-ef8e3a3140b8/dqc_reference/reference_markers.fasta -out OceanDNA-b22917/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 23:35:55,940] [INFO] Task succeeded: Blastn
[2023-03-16 23:35:55,941] [INFO] Selected 14 target genomes.
[2023-03-16 23:35:55,941] [INFO] Target genome list was writen to OceanDNA-b22917/target_genomes.txt
[2023-03-16 23:35:55,947] [INFO] Task started: fastANI
[2023-03-16 23:35:55,947] [INFO] Running command: fastANI --query /var/lib/cwl/stg942eb126-d204-482e-ae6d-cdb43303d34b/OceanDNA-b22917.fa --refList OceanDNA-b22917/target_genomes.txt --output OceanDNA-b22917/fastani_result.tsv --threads 1
[2023-03-16 23:36:12,875] [INFO] Task succeeded: fastANI
[2023-03-16 23:36:12,875] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc12a26f0-5e9a-435f-bdcf-ef8e3a3140b8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 23:36:12,875] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc12a26f0-5e9a-435f-bdcf-ef8e3a3140b8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 23:36:12,882] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 23:36:12,882] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 23:36:12,882] [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
Gimesia algae	strain=Pan161	GCA_007746795.1	2527971	2527971	type	True	85.1311	1864	2293	95	below_threshold
Gimesia maris	strain=DSM 8797	GCA_009720545.1	122	122	type	True	85.0165	1857	2293	95	below_threshold
Gimesia maris	strain=DSM 8797	GCA_000181475.1	122	122	type	True	84.9915	1820	2293	95	below_threshold
Gimesia maris	strain=DSM 8797	GCA_008298035.1	122	122	type	True	84.9802	1856	2293	95	below_threshold
Gimesia fumaroli	strain=Enr17	GCA_007754425.1	2527976	2527976	type	True	78.6706	890	2293	95	below_threshold
Gimesia benthica	strain=E7	GCA_009720525.1	2608982	2608982	type	True	78.669	932	2293	95	below_threshold
Gimesia panareensis	strain=Enr10	GCA_007748155.1	2527978	2527978	type	True	78.6307	970	2293	95	below_threshold
Gimesia alba	strain=Pan241w	GCA_007744675.1	2527973	2527973	type	True	78.5627	933	2293	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 23:36:12,882] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22917/tc_result.tsv
[2023-03-16 23:36:12,882] [INFO] ===== Taxonomy check completed =====
[2023-03-16 23:36:12,882] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 23:36:12,882] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc12a26f0-5e9a-435f-bdcf-ef8e3a3140b8/dqc_reference/checkm_data
[2023-03-16 23:36:12,883] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 23:36:12,891] [INFO] Task started: CheckM
[2023-03-16 23:36:12,891] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22917/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22917/checkm_input OceanDNA-b22917/checkm_result
[2023-03-16 23:37:51,085] [INFO] Task succeeded: CheckM
[2023-03-16 23:37:51,086] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 23:37:51,098] [INFO] ===== Completeness check finished =====
[2023-03-16 23:37:51,098] [INFO] ===== Start GTDB Search =====
[2023-03-16 23:37:51,098] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22917/markers.fasta)
[2023-03-16 23:37:51,099] [INFO] Task started: Blastn
[2023-03-16 23:37:51,099] [INFO] Running command: blastn -query OceanDNA-b22917/markers.fasta -db /var/lib/cwl/stgc12a26f0-5e9a-435f-bdcf-ef8e3a3140b8/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22917/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 23:37:51,835] [INFO] Task succeeded: Blastn
[2023-03-16 23:37:51,838] [INFO] Selected 8 target genomes.
[2023-03-16 23:37:51,838] [INFO] Target genome list was writen to OceanDNA-b22917/target_genomes_gtdb.txt
[2023-03-16 23:37:51,990] [INFO] Task started: fastANI
[2023-03-16 23:37:51,991] [INFO] Running command: fastANI --query /var/lib/cwl/stg942eb126-d204-482e-ae6d-cdb43303d34b/OceanDNA-b22917.fa --refList OceanDNA-b22917/target_genomes_gtdb.txt --output OceanDNA-b22917/fastani_result_gtdb.tsv --threads 1
[2023-03-16 23:38:05,052] [INFO] Task succeeded: fastANI
[2023-03-16 23:38:05,057] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 23:38:05,057] [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_002706765.1	s__Gimesia sp002706765	99.9674	2244	2293	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Gimesia	95.0	99.96	99.96	0.97	0.97	2	conclusive
GCF_007746795.1	s__Gimesia algae	85.1518	1859	2293	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Gimesia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008298035.1	s__Gimesia maris	84.9804	1856	2293	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Gimesia	95.0	98.48	97.03	0.94	0.89	7	-
GCF_007754425.1	s__Gimesia fumaroli	78.6677	890	2293	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Gimesia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009720525.1	s__Gimesia benthica	78.6632	934	2293	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Gimesia	95.0249	95.18	95.18	0.86	0.86	2	-
GCF_007748155.1	s__Gimesia panareensis	78.6366	968	2293	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Gimesia	95.0	96.61	95.86	0.91	0.90	3	-
GCF_008329715.1	s__Gimesia chilikensis	78.5965	896	2293	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Gimesia	95.0249	95.30	95.11	0.90	0.87	4	-
GCF_007744675.1	s__Gimesia alba	78.572	929	2293	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Gimesia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 23:38:05,058] [INFO] GTDB search result was written to OceanDNA-b22917/result_gtdb.tsv
[2023-03-16 23:38:05,059] [INFO] ===== GTDB Search completed =====
[2023-03-16 23:38:05,061] [INFO] DFAST_QC result json was written to OceanDNA-b22917/dqc_result.json
[2023-03-16 23:38:05,061] [INFO] DFAST_QC completed!
[2023-03-16 23:38:05,062] [INFO] Total running time: 0h2m52s