[2023-03-18 04:16:53,211] [INFO] DFAST_QC pipeline started.
[2023-03-18 04:16:53,211] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 04:16:53,211] [INFO] DQC Reference Directory: /var/lib/cwl/stgfa1abb7a-8bbf-49fa-8ae7-f94d11150992/dqc_reference
[2023-03-18 04:16:54,294] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 04:16:54,294] [INFO] Task started: Prodigal
[2023-03-18 04:16:54,294] [INFO] Running command: cat /var/lib/cwl/stg83fe73ec-d7f3-49df-944a-3f9e59d36c29/OceanDNA-b43904.fa | prodigal -d OceanDNA-b43904/cds.fna -a OceanDNA-b43904/protein.faa -g 11 -q > /dev/null
[2023-03-18 04:17:04,977] [INFO] Task succeeded: Prodigal
[2023-03-18 04:17:04,977] [INFO] Task started: HMMsearch
[2023-03-18 04:17:04,977] [INFO] Running command: hmmsearch --tblout OceanDNA-b43904/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfa1abb7a-8bbf-49fa-8ae7-f94d11150992/dqc_reference/reference_markers.hmm OceanDNA-b43904/protein.faa > /dev/null
[2023-03-18 04:17:05,140] [INFO] Task succeeded: HMMsearch
[2023-03-18 04:17:05,140] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg83fe73ec-d7f3-49df-944a-3f9e59d36c29/OceanDNA-b43904.fa]
[2023-03-18 04:17:05,152] [INFO] Query marker FASTA was written to OceanDNA-b43904/markers.fasta
[2023-03-18 04:17:05,153] [INFO] Task started: Blastn
[2023-03-18 04:17:05,153] [INFO] Running command: blastn -query OceanDNA-b43904/markers.fasta -db /var/lib/cwl/stgfa1abb7a-8bbf-49fa-8ae7-f94d11150992/dqc_reference/reference_markers.fasta -out OceanDNA-b43904/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 04:17:05,581] [INFO] Task succeeded: Blastn
[2023-03-18 04:17:05,581] [INFO] Selected 15 target genomes.
[2023-03-18 04:17:05,582] [INFO] Target genome list was writen to OceanDNA-b43904/target_genomes.txt
[2023-03-18 04:17:05,592] [INFO] Task started: fastANI
[2023-03-18 04:17:05,593] [INFO] Running command: fastANI --query /var/lib/cwl/stg83fe73ec-d7f3-49df-944a-3f9e59d36c29/OceanDNA-b43904.fa --refList OceanDNA-b43904/target_genomes.txt --output OceanDNA-b43904/fastani_result.tsv --threads 1
[2023-03-18 04:17:13,624] [INFO] Task succeeded: fastANI
[2023-03-18 04:17:13,625] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfa1abb7a-8bbf-49fa-8ae7-f94d11150992/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 04:17:13,625] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfa1abb7a-8bbf-49fa-8ae7-f94d11150992/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 04:17:13,625] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 04:17:13,625] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 04:17:13,625] [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 04:17:13,625] [INFO] DFAST Taxonomy check result was written to OceanDNA-b43904/tc_result.tsv
[2023-03-18 04:17:13,625] [INFO] ===== Taxonomy check completed =====
[2023-03-18 04:17:13,625] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 04:17:13,626] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfa1abb7a-8bbf-49fa-8ae7-f94d11150992/dqc_reference/checkm_data
[2023-03-18 04:17:13,629] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 04:17:13,637] [INFO] Task started: CheckM
[2023-03-18 04:17:13,637] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b43904/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b43904/checkm_input OceanDNA-b43904/checkm_result
[2023-03-18 04:17:44,699] [INFO] Task succeeded: CheckM
[2023-03-18 04:17:44,699] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 04:17:44,786] [INFO] ===== Completeness check finished =====
[2023-03-18 04:17:44,786] [INFO] ===== Start GTDB Search =====
[2023-03-18 04:17:44,786] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b43904/markers.fasta)
[2023-03-18 04:17:44,787] [INFO] Task started: Blastn
[2023-03-18 04:17:44,787] [INFO] Running command: blastn -query OceanDNA-b43904/markers.fasta -db /var/lib/cwl/stgfa1abb7a-8bbf-49fa-8ae7-f94d11150992/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b43904/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 04:17:45,201] [INFO] Task succeeded: Blastn
[2023-03-18 04:17:45,202] [INFO] Selected 13 target genomes.
[2023-03-18 04:17:45,202] [INFO] Target genome list was writen to OceanDNA-b43904/target_genomes_gtdb.txt
[2023-03-18 04:17:45,387] [INFO] Task started: fastANI
[2023-03-18 04:17:45,387] [INFO] Running command: fastANI --query /var/lib/cwl/stg83fe73ec-d7f3-49df-944a-3f9e59d36c29/OceanDNA-b43904.fa --refList OceanDNA-b43904/target_genomes_gtdb.txt --output OceanDNA-b43904/fastani_result_gtdb.tsv --threads 1
[2023-03-18 04:17:52,369] [INFO] Task succeeded: fastANI
[2023-03-18 04:17:52,371] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 04:17:52,371] [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_002709565.1	s__GCA-2709565 sp002709565	99.9584	581	608	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__UBA1113;f__UBA1113;g__GCA-2709565	95.0	99.99	99.99	0.97	0.97	2	conclusive
--------------------------------------------------------------------------------
[2023-03-18 04:17:52,371] [INFO] GTDB search result was written to OceanDNA-b43904/result_gtdb.tsv
[2023-03-18 04:17:52,371] [INFO] ===== GTDB Search completed =====
[2023-03-18 04:17:52,371] [INFO] DFAST_QC result json was written to OceanDNA-b43904/dqc_result.json
[2023-03-18 04:17:52,372] [INFO] DFAST_QC completed!
[2023-03-18 04:17:52,372] [INFO] Total running time: 0h0m59s