[2023-03-18 09:26:42,702] [INFO] DFAST_QC pipeline started.
[2023-03-18 09:26:42,702] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 09:26:42,702] [INFO] DQC Reference Directory: /var/lib/cwl/stg3c73bff8-cc11-4152-aa2d-034d7f9d93a1/dqc_reference
[2023-03-18 09:26:43,804] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 09:26:43,804] [INFO] Task started: Prodigal
[2023-03-18 09:26:43,804] [INFO] Running command: cat /var/lib/cwl/stg45099882-1217-4e33-b514-5362e5770e16/OceanDNA-b22229.fa | prodigal -d OceanDNA-b22229/cds.fna -a OceanDNA-b22229/protein.faa -g 11 -q > /dev/null
[2023-03-18 09:27:03,524] [INFO] Task succeeded: Prodigal
[2023-03-18 09:27:03,524] [INFO] Task started: HMMsearch
[2023-03-18 09:27:03,524] [INFO] Running command: hmmsearch --tblout OceanDNA-b22229/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3c73bff8-cc11-4152-aa2d-034d7f9d93a1/dqc_reference/reference_markers.hmm OceanDNA-b22229/protein.faa > /dev/null
[2023-03-18 09:27:03,712] [INFO] Task succeeded: HMMsearch
[2023-03-18 09:27:03,712] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg45099882-1217-4e33-b514-5362e5770e16/OceanDNA-b22229.fa]
[2023-03-18 09:27:03,731] [INFO] Query marker FASTA was written to OceanDNA-b22229/markers.fasta
[2023-03-18 09:27:03,732] [INFO] Task started: Blastn
[2023-03-18 09:27:03,732] [INFO] Running command: blastn -query OceanDNA-b22229/markers.fasta -db /var/lib/cwl/stg3c73bff8-cc11-4152-aa2d-034d7f9d93a1/dqc_reference/reference_markers.fasta -out OceanDNA-b22229/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:27:04,255] [INFO] Task succeeded: Blastn
[2023-03-18 09:27:04,255] [INFO] Selected 19 target genomes.
[2023-03-18 09:27:04,256] [INFO] Target genome list was writen to OceanDNA-b22229/target_genomes.txt
[2023-03-18 09:27:04,265] [INFO] Task started: fastANI
[2023-03-18 09:27:04,265] [INFO] Running command: fastANI --query /var/lib/cwl/stg45099882-1217-4e33-b514-5362e5770e16/OceanDNA-b22229.fa --refList OceanDNA-b22229/target_genomes.txt --output OceanDNA-b22229/fastani_result.tsv --threads 1
[2023-03-18 09:27:19,027] [INFO] Task succeeded: fastANI
[2023-03-18 09:27:19,028] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3c73bff8-cc11-4152-aa2d-034d7f9d93a1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 09:27:19,028] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3c73bff8-cc11-4152-aa2d-034d7f9d93a1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 09:27:19,028] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 09:27:19,028] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 09:27:19,028] [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
--------------------------------------------------------------------------------
[2023-03-18 09:27:19,028] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22229/tc_result.tsv
[2023-03-18 09:27:19,029] [INFO] ===== Taxonomy check completed =====
[2023-03-18 09:27:19,029] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 09:27:19,029] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3c73bff8-cc11-4152-aa2d-034d7f9d93a1/dqc_reference/checkm_data
[2023-03-18 09:27:19,031] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 09:27:19,035] [INFO] Task started: CheckM
[2023-03-18 09:27:19,035] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22229/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22229/checkm_input OceanDNA-b22229/checkm_result
[2023-03-18 09:28:11,788] [INFO] Task succeeded: CheckM
[2023-03-18 09:28:11,788] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 09:28:11,790] [INFO] ===== Completeness check finished =====
[2023-03-18 09:28:11,790] [INFO] ===== Start GTDB Search =====
[2023-03-18 09:28:11,791] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22229/markers.fasta)
[2023-03-18 09:28:11,791] [INFO] Task started: Blastn
[2023-03-18 09:28:11,791] [INFO] Running command: blastn -query OceanDNA-b22229/markers.fasta -db /var/lib/cwl/stg3c73bff8-cc11-4152-aa2d-034d7f9d93a1/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22229/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:28:12,497] [INFO] Task succeeded: Blastn
[2023-03-18 09:28:12,498] [INFO] Selected 14 target genomes.
[2023-03-18 09:28:12,498] [INFO] Target genome list was writen to OceanDNA-b22229/target_genomes_gtdb.txt
[2023-03-18 09:28:12,556] [INFO] Task started: fastANI
[2023-03-18 09:28:12,556] [INFO] Running command: fastANI --query /var/lib/cwl/stg45099882-1217-4e33-b514-5362e5770e16/OceanDNA-b22229.fa --refList OceanDNA-b22229/target_genomes_gtdb.txt --output OceanDNA-b22229/fastani_result_gtdb.tsv --threads 1
[2023-03-18 09:28:19,410] [INFO] Task succeeded: fastANI
[2023-03-18 09:28:19,416] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 09:28:19,416] [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_015487555.1	s__UBA1924 sp015487555	77.6287	269	1004	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__UBA1924	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002337545.1	s__UBA1924 sp002337545	77.0121	195	1004	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__UBA1924	95.0	98.57	98.49	0.90	0.89	3	-
GCA_002364005.1	s__UBA1924 sp002364005	76.988	212	1004	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__UBA1924	95.0	99.92	99.89	0.95	0.91	4	-
GCA_017640485.1	s__UBA1924 sp017640485	76.8574	123	1004	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__UBA1924	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017642965.1	s__UBA1924 sp017642965	76.8243	152	1004	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__UBA1924	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016764895.1	s__UBA1924 sp016764895	76.5595	93	1004	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__UBA1924	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009827215.1	s__UBA1924 sp009827215	76.4995	129	1004	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__UBA1924	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016763115.1	s__UBA1924 sp016763115	76.1772	70	1004	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__UBA1924	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003696675.1	s__UBA6054 sp003696675	76.102	57	1004	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__UBA6054	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 09:28:19,416] [INFO] GTDB search result was written to OceanDNA-b22229/result_gtdb.tsv
[2023-03-18 09:28:19,416] [INFO] ===== GTDB Search completed =====
[2023-03-18 09:28:19,417] [INFO] DFAST_QC result json was written to OceanDNA-b22229/dqc_result.json
[2023-03-18 09:28:19,417] [INFO] DFAST_QC completed!
[2023-03-18 09:28:19,417] [INFO] Total running time: 0h1m37s