[2023-03-15 11:22:20,467] [INFO] DFAST_QC pipeline started.
[2023-03-15 11:22:20,467] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 11:22:20,467] [INFO] DQC Reference Directory: /var/lib/cwl/stg6af17729-10a6-401e-be59-adba96daed33/dqc_reference
[2023-03-15 11:22:21,951] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 11:22:21,951] [INFO] Task started: Prodigal
[2023-03-15 11:22:21,952] [INFO] Running command: cat /var/lib/cwl/stg5a784ee8-ef45-49f0-9aef-b1280d0aa9d4/OceanDNA-b13598.fa | prodigal -d OceanDNA-b13598/cds.fna -a OceanDNA-b13598/protein.faa -g 11 -q > /dev/null
[2023-03-15 11:22:26,416] [INFO] Task succeeded: Prodigal
[2023-03-15 11:22:26,417] [INFO] Task started: HMMsearch
[2023-03-15 11:22:26,417] [INFO] Running command: hmmsearch --tblout OceanDNA-b13598/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6af17729-10a6-401e-be59-adba96daed33/dqc_reference/reference_markers.hmm OceanDNA-b13598/protein.faa > /dev/null
[2023-03-15 11:22:26,602] [INFO] Task succeeded: HMMsearch
[2023-03-15 11:22:26,602] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg5a784ee8-ef45-49f0-9aef-b1280d0aa9d4/OceanDNA-b13598.fa]
[2023-03-15 11:22:26,612] [INFO] Query marker FASTA was written to OceanDNA-b13598/markers.fasta
[2023-03-15 11:22:26,614] [INFO] Task started: Blastn
[2023-03-15 11:22:26,614] [INFO] Running command: blastn -query OceanDNA-b13598/markers.fasta -db /var/lib/cwl/stg6af17729-10a6-401e-be59-adba96daed33/dqc_reference/reference_markers.fasta -out OceanDNA-b13598/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:22:29,529] [INFO] Task succeeded: Blastn
[2023-03-15 11:22:29,529] [INFO] Selected 11 target genomes.
[2023-03-15 11:22:29,530] [INFO] Target genome list was writen to OceanDNA-b13598/target_genomes.txt
[2023-03-15 11:22:29,538] [INFO] Task started: fastANI
[2023-03-15 11:22:29,538] [INFO] Running command: fastANI --query /var/lib/cwl/stg5a784ee8-ef45-49f0-9aef-b1280d0aa9d4/OceanDNA-b13598.fa --refList OceanDNA-b13598/target_genomes.txt --output OceanDNA-b13598/fastani_result.tsv --threads 1
[2023-03-15 11:22:35,424] [INFO] Task succeeded: fastANI
[2023-03-15 11:22:35,424] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6af17729-10a6-401e-be59-adba96daed33/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 11:22:35,424] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6af17729-10a6-401e-be59-adba96daed33/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 11:22:35,424] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 11:22:35,424] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 11:22:35,425] [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 11:22:35,425] [INFO] DFAST Taxonomy check result was written to OceanDNA-b13598/tc_result.tsv
[2023-03-15 11:22:35,425] [INFO] ===== Taxonomy check completed =====
[2023-03-15 11:22:35,425] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 11:22:35,425] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6af17729-10a6-401e-be59-adba96daed33/dqc_reference/checkm_data
[2023-03-15 11:22:35,428] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 11:22:35,502] [INFO] Task started: CheckM
[2023-03-15 11:22:35,502] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b13598/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b13598/checkm_input OceanDNA-b13598/checkm_result
[2023-03-15 11:22:53,503] [INFO] Task succeeded: CheckM
[2023-03-15 11:22:53,504] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.84%
Contamintation: 1.42%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-15 11:22:53,505] [INFO] ===== Completeness check finished =====
[2023-03-15 11:22:53,506] [INFO] ===== Start GTDB Search =====
[2023-03-15 11:22:53,506] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b13598/markers.fasta)
[2023-03-15 11:22:53,507] [INFO] Task started: Blastn
[2023-03-15 11:22:53,508] [INFO] Running command: blastn -query OceanDNA-b13598/markers.fasta -db /var/lib/cwl/stg6af17729-10a6-401e-be59-adba96daed33/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b13598/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:22:54,200] [INFO] Task succeeded: Blastn
[2023-03-15 11:22:54,201] [INFO] Selected 15 target genomes.
[2023-03-15 11:22:54,201] [INFO] Target genome list was writen to OceanDNA-b13598/target_genomes_gtdb.txt
[2023-03-15 11:22:54,213] [INFO] Task started: fastANI
[2023-03-15 11:22:54,213] [INFO] Running command: fastANI --query /var/lib/cwl/stg5a784ee8-ef45-49f0-9aef-b1280d0aa9d4/OceanDNA-b13598.fa --refList OceanDNA-b13598/target_genomes_gtdb.txt --output OceanDNA-b13598/fastani_result_gtdb.tsv --threads 1
[2023-03-15 11:22:59,314] [INFO] Task succeeded: fastANI
[2023-03-15 11:22:59,316] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 11:22:59,316] [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_016199495.1	s__JACQGQ01 sp016199495	81.094	106	230	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__Dehalococcoidales;f__UBA2162;g__JACQGQ01	95.0	98.63	98.63	0.73	0.73	2	-
--------------------------------------------------------------------------------
[2023-03-15 11:22:59,488] [INFO] GTDB search result was written to OceanDNA-b13598/result_gtdb.tsv
[2023-03-15 11:22:59,488] [INFO] ===== GTDB Search completed =====
[2023-03-15 11:22:59,489] [INFO] DFAST_QC result json was written to OceanDNA-b13598/dqc_result.json
[2023-03-15 11:22:59,489] [INFO] DFAST_QC completed!
[2023-03-15 11:22:59,489] [INFO] Total running time: 0h0m39s