[2023-03-15 15:06:33,520] [INFO] DFAST_QC pipeline started.
[2023-03-15 15:06:33,538] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 15:06:33,538] [INFO] DQC Reference Directory: /var/lib/cwl/stg19bf23b1-c24f-4616-a42f-b9f42c52f741/dqc_reference
[2023-03-15 15:06:34,684] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 15:06:34,685] [INFO] Task started: Prodigal
[2023-03-15 15:06:34,685] [INFO] Running command: cat /var/lib/cwl/stg8e1c5189-556f-46aa-be01-10e1d461df9a/OceanDNA-b17035.fa | prodigal -d OceanDNA-b17035/cds.fna -a OceanDNA-b17035/protein.faa -g 11 -q > /dev/null
[2023-03-15 15:06:48,241] [INFO] Task succeeded: Prodigal
[2023-03-15 15:06:48,241] [INFO] Task started: HMMsearch
[2023-03-15 15:06:48,241] [INFO] Running command: hmmsearch --tblout OceanDNA-b17035/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg19bf23b1-c24f-4616-a42f-b9f42c52f741/dqc_reference/reference_markers.hmm OceanDNA-b17035/protein.faa > /dev/null
[2023-03-15 15:06:48,427] [INFO] Task succeeded: HMMsearch
[2023-03-15 15:06:48,427] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg8e1c5189-556f-46aa-be01-10e1d461df9a/OceanDNA-b17035.fa]
[2023-03-15 15:06:48,554] [INFO] Query marker FASTA was written to OceanDNA-b17035/markers.fasta
[2023-03-15 15:06:48,555] [INFO] Task started: Blastn
[2023-03-15 15:06:48,555] [INFO] Running command: blastn -query OceanDNA-b17035/markers.fasta -db /var/lib/cwl/stg19bf23b1-c24f-4616-a42f-b9f42c52f741/dqc_reference/reference_markers.fasta -out OceanDNA-b17035/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 15:06:49,162] [INFO] Task succeeded: Blastn
[2023-03-15 15:06:49,202] [INFO] Selected 24 target genomes.
[2023-03-15 15:06:49,202] [INFO] Target genome list was writen to OceanDNA-b17035/target_genomes.txt
[2023-03-15 15:06:49,217] [INFO] Task started: fastANI
[2023-03-15 15:06:49,218] [INFO] Running command: fastANI --query /var/lib/cwl/stg8e1c5189-556f-46aa-be01-10e1d461df9a/OceanDNA-b17035.fa --refList OceanDNA-b17035/target_genomes.txt --output OceanDNA-b17035/fastani_result.tsv --threads 1
[2023-03-15 15:07:04,229] [INFO] Task succeeded: fastANI
[2023-03-15 15:07:04,229] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg19bf23b1-c24f-4616-a42f-b9f42c52f741/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 15:07:04,229] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg19bf23b1-c24f-4616-a42f-b9f42c52f741/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 15:07:04,229] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 15:07:04,229] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 15:07:04,229] [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 15:07:04,240] [INFO] DFAST Taxonomy check result was written to OceanDNA-b17035/tc_result.tsv
[2023-03-15 15:07:04,263] [INFO] ===== Taxonomy check completed =====
[2023-03-15 15:07:04,263] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 15:07:04,263] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg19bf23b1-c24f-4616-a42f-b9f42c52f741/dqc_reference/checkm_data
[2023-03-15 15:07:04,266] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 15:07:04,273] [INFO] Task started: CheckM
[2023-03-15 15:07:04,273] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b17035/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b17035/checkm_input OceanDNA-b17035/checkm_result
[2023-03-15 15:07:41,428] [INFO] Task succeeded: CheckM
[2023-03-15 15:07:41,428] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.79%
Contamintation: 4.63%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-15 15:07:41,584] [INFO] ===== Completeness check finished =====
[2023-03-15 15:07:41,584] [INFO] ===== Start GTDB Search =====
[2023-03-15 15:07:41,584] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b17035/markers.fasta)
[2023-03-15 15:07:41,585] [INFO] Task started: Blastn
[2023-03-15 15:07:41,585] [INFO] Running command: blastn -query OceanDNA-b17035/markers.fasta -db /var/lib/cwl/stg19bf23b1-c24f-4616-a42f-b9f42c52f741/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b17035/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 15:07:42,605] [INFO] Task succeeded: Blastn
[2023-03-15 15:07:42,649] [INFO] Selected 24 target genomes.
[2023-03-15 15:07:42,650] [INFO] Target genome list was writen to OceanDNA-b17035/target_genomes_gtdb.txt
[2023-03-15 15:07:42,747] [INFO] Task started: fastANI
[2023-03-15 15:07:42,747] [INFO] Running command: fastANI --query /var/lib/cwl/stg8e1c5189-556f-46aa-be01-10e1d461df9a/OceanDNA-b17035.fa --refList OceanDNA-b17035/target_genomes_gtdb.txt --output OceanDNA-b17035/fastani_result_gtdb.tsv --threads 1
[2023-03-15 15:07:56,501] [INFO] Task succeeded: fastANI
[2023-03-15 15:07:56,502] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 15:07:56,502] [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
--------------------------------------------------------------------------------
[2023-03-15 15:07:56,519] [INFO] GTDB search result was written to OceanDNA-b17035/result_gtdb.tsv
[2023-03-15 15:07:56,549] [INFO] ===== GTDB Search completed =====
[2023-03-15 15:07:56,564] [INFO] DFAST_QC result json was written to OceanDNA-b17035/dqc_result.json
[2023-03-15 15:07:56,564] [INFO] DFAST_QC completed!
[2023-03-15 15:07:56,564] [INFO] Total running time: 0h1m23s