[2023-03-17 05:16:57,860] [INFO] DFAST_QC pipeline started.
[2023-03-17 05:16:57,860] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 05:16:57,860] [INFO] DQC Reference Directory: /var/lib/cwl/stg16b53db6-1786-41d5-9221-9611a20cedd8/dqc_reference
[2023-03-17 05:16:59,366] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 05:16:59,367] [INFO] Task started: Prodigal
[2023-03-17 05:16:59,367] [INFO] Running command: cat /var/lib/cwl/stgcea51b01-ec1e-44a5-94bc-0d2a5dc308bd/OceanDNA-b37058.fa | prodigal -d OceanDNA-b37058/cds.fna -a OceanDNA-b37058/protein.faa -g 11 -q > /dev/null
[2023-03-17 05:17:12,599] [INFO] Task succeeded: Prodigal
[2023-03-17 05:17:12,599] [INFO] Task started: HMMsearch
[2023-03-17 05:17:12,599] [INFO] Running command: hmmsearch --tblout OceanDNA-b37058/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg16b53db6-1786-41d5-9221-9611a20cedd8/dqc_reference/reference_markers.hmm OceanDNA-b37058/protein.faa > /dev/null
[2023-03-17 05:17:12,777] [INFO] Task succeeded: HMMsearch
[2023-03-17 05:17:12,778] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgcea51b01-ec1e-44a5-94bc-0d2a5dc308bd/OceanDNA-b37058.fa]
[2023-03-17 05:17:12,794] [INFO] Query marker FASTA was written to OceanDNA-b37058/markers.fasta
[2023-03-17 05:17:12,795] [INFO] Task started: Blastn
[2023-03-17 05:17:12,795] [INFO] Running command: blastn -query OceanDNA-b37058/markers.fasta -db /var/lib/cwl/stg16b53db6-1786-41d5-9221-9611a20cedd8/dqc_reference/reference_markers.fasta -out OceanDNA-b37058/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:17:13,367] [INFO] Task succeeded: Blastn
[2023-03-17 05:17:13,368] [INFO] Selected 21 target genomes.
[2023-03-17 05:17:13,368] [INFO] Target genome list was writen to OceanDNA-b37058/target_genomes.txt
[2023-03-17 05:17:13,452] [INFO] Task started: fastANI
[2023-03-17 05:17:13,452] [INFO] Running command: fastANI --query /var/lib/cwl/stgcea51b01-ec1e-44a5-94bc-0d2a5dc308bd/OceanDNA-b37058.fa --refList OceanDNA-b37058/target_genomes.txt --output OceanDNA-b37058/fastani_result.tsv --threads 1
[2023-03-17 05:17:26,026] [INFO] Task succeeded: fastANI
[2023-03-17 05:17:26,026] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg16b53db6-1786-41d5-9221-9611a20cedd8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 05:17:26,026] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg16b53db6-1786-41d5-9221-9611a20cedd8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 05:17:26,026] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 05:17:26,027] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 05:17:26,027] [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
--------------------------------------------------------------------------------
[2023-03-17 05:17:26,027] [INFO] DFAST Taxonomy check result was written to OceanDNA-b37058/tc_result.tsv
[2023-03-17 05:17:26,027] [INFO] ===== Taxonomy check completed =====
[2023-03-17 05:17:26,027] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 05:17:26,027] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg16b53db6-1786-41d5-9221-9611a20cedd8/dqc_reference/checkm_data
[2023-03-17 05:17:26,030] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 05:17:26,034] [INFO] Task started: CheckM
[2023-03-17 05:17:26,034] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b37058/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b37058/checkm_input OceanDNA-b37058/checkm_result
[2023-03-17 05:18:02,352] [INFO] Task succeeded: CheckM
[2023-03-17 05:18:02,353] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 05:18:02,359] [INFO] ===== Completeness check finished =====
[2023-03-17 05:18:02,359] [INFO] ===== Start GTDB Search =====
[2023-03-17 05:18:02,359] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b37058/markers.fasta)
[2023-03-17 05:18:02,361] [INFO] Task started: Blastn
[2023-03-17 05:18:02,361] [INFO] Running command: blastn -query OceanDNA-b37058/markers.fasta -db /var/lib/cwl/stg16b53db6-1786-41d5-9221-9611a20cedd8/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b37058/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:18:03,293] [INFO] Task succeeded: Blastn
[2023-03-17 05:18:03,293] [INFO] Selected 12 target genomes.
[2023-03-17 05:18:03,294] [INFO] Target genome list was writen to OceanDNA-b37058/target_genomes_gtdb.txt
[2023-03-17 05:18:03,416] [INFO] Task started: fastANI
[2023-03-17 05:18:03,416] [INFO] Running command: fastANI --query /var/lib/cwl/stgcea51b01-ec1e-44a5-94bc-0d2a5dc308bd/OceanDNA-b37058.fa --refList OceanDNA-b37058/target_genomes_gtdb.txt --output OceanDNA-b37058/fastani_result_gtdb.tsv --threads 1
[2023-03-17 05:18:10,115] [INFO] Task succeeded: fastANI
[2023-03-17 05:18:10,118] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 05:18:10,118] [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_002336645.1	s__UBA4421 sp002336645	99.2624	640	762	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA4421	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_009886205.1	s__UBA4421 sp009886205	83.6952	575	762	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA4421	95.0	98.44	96.05	0.88	0.79	9	-
GCA_905182095.1	s__UBA4421 sp905182095	80.0106	360	762	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA4421	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905182905.1	s__UBA4421 sp002390555	78.3417	276	762	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA4421	95.0	99.65	99.65	0.88	0.88	2	-
--------------------------------------------------------------------------------
[2023-03-17 05:18:10,119] [INFO] GTDB search result was written to OceanDNA-b37058/result_gtdb.tsv
[2023-03-17 05:18:10,119] [INFO] ===== GTDB Search completed =====
[2023-03-17 05:18:10,119] [INFO] DFAST_QC result json was written to OceanDNA-b37058/dqc_result.json
[2023-03-17 05:18:10,119] [INFO] DFAST_QC completed!
[2023-03-17 05:18:10,119] [INFO] Total running time: 0h1m12s