[2023-03-17 02:49:37,389] [INFO] DFAST_QC pipeline started.
[2023-03-17 02:49:37,390] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 02:49:37,390] [INFO] DQC Reference Directory: /var/lib/cwl/stge6b0b99c-b79e-41c4-94bd-2c00bd72e839/dqc_reference
[2023-03-17 02:49:38,568] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 02:49:38,568] [INFO] Task started: Prodigal
[2023-03-17 02:49:38,568] [INFO] Running command: cat /var/lib/cwl/stgf4f5e519-0519-4d43-b251-70b17361cae7/OceanDNA-b37094.fa | prodigal -d OceanDNA-b37094/cds.fna -a OceanDNA-b37094/protein.faa -g 11 -q > /dev/null
[2023-03-17 02:49:54,983] [INFO] Task succeeded: Prodigal
[2023-03-17 02:49:54,984] [INFO] Task started: HMMsearch
[2023-03-17 02:49:54,984] [INFO] Running command: hmmsearch --tblout OceanDNA-b37094/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge6b0b99c-b79e-41c4-94bd-2c00bd72e839/dqc_reference/reference_markers.hmm OceanDNA-b37094/protein.faa > /dev/null
[2023-03-17 02:49:55,178] [INFO] Task succeeded: HMMsearch
[2023-03-17 02:49:55,179] [INFO] Found 6/6 markers.
[2023-03-17 02:49:55,199] [INFO] Query marker FASTA was written to OceanDNA-b37094/markers.fasta
[2023-03-17 02:49:55,200] [INFO] Task started: Blastn
[2023-03-17 02:49:55,200] [INFO] Running command: blastn -query OceanDNA-b37094/markers.fasta -db /var/lib/cwl/stge6b0b99c-b79e-41c4-94bd-2c00bd72e839/dqc_reference/reference_markers.fasta -out OceanDNA-b37094/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 02:49:55,847] [INFO] Task succeeded: Blastn
[2023-03-17 02:49:55,848] [INFO] Selected 30 target genomes.
[2023-03-17 02:49:55,848] [INFO] Target genome list was writen to OceanDNA-b37094/target_genomes.txt
[2023-03-17 02:49:56,004] [INFO] Task started: fastANI
[2023-03-17 02:49:56,004] [INFO] Running command: fastANI --query /var/lib/cwl/stgf4f5e519-0519-4d43-b251-70b17361cae7/OceanDNA-b37094.fa --refList OceanDNA-b37094/target_genomes.txt --output OceanDNA-b37094/fastani_result.tsv --threads 1
[2023-03-17 02:50:12,619] [INFO] Task succeeded: fastANI
[2023-03-17 02:50:12,620] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge6b0b99c-b79e-41c4-94bd-2c00bd72e839/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 02:50:12,620] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge6b0b99c-b79e-41c4-94bd-2c00bd72e839/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 02:50:12,620] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 02:50:12,620] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 02:50:12,620] [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 02:50:12,620] [INFO] DFAST Taxonomy check result was written to OceanDNA-b37094/tc_result.tsv
[2023-03-17 02:50:12,621] [INFO] ===== Taxonomy check completed =====
[2023-03-17 02:50:12,621] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 02:50:12,621] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge6b0b99c-b79e-41c4-94bd-2c00bd72e839/dqc_reference/checkm_data
[2023-03-17 02:50:12,631] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 02:50:12,653] [INFO] Task started: CheckM
[2023-03-17 02:50:12,654] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b37094/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b37094/checkm_input OceanDNA-b37094/checkm_result
[2023-03-17 02:50:57,192] [INFO] Task succeeded: CheckM
[2023-03-17 02:50:57,193] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 82.29%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 02:50:57,199] [INFO] ===== Completeness check finished =====
[2023-03-17 02:50:57,199] [INFO] ===== Start GTDB Search =====
[2023-03-17 02:50:57,199] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b37094/markers.fasta)
[2023-03-17 02:50:57,200] [INFO] Task started: Blastn
[2023-03-17 02:50:57,200] [INFO] Running command: blastn -query OceanDNA-b37094/markers.fasta -db /var/lib/cwl/stge6b0b99c-b79e-41c4-94bd-2c00bd72e839/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b37094/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 02:50:58,601] [INFO] Task succeeded: Blastn
[2023-03-17 02:50:58,602] [INFO] Selected 26 target genomes.
[2023-03-17 02:50:58,602] [INFO] Target genome list was writen to OceanDNA-b37094/target_genomes_gtdb.txt
[2023-03-17 02:50:58,820] [INFO] Task started: fastANI
[2023-03-17 02:50:58,820] [INFO] Running command: fastANI --query /var/lib/cwl/stgf4f5e519-0519-4d43-b251-70b17361cae7/OceanDNA-b37094.fa --refList OceanDNA-b37094/target_genomes_gtdb.txt --output OceanDNA-b37094/fastani_result_gtdb.tsv --threads 1
[2023-03-17 02:51:12,057] [INFO] Task succeeded: fastANI
[2023-03-17 02:51:12,059] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 02:51:12,059] [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_002450255.1	s__UBA4421 sp002450255	99.5871	798	923	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA4421	95.0	N/A	N/A	N/A	N/A	1	conclusive
--------------------------------------------------------------------------------
[2023-03-17 02:51:12,060] [INFO] GTDB search result was written to OceanDNA-b37094/result_gtdb.tsv
[2023-03-17 02:51:12,062] [INFO] ===== GTDB Search completed =====
[2023-03-17 02:51:12,063] [INFO] DFAST_QC result json was written to OceanDNA-b37094/dqc_result.json
[2023-03-17 02:51:12,063] [INFO] DFAST_QC completed!
[2023-03-17 02:51:12,063] [INFO] Total running time: 0h1m35s