[2023-03-15 19:27:48,484] [INFO] DFAST_QC pipeline started.
[2023-03-15 19:27:48,484] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 19:27:48,484] [INFO] DQC Reference Directory: /var/lib/cwl/stgc4d9b5f9-4a82-4f0e-aa22-bb1137403148/dqc_reference
[2023-03-15 19:28:00,517] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 19:28:00,518] [INFO] Task started: Prodigal
[2023-03-15 19:28:00,518] [INFO] Running command: cat /var/lib/cwl/stg60765138-39e9-419c-aaef-688a5c34bea1/OceanDNA-b36755.fa | prodigal -d OceanDNA-b36755/cds.fna -a OceanDNA-b36755/protein.faa -g 11 -q > /dev/null
[2023-03-15 19:31:47,690] [INFO] Task succeeded: Prodigal
[2023-03-15 19:31:47,690] [INFO] Task started: HMMsearch
[2023-03-15 19:31:47,690] [INFO] Running command: hmmsearch --tblout OceanDNA-b36755/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc4d9b5f9-4a82-4f0e-aa22-bb1137403148/dqc_reference/reference_markers.hmm OceanDNA-b36755/protein.faa > /dev/null
[2023-03-15 19:31:48,480] [INFO] Task succeeded: HMMsearch
[2023-03-15 19:31:48,480] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg60765138-39e9-419c-aaef-688a5c34bea1/OceanDNA-b36755.fa]
[2023-03-15 19:31:48,555] [INFO] Query marker FASTA was written to OceanDNA-b36755/markers.fasta
[2023-03-15 19:31:48,584] [INFO] Task started: Blastn
[2023-03-15 19:31:48,584] [INFO] Running command: blastn -query OceanDNA-b36755/markers.fasta -db /var/lib/cwl/stgc4d9b5f9-4a82-4f0e-aa22-bb1137403148/dqc_reference/reference_markers.fasta -out OceanDNA-b36755/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 19:31:50,640] [INFO] Task succeeded: Blastn
[2023-03-15 19:31:50,641] [INFO] Selected 26 target genomes.
[2023-03-15 19:31:50,641] [INFO] Target genome list was writen to OceanDNA-b36755/target_genomes.txt
[2023-03-15 19:31:50,931] [INFO] Task started: fastANI
[2023-03-15 19:31:50,931] [INFO] Running command: fastANI --query /var/lib/cwl/stg60765138-39e9-419c-aaef-688a5c34bea1/OceanDNA-b36755.fa --refList OceanDNA-b36755/target_genomes.txt --output OceanDNA-b36755/fastani_result.tsv --threads 1
[2023-03-15 19:32:34,674] [INFO] Task succeeded: fastANI
[2023-03-15 19:32:34,675] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc4d9b5f9-4a82-4f0e-aa22-bb1137403148/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 19:32:34,675] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc4d9b5f9-4a82-4f0e-aa22-bb1137403148/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 19:32:34,675] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 19:32:34,675] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 19:32:34,675] [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
--------------------------------------------------------------------------------
[2023-03-15 19:32:34,675] [INFO] DFAST Taxonomy check result was written to OceanDNA-b36755/tc_result.tsv
[2023-03-15 19:32:34,676] [INFO] ===== Taxonomy check completed =====
[2023-03-15 19:32:34,676] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 19:32:34,676] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc4d9b5f9-4a82-4f0e-aa22-bb1137403148/dqc_reference/checkm_data
[2023-03-15 19:32:34,679] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 19:32:34,694] [INFO] Task started: CheckM
[2023-03-15 19:32:34,694] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b36755/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b36755/checkm_input OceanDNA-b36755/checkm_result
[2023-03-15 19:33:28,770] [INFO] Task succeeded: CheckM
[2023-03-15 19:33:28,770] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 63.89%
Contamintation: 5.21%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-15 19:33:28,773] [INFO] ===== Completeness check finished =====
[2023-03-15 19:33:28,773] [INFO] ===== Start GTDB Search =====
[2023-03-15 19:33:28,773] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b36755/markers.fasta)
[2023-03-15 19:33:28,774] [INFO] Task started: Blastn
[2023-03-15 19:33:28,775] [INFO] Running command: blastn -query OceanDNA-b36755/markers.fasta -db /var/lib/cwl/stgc4d9b5f9-4a82-4f0e-aa22-bb1137403148/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b36755/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 19:33:29,629] [INFO] Task succeeded: Blastn
[2023-03-15 19:33:29,630] [INFO] Selected 26 target genomes.
[2023-03-15 19:33:29,630] [INFO] Target genome list was writen to OceanDNA-b36755/target_genomes_gtdb.txt
[2023-03-15 19:33:31,081] [INFO] Task started: fastANI
[2023-03-15 19:33:31,081] [INFO] Running command: fastANI --query /var/lib/cwl/stg60765138-39e9-419c-aaef-688a5c34bea1/OceanDNA-b36755.fa --refList OceanDNA-b36755/target_genomes_gtdb.txt --output OceanDNA-b36755/fastani_result_gtdb.tsv --threads 1
[2023-03-15 19:33:46,648] [INFO] Task succeeded: fastANI
[2023-03-15 19:33:46,651] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 19:33:46,651] [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_002728675.1	s__GCA-002728675 sp002728675	78.2479	431	1124	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__GCA-002728675	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002714125.1	s__GCA-002728675 sp002714125	76.4704	129	1124	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__GCA-002728675	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002480525.1	s__UBA7803 sp002480525	75.3575	58	1124	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA7803	95.0	99.35	98.95	0.83	0.81	3	-
--------------------------------------------------------------------------------
[2023-03-15 19:33:46,651] [INFO] GTDB search result was written to OceanDNA-b36755/result_gtdb.tsv
[2023-03-15 19:33:46,651] [INFO] ===== GTDB Search completed =====
[2023-03-15 19:33:46,652] [INFO] DFAST_QC result json was written to OceanDNA-b36755/dqc_result.json
[2023-03-15 19:33:46,652] [INFO] DFAST_QC completed!
[2023-03-15 19:33:46,652] [INFO] Total running time: 0h5m58s