[2023-03-14 11:33:34,886] [INFO] DFAST_QC pipeline started.
[2023-03-14 11:33:34,886] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 11:33:34,886] [INFO] DQC Reference Directory: /var/lib/cwl/stg6fb6939e-5b8c-4e42-89a0-370bf5d50ee1/dqc_reference
[2023-03-14 11:33:36,058] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 11:33:36,060] [INFO] Task started: Prodigal
[2023-03-14 11:33:36,060] [INFO] Running command: cat /var/lib/cwl/stg342e1a03-9b7c-4e27-b367-de7cd5c9b568/OceanDNA-b21511.fa | prodigal -d OceanDNA-b21511/cds.fna -a OceanDNA-b21511/protein.faa -g 11 -q > /dev/null
[2023-03-14 11:33:42,577] [INFO] Task succeeded: Prodigal
[2023-03-14 11:33:42,578] [INFO] Task started: HMMsearch
[2023-03-14 11:33:42,578] [INFO] Running command: hmmsearch --tblout OceanDNA-b21511/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6fb6939e-5b8c-4e42-89a0-370bf5d50ee1/dqc_reference/reference_markers.hmm OceanDNA-b21511/protein.faa > /dev/null
[2023-03-14 11:33:42,749] [INFO] Task succeeded: HMMsearch
[2023-03-14 11:33:42,750] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg342e1a03-9b7c-4e27-b367-de7cd5c9b568/OceanDNA-b21511.fa]
[2023-03-14 11:33:42,757] [INFO] Query marker FASTA was written to OceanDNA-b21511/markers.fasta
[2023-03-14 11:33:42,758] [INFO] Task started: Blastn
[2023-03-14 11:33:42,758] [INFO] Running command: blastn -query OceanDNA-b21511/markers.fasta -db /var/lib/cwl/stg6fb6939e-5b8c-4e42-89a0-370bf5d50ee1/dqc_reference/reference_markers.fasta -out OceanDNA-b21511/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:33:43,193] [INFO] Task succeeded: Blastn
[2023-03-14 11:33:43,196] [INFO] Selected 3 target genomes.
[2023-03-14 11:33:43,197] [INFO] Target genome list was writen to OceanDNA-b21511/target_genomes.txt
[2023-03-14 11:33:43,199] [INFO] Task started: fastANI
[2023-03-14 11:33:43,199] [INFO] Running command: fastANI --query /var/lib/cwl/stg342e1a03-9b7c-4e27-b367-de7cd5c9b568/OceanDNA-b21511.fa --refList OceanDNA-b21511/target_genomes.txt --output OceanDNA-b21511/fastani_result.tsv --threads 1
[2023-03-14 11:33:45,535] [INFO] Task succeeded: fastANI
[2023-03-14 11:33:45,536] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6fb6939e-5b8c-4e42-89a0-370bf5d50ee1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 11:33:45,536] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6fb6939e-5b8c-4e42-89a0-370bf5d50ee1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 11:33:45,536] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 11:33:45,536] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 11:33:45,536] [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
--------------------------------------------------------------------------------
[2023-03-14 11:33:45,536] [INFO] DFAST Taxonomy check result was written to OceanDNA-b21511/tc_result.tsv
[2023-03-14 11:33:45,536] [INFO] ===== Taxonomy check completed =====
[2023-03-14 11:33:45,537] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 11:33:45,537] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6fb6939e-5b8c-4e42-89a0-370bf5d50ee1/dqc_reference/checkm_data
[2023-03-14 11:33:45,539] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 11:33:45,541] [INFO] Task started: CheckM
[2023-03-14 11:33:45,541] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b21511/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b21511/checkm_input OceanDNA-b21511/checkm_result
[2023-03-14 11:34:07,843] [INFO] Task succeeded: CheckM
[2023-03-14 11:34:07,843] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 84.72%
Contamintation: 2.08%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 11:34:07,844] [INFO] ===== Completeness check finished =====
[2023-03-14 11:34:07,845] [INFO] ===== Start GTDB Search =====
[2023-03-14 11:34:07,845] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b21511/markers.fasta)
[2023-03-14 11:34:07,845] [INFO] Task started: Blastn
[2023-03-14 11:34:07,845] [INFO] Running command: blastn -query OceanDNA-b21511/markers.fasta -db /var/lib/cwl/stg6fb6939e-5b8c-4e42-89a0-370bf5d50ee1/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b21511/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:34:08,295] [INFO] Task succeeded: Blastn
[2023-03-14 11:34:08,322] [INFO] Selected 7 target genomes.
[2023-03-14 11:34:08,323] [INFO] Target genome list was writen to OceanDNA-b21511/target_genomes_gtdb.txt
[2023-03-14 11:34:08,351] [INFO] Task started: fastANI
[2023-03-14 11:34:08,351] [INFO] Running command: fastANI --query /var/lib/cwl/stg342e1a03-9b7c-4e27-b367-de7cd5c9b568/OceanDNA-b21511.fa --refList OceanDNA-b21511/target_genomes_gtdb.txt --output OceanDNA-b21511/fastani_result_gtdb.tsv --threads 1
[2023-03-14 11:34:12,266] [INFO] Task succeeded: fastANI
[2023-03-14 11:34:12,268] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 11:34:12,269] [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_002686445.1	s__GCA-2686445 sp002686445	99.95	210	256	d__Bacteria;p__Patescibacteria;c__Andersenbacteria;o__UBA10190;f__UBA10190;g__GCA-2686445	95.0	N/A	N/A	N/A	N/A	1	conclusive
--------------------------------------------------------------------------------
[2023-03-14 11:34:12,269] [INFO] GTDB search result was written to OceanDNA-b21511/result_gtdb.tsv
[2023-03-14 11:34:12,269] [INFO] ===== GTDB Search completed =====
[2023-03-14 11:34:12,269] [INFO] DFAST_QC result json was written to OceanDNA-b21511/dqc_result.json
[2023-03-14 11:34:12,269] [INFO] DFAST_QC completed!
[2023-03-14 11:34:12,270] [INFO] Total running time: 0h0m37s