[2023-03-17 10:19:15,246] [INFO] DFAST_QC pipeline started.
[2023-03-17 10:19:15,247] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 10:19:15,247] [INFO] DQC Reference Directory: /var/lib/cwl/stg82ac3392-82ae-4265-a7b1-f054c0f52fe2/dqc_reference
[2023-03-17 10:19:16,990] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 10:19:16,990] [INFO] Task started: Prodigal
[2023-03-17 10:19:16,991] [INFO] Running command: cat /var/lib/cwl/stg57247900-bbeb-466d-87f6-072ec3d27c74/OceanDNA-b13246.fa | prodigal -d OceanDNA-b13246/cds.fna -a OceanDNA-b13246/protein.faa -g 11 -q > /dev/null
[2023-03-17 10:19:21,795] [INFO] Task succeeded: Prodigal
[2023-03-17 10:19:21,795] [INFO] Task started: HMMsearch
[2023-03-17 10:19:21,796] [INFO] Running command: hmmsearch --tblout OceanDNA-b13246/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg82ac3392-82ae-4265-a7b1-f054c0f52fe2/dqc_reference/reference_markers.hmm OceanDNA-b13246/protein.faa > /dev/null
[2023-03-17 10:19:21,946] [INFO] Task succeeded: HMMsearch
[2023-03-17 10:19:21,946] [INFO] Found 6/6 markers.
[2023-03-17 10:19:21,962] [INFO] Query marker FASTA was written to OceanDNA-b13246/markers.fasta
[2023-03-17 10:19:21,963] [INFO] Task started: Blastn
[2023-03-17 10:19:21,963] [INFO] Running command: blastn -query OceanDNA-b13246/markers.fasta -db /var/lib/cwl/stg82ac3392-82ae-4265-a7b1-f054c0f52fe2/dqc_reference/reference_markers.fasta -out OceanDNA-b13246/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 10:19:23,569] [INFO] Task succeeded: Blastn
[2023-03-17 10:19:23,571] [INFO] Selected 7 target genomes.
[2023-03-17 10:19:23,572] [INFO] Target genome list was writen to OceanDNA-b13246/target_genomes.txt
[2023-03-17 10:19:23,575] [INFO] Task started: fastANI
[2023-03-17 10:19:23,575] [INFO] Running command: fastANI --query /var/lib/cwl/stg57247900-bbeb-466d-87f6-072ec3d27c74/OceanDNA-b13246.fa --refList OceanDNA-b13246/target_genomes.txt --output OceanDNA-b13246/fastani_result.tsv --threads 1
[2023-03-17 10:19:26,677] [INFO] Task succeeded: fastANI
[2023-03-17 10:19:26,678] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg82ac3392-82ae-4265-a7b1-f054c0f52fe2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 10:19:26,678] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg82ac3392-82ae-4265-a7b1-f054c0f52fe2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 10:19:26,678] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 10:19:26,678] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 10:19:26,678] [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 10:19:26,680] [INFO] DFAST Taxonomy check result was written to OceanDNA-b13246/tc_result.tsv
[2023-03-17 10:19:26,681] [INFO] ===== Taxonomy check completed =====
[2023-03-17 10:19:26,681] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 10:19:26,681] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg82ac3392-82ae-4265-a7b1-f054c0f52fe2/dqc_reference/checkm_data
[2023-03-17 10:19:26,684] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 10:19:26,689] [INFO] Task started: CheckM
[2023-03-17 10:19:26,689] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b13246/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b13246/checkm_input OceanDNA-b13246/checkm_result
[2023-03-17 10:19:45,069] [INFO] Task succeeded: CheckM
[2023-03-17 10:19:45,070] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 85.06%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 10:19:45,086] [INFO] ===== Completeness check finished =====
[2023-03-17 10:19:45,086] [INFO] ===== Start GTDB Search =====
[2023-03-17 10:19:45,086] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b13246/markers.fasta)
[2023-03-17 10:19:45,088] [INFO] Task started: Blastn
[2023-03-17 10:19:45,088] [INFO] Running command: blastn -query OceanDNA-b13246/markers.fasta -db /var/lib/cwl/stg82ac3392-82ae-4265-a7b1-f054c0f52fe2/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b13246/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 10:19:45,715] [INFO] Task succeeded: Blastn
[2023-03-17 10:19:45,717] [INFO] Selected 13 target genomes.
[2023-03-17 10:19:45,717] [INFO] Target genome list was writen to OceanDNA-b13246/target_genomes_gtdb.txt
[2023-03-17 10:19:46,169] [INFO] Task started: fastANI
[2023-03-17 10:19:46,169] [INFO] Running command: fastANI --query /var/lib/cwl/stg57247900-bbeb-466d-87f6-072ec3d27c74/OceanDNA-b13246.fa --refList OceanDNA-b13246/target_genomes_gtdb.txt --output OceanDNA-b13246/fastani_result_gtdb.tsv --threads 1
[2023-03-17 10:19:50,636] [INFO] Task succeeded: fastANI
[2023-03-17 10:19:50,639] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 10:19:50,639] [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_002711925.1	s__GCA-2711925 sp002711925	99.5067	194	228	d__Bacteria;p__Bdellovibrionota;c__Oligoflexia;o__Oligoflexales;f__Bog-1112;g__GCA-2711925	95.0	N/A	N/A	N/A	N/A	1	conclusive
--------------------------------------------------------------------------------
[2023-03-17 10:19:50,640] [INFO] GTDB search result was written to OceanDNA-b13246/result_gtdb.tsv
[2023-03-17 10:19:50,641] [INFO] ===== GTDB Search completed =====
[2023-03-17 10:19:50,643] [INFO] DFAST_QC result json was written to OceanDNA-b13246/dqc_result.json
[2023-03-17 10:19:50,643] [INFO] DFAST_QC completed!
[2023-03-17 10:19:50,643] [INFO] Total running time: 0h0m35s