[2023-03-15 17:09:05,939] [INFO] DFAST_QC pipeline started.
[2023-03-15 17:09:05,940] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 17:09:05,940] [INFO] DQC Reference Directory: /var/lib/cwl/stg49b78825-04ab-405d-a22c-26c098b97943/dqc_reference
[2023-03-15 17:09:07,761] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 17:09:07,761] [INFO] Task started: Prodigal
[2023-03-15 17:09:07,762] [INFO] Running command: cat /var/lib/cwl/stg7b872ddb-b600-4170-918a-c5a477d596ae/OceanDNA-b45320.fa | prodigal -d OceanDNA-b45320/cds.fna -a OceanDNA-b45320/protein.faa -g 11 -q > /dev/null
[2023-03-15 17:09:13,188] [INFO] Task succeeded: Prodigal
[2023-03-15 17:09:13,188] [INFO] Task started: HMMsearch
[2023-03-15 17:09:13,188] [INFO] Running command: hmmsearch --tblout OceanDNA-b45320/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg49b78825-04ab-405d-a22c-26c098b97943/dqc_reference/reference_markers.hmm OceanDNA-b45320/protein.faa > /dev/null
[2023-03-15 17:09:13,431] [INFO] Task succeeded: HMMsearch
[2023-03-15 17:09:13,431] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg7b872ddb-b600-4170-918a-c5a477d596ae/OceanDNA-b45320.fa]
[2023-03-15 17:09:13,440] [INFO] Query marker FASTA was written to OceanDNA-b45320/markers.fasta
[2023-03-15 17:09:13,441] [INFO] Task started: Blastn
[2023-03-15 17:09:13,442] [INFO] Running command: blastn -query OceanDNA-b45320/markers.fasta -db /var/lib/cwl/stg49b78825-04ab-405d-a22c-26c098b97943/dqc_reference/reference_markers.fasta -out OceanDNA-b45320/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:09:14,271] [INFO] Task succeeded: Blastn
[2023-03-15 17:09:14,273] [INFO] Selected 10 target genomes.
[2023-03-15 17:09:14,273] [INFO] Target genome list was writen to OceanDNA-b45320/target_genomes.txt
[2023-03-15 17:09:14,282] [INFO] Task started: fastANI
[2023-03-15 17:09:14,282] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b872ddb-b600-4170-918a-c5a477d596ae/OceanDNA-b45320.fa --refList OceanDNA-b45320/target_genomes.txt --output OceanDNA-b45320/fastani_result.tsv --threads 1
[2023-03-15 17:09:19,279] [INFO] Task succeeded: fastANI
[2023-03-15 17:09:19,279] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg49b78825-04ab-405d-a22c-26c098b97943/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 17:09:19,279] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg49b78825-04ab-405d-a22c-26c098b97943/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 17:09:19,279] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 17:09:19,279] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 17:09:19,279] [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 17:09:19,280] [INFO] DFAST Taxonomy check result was written to OceanDNA-b45320/tc_result.tsv
[2023-03-15 17:09:19,281] [INFO] ===== Taxonomy check completed =====
[2023-03-15 17:09:19,281] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 17:09:19,282] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg49b78825-04ab-405d-a22c-26c098b97943/dqc_reference/checkm_data
[2023-03-15 17:09:19,336] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 17:09:19,371] [INFO] Task started: CheckM
[2023-03-15 17:09:19,371] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b45320/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b45320/checkm_input OceanDNA-b45320/checkm_result
[2023-03-15 17:09:41,886] [INFO] Task succeeded: CheckM
[2023-03-15 17:09:41,887] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 17:09:41,898] [INFO] ===== Completeness check finished =====
[2023-03-15 17:09:41,898] [INFO] ===== Start GTDB Search =====
[2023-03-15 17:09:41,898] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b45320/markers.fasta)
[2023-03-15 17:09:41,900] [INFO] Task started: Blastn
[2023-03-15 17:09:41,900] [INFO] Running command: blastn -query OceanDNA-b45320/markers.fasta -db /var/lib/cwl/stg49b78825-04ab-405d-a22c-26c098b97943/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b45320/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:09:42,831] [INFO] Task succeeded: Blastn
[2023-03-15 17:09:42,833] [INFO] Selected 17 target genomes.
[2023-03-15 17:09:42,833] [INFO] Target genome list was writen to OceanDNA-b45320/target_genomes_gtdb.txt
[2023-03-15 17:09:42,897] [INFO] Task started: fastANI
[2023-03-15 17:09:42,897] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b872ddb-b600-4170-918a-c5a477d596ae/OceanDNA-b45320.fa --refList OceanDNA-b45320/target_genomes_gtdb.txt --output OceanDNA-b45320/fastani_result_gtdb.tsv --threads 1
[2023-03-15 17:09:48,417] [INFO] Task succeeded: fastANI
[2023-03-15 17:09:48,419] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 17:09:48,419] [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_002712105.1	s__GCA-2712105 sp002712105	81.1179	233	361	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__Kiritimatiellales;f__Pontiellaceae;g__GCA-2712105	95.0	97.04	97.04	0.84	0.84	2	-
--------------------------------------------------------------------------------
[2023-03-15 17:09:48,420] [INFO] GTDB search result was written to OceanDNA-b45320/result_gtdb.tsv
[2023-03-15 17:09:48,420] [INFO] ===== GTDB Search completed =====
[2023-03-15 17:09:48,422] [INFO] DFAST_QC result json was written to OceanDNA-b45320/dqc_result.json
[2023-03-15 17:09:48,422] [INFO] DFAST_QC completed!
[2023-03-15 17:09:48,422] [INFO] Total running time: 0h0m42s