[2023-03-15 14:06:11,277] [INFO] DFAST_QC pipeline started.
[2023-03-15 14:06:11,278] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 14:06:11,278] [INFO] DQC Reference Directory: /var/lib/cwl/stg7da2edda-4c8a-4883-a477-f0fe9b6f27f6/dqc_reference
[2023-03-15 14:06:12,390] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 14:06:12,390] [INFO] Task started: Prodigal
[2023-03-15 14:06:12,391] [INFO] Running command: cat /var/lib/cwl/stgd72698af-dc10-4a53-ab9b-49317323aa82/OceanDNA-b33605.fa | prodigal -d OceanDNA-b33605/cds.fna -a OceanDNA-b33605/protein.faa -g 11 -q > /dev/null
[2023-03-15 14:06:16,429] [INFO] Task succeeded: Prodigal
[2023-03-15 14:06:16,430] [INFO] Task started: HMMsearch
[2023-03-15 14:06:16,430] [INFO] Running command: hmmsearch --tblout OceanDNA-b33605/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7da2edda-4c8a-4883-a477-f0fe9b6f27f6/dqc_reference/reference_markers.hmm OceanDNA-b33605/protein.faa > /dev/null
[2023-03-15 14:06:16,612] [INFO] Task succeeded: HMMsearch
[2023-03-15 14:06:16,612] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgd72698af-dc10-4a53-ab9b-49317323aa82/OceanDNA-b33605.fa]
[2023-03-15 14:06:16,621] [INFO] Query marker FASTA was written to OceanDNA-b33605/markers.fasta
[2023-03-15 14:06:16,623] [INFO] Task started: Blastn
[2023-03-15 14:06:16,623] [INFO] Running command: blastn -query OceanDNA-b33605/markers.fasta -db /var/lib/cwl/stg7da2edda-4c8a-4883-a477-f0fe9b6f27f6/dqc_reference/reference_markers.fasta -out OceanDNA-b33605/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 14:06:17,164] [INFO] Task succeeded: Blastn
[2023-03-15 14:06:17,165] [INFO] Selected 11 target genomes.
[2023-03-15 14:06:17,165] [INFO] Target genome list was writen to OceanDNA-b33605/target_genomes.txt
[2023-03-15 14:06:17,172] [INFO] Task started: fastANI
[2023-03-15 14:06:17,172] [INFO] Running command: fastANI --query /var/lib/cwl/stgd72698af-dc10-4a53-ab9b-49317323aa82/OceanDNA-b33605.fa --refList OceanDNA-b33605/target_genomes.txt --output OceanDNA-b33605/fastani_result.tsv --threads 1
[2023-03-15 14:06:23,117] [INFO] Task succeeded: fastANI
[2023-03-15 14:06:23,117] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7da2edda-4c8a-4883-a477-f0fe9b6f27f6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 14:06:23,117] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7da2edda-4c8a-4883-a477-f0fe9b6f27f6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 14:06:23,118] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 14:06:23,118] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 14:06:23,118] [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 14:06:23,119] [INFO] DFAST Taxonomy check result was written to OceanDNA-b33605/tc_result.tsv
[2023-03-15 14:06:23,119] [INFO] ===== Taxonomy check completed =====
[2023-03-15 14:06:23,119] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 14:06:23,119] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7da2edda-4c8a-4883-a477-f0fe9b6f27f6/dqc_reference/checkm_data
[2023-03-15 14:06:23,121] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 14:06:23,126] [INFO] Task started: CheckM
[2023-03-15 14:06:23,126] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b33605/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b33605/checkm_input OceanDNA-b33605/checkm_result
[2023-03-15 14:06:39,853] [INFO] Task succeeded: CheckM
[2023-03-15 14:06:39,854] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 55.09%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 14:06:39,856] [INFO] ===== Completeness check finished =====
[2023-03-15 14:06:39,856] [INFO] ===== Start GTDB Search =====
[2023-03-15 14:06:39,856] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b33605/markers.fasta)
[2023-03-15 14:06:39,857] [INFO] Task started: Blastn
[2023-03-15 14:06:39,857] [INFO] Running command: blastn -query OceanDNA-b33605/markers.fasta -db /var/lib/cwl/stg7da2edda-4c8a-4883-a477-f0fe9b6f27f6/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b33605/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 14:06:40,502] [INFO] Task succeeded: Blastn
[2023-03-15 14:06:40,503] [INFO] Selected 24 target genomes.
[2023-03-15 14:06:40,504] [INFO] Target genome list was writen to OceanDNA-b33605/target_genomes_gtdb.txt
[2023-03-15 14:06:40,528] [INFO] Task started: fastANI
[2023-03-15 14:06:40,528] [INFO] Running command: fastANI --query /var/lib/cwl/stgd72698af-dc10-4a53-ab9b-49317323aa82/OceanDNA-b33605.fa --refList OceanDNA-b33605/target_genomes_gtdb.txt --output OceanDNA-b33605/fastani_result_gtdb.tsv --threads 1
[2023-03-15 14:06:50,649] [INFO] Task succeeded: fastANI
[2023-03-15 14:06:50,651] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 14:06:50,651] [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_002171155.1	s__UBA7377 sp002171155	99.8593	204	251	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae_A;g__UBA7377	95.0	N/A	N/A	N/A	N/A	1	conclusive
--------------------------------------------------------------------------------
[2023-03-15 14:06:50,652] [INFO] GTDB search result was written to OceanDNA-b33605/result_gtdb.tsv
[2023-03-15 14:06:50,652] [INFO] ===== GTDB Search completed =====
[2023-03-15 14:06:50,652] [INFO] DFAST_QC result json was written to OceanDNA-b33605/dqc_result.json
[2023-03-15 14:06:50,652] [INFO] DFAST_QC completed!
[2023-03-15 14:06:50,653] [INFO] Total running time: 0h0m39s