[2023-03-18 06:30:24,714] [INFO] DFAST_QC pipeline started.
[2023-03-18 06:30:24,714] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 06:30:24,714] [INFO] DQC Reference Directory: /var/lib/cwl/stgdbea06cc-9698-4f27-9b92-1a1523540f15/dqc_reference
[2023-03-18 06:30:25,871] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 06:30:25,871] [INFO] Task started: Prodigal
[2023-03-18 06:30:25,871] [INFO] Running command: cat /var/lib/cwl/stg2bf30ef9-9165-4818-a7e1-3a5488e37e6b/OceanDNA-b34165.fa | prodigal -d OceanDNA-b34165/cds.fna -a OceanDNA-b34165/protein.faa -g 11 -q > /dev/null
[2023-03-18 06:30:33,276] [INFO] Task succeeded: Prodigal
[2023-03-18 06:30:33,277] [INFO] Task started: HMMsearch
[2023-03-18 06:30:33,277] [INFO] Running command: hmmsearch --tblout OceanDNA-b34165/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdbea06cc-9698-4f27-9b92-1a1523540f15/dqc_reference/reference_markers.hmm OceanDNA-b34165/protein.faa > /dev/null
[2023-03-18 06:30:33,451] [INFO] Task succeeded: HMMsearch
[2023-03-18 06:30:33,451] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg2bf30ef9-9165-4818-a7e1-3a5488e37e6b/OceanDNA-b34165.fa]
[2023-03-18 06:30:33,464] [INFO] Query marker FASTA was written to OceanDNA-b34165/markers.fasta
[2023-03-18 06:30:33,465] [INFO] Task started: Blastn
[2023-03-18 06:30:33,465] [INFO] Running command: blastn -query OceanDNA-b34165/markers.fasta -db /var/lib/cwl/stgdbea06cc-9698-4f27-9b92-1a1523540f15/dqc_reference/reference_markers.fasta -out OceanDNA-b34165/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 06:30:33,993] [INFO] Task succeeded: Blastn
[2023-03-18 06:30:33,994] [INFO] Selected 16 target genomes.
[2023-03-18 06:30:33,994] [INFO] Target genome list was writen to OceanDNA-b34165/target_genomes.txt
[2023-03-18 06:30:34,085] [INFO] Task started: fastANI
[2023-03-18 06:30:34,085] [INFO] Running command: fastANI --query /var/lib/cwl/stg2bf30ef9-9165-4818-a7e1-3a5488e37e6b/OceanDNA-b34165.fa --refList OceanDNA-b34165/target_genomes.txt --output OceanDNA-b34165/fastani_result.tsv --threads 1
[2023-03-18 06:30:42,428] [INFO] Task succeeded: fastANI
[2023-03-18 06:30:42,428] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdbea06cc-9698-4f27-9b92-1a1523540f15/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 06:30:42,428] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdbea06cc-9698-4f27-9b92-1a1523540f15/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 06:30:42,428] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 06:30:42,428] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 06:30:42,429] [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 06:30:42,429] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34165/tc_result.tsv
[2023-03-18 06:30:42,431] [INFO] ===== Taxonomy check completed =====
[2023-03-18 06:30:42,431] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 06:30:42,431] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdbea06cc-9698-4f27-9b92-1a1523540f15/dqc_reference/checkm_data
[2023-03-18 06:30:42,434] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 06:30:42,441] [INFO] Task started: CheckM
[2023-03-18 06:30:42,441] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34165/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34165/checkm_input OceanDNA-b34165/checkm_result
[2023-03-18 06:31:06,358] [INFO] Task succeeded: CheckM
[2023-03-18 06:31:06,359] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.28%
Contamintation: 8.85%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2023-03-18 06:31:06,371] [INFO] ===== Completeness check finished =====
[2023-03-18 06:31:06,371] [INFO] ===== Start GTDB Search =====
[2023-03-18 06:31:06,371] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34165/markers.fasta)
[2023-03-18 06:31:06,371] [INFO] Task started: Blastn
[2023-03-18 06:31:06,372] [INFO] Running command: blastn -query OceanDNA-b34165/markers.fasta -db /var/lib/cwl/stgdbea06cc-9698-4f27-9b92-1a1523540f15/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34165/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 06:31:07,178] [INFO] Task succeeded: Blastn
[2023-03-18 06:31:07,185] [INFO] Selected 24 target genomes.
[2023-03-18 06:31:07,185] [INFO] Target genome list was writen to OceanDNA-b34165/target_genomes_gtdb.txt
[2023-03-18 06:31:07,372] [INFO] Task started: fastANI
[2023-03-18 06:31:07,372] [INFO] Running command: fastANI --query /var/lib/cwl/stg2bf30ef9-9165-4818-a7e1-3a5488e37e6b/OceanDNA-b34165.fa --refList OceanDNA-b34165/target_genomes_gtdb.txt --output OceanDNA-b34165/fastani_result_gtdb.tsv --threads 1
[2023-03-18 06:31:17,179] [INFO] Task succeeded: fastANI
[2023-03-18 06:31:17,182] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 06:31:17,182] [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_905479505.1	s__UBA3031 sp905479505	97.2523	237	445	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__UBA3031;g__UBA3031	95.0	98.43	98.37	0.67	0.60	4	conclusive
GCA_002367635.1	s__UBA3031 sp002367635	77.1705	54	445	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__UBA3031;g__UBA3031	95.0	99.64	99.62	0.86	0.85	3	-
--------------------------------------------------------------------------------
[2023-03-18 06:31:17,184] [INFO] GTDB search result was written to OceanDNA-b34165/result_gtdb.tsv
[2023-03-18 06:31:17,187] [INFO] ===== GTDB Search completed =====
[2023-03-18 06:31:17,189] [INFO] DFAST_QC result json was written to OceanDNA-b34165/dqc_result.json
[2023-03-18 06:31:17,189] [INFO] DFAST_QC completed!
[2023-03-18 06:31:17,189] [INFO] Total running time: 0h0m52s