[2023-03-18 08:59:03,331] [INFO] DFAST_QC pipeline started.
[2023-03-18 08:59:03,331] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 08:59:03,331] [INFO] DQC Reference Directory: /var/lib/cwl/stg7e13bf26-25b3-4feb-b59d-83f54f204f29/dqc_reference
[2023-03-18 08:59:04,427] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 08:59:04,428] [INFO] Task started: Prodigal
[2023-03-18 08:59:04,428] [INFO] Running command: cat /var/lib/cwl/stg8777a97a-42c3-469d-84ba-23ffd34a73d8/OceanDNA-b54.fa | prodigal -d OceanDNA-b54/cds.fna -a OceanDNA-b54/protein.faa -g 11 -q > /dev/null
[2023-03-18 08:59:09,557] [INFO] Task succeeded: Prodigal
[2023-03-18 08:59:09,558] [INFO] Task started: HMMsearch
[2023-03-18 08:59:09,558] [INFO] Running command: hmmsearch --tblout OceanDNA-b54/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7e13bf26-25b3-4feb-b59d-83f54f204f29/dqc_reference/reference_markers.hmm OceanDNA-b54/protein.faa > /dev/null
[2023-03-18 08:59:09,698] [INFO] Task succeeded: HMMsearch
[2023-03-18 08:59:09,699] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg8777a97a-42c3-469d-84ba-23ffd34a73d8/OceanDNA-b54.fa]
[2023-03-18 08:59:09,715] [INFO] Query marker FASTA was written to OceanDNA-b54/markers.fasta
[2023-03-18 08:59:09,716] [INFO] Task started: Blastn
[2023-03-18 08:59:09,716] [INFO] Running command: blastn -query OceanDNA-b54/markers.fasta -db /var/lib/cwl/stg7e13bf26-25b3-4feb-b59d-83f54f204f29/dqc_reference/reference_markers.fasta -out OceanDNA-b54/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:59:10,288] [INFO] Task succeeded: Blastn
[2023-03-18 08:59:10,294] [INFO] Selected 10 target genomes.
[2023-03-18 08:59:10,294] [INFO] Target genome list was writen to OceanDNA-b54/target_genomes.txt
[2023-03-18 08:59:10,304] [INFO] Task started: fastANI
[2023-03-18 08:59:10,304] [INFO] Running command: fastANI --query /var/lib/cwl/stg8777a97a-42c3-469d-84ba-23ffd34a73d8/OceanDNA-b54.fa --refList OceanDNA-b54/target_genomes.txt --output OceanDNA-b54/fastani_result.tsv --threads 1
[2023-03-18 08:59:16,103] [INFO] Task succeeded: fastANI
[2023-03-18 08:59:16,103] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7e13bf26-25b3-4feb-b59d-83f54f204f29/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 08:59:16,103] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7e13bf26-25b3-4feb-b59d-83f54f204f29/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 08:59:16,104] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 08:59:16,104] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 08:59:16,104] [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
--------------------------------------------------------------------------------
[2023-03-18 08:59:16,105] [INFO] DFAST Taxonomy check result was written to OceanDNA-b54/tc_result.tsv
[2023-03-18 08:59:16,106] [INFO] ===== Taxonomy check completed =====
[2023-03-18 08:59:16,106] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 08:59:16,106] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7e13bf26-25b3-4feb-b59d-83f54f204f29/dqc_reference/checkm_data
[2023-03-18 08:59:16,109] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 08:59:16,119] [INFO] Task started: CheckM
[2023-03-18 08:59:16,119] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b54/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b54/checkm_input OceanDNA-b54/checkm_result
[2023-03-18 08:59:34,743] [INFO] Task succeeded: CheckM
[2023-03-18 08:59:34,743] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 65.74%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 08:59:34,759] [INFO] ===== Completeness check finished =====
[2023-03-18 08:59:34,760] [INFO] ===== Start GTDB Search =====
[2023-03-18 08:59:34,760] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b54/markers.fasta)
[2023-03-18 08:59:34,761] [INFO] Task started: Blastn
[2023-03-18 08:59:34,761] [INFO] Running command: blastn -query OceanDNA-b54/markers.fasta -db /var/lib/cwl/stg7e13bf26-25b3-4feb-b59d-83f54f204f29/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b54/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:59:35,562] [INFO] Task succeeded: Blastn
[2023-03-18 08:59:35,566] [INFO] Selected 25 target genomes.
[2023-03-18 08:59:35,566] [INFO] Target genome list was writen to OceanDNA-b54/target_genomes_gtdb.txt
[2023-03-18 08:59:35,597] [INFO] Task started: fastANI
[2023-03-18 08:59:35,598] [INFO] Running command: fastANI --query /var/lib/cwl/stg8777a97a-42c3-469d-84ba-23ffd34a73d8/OceanDNA-b54.fa --refList OceanDNA-b54/target_genomes_gtdb.txt --output OceanDNA-b54/fastani_result_gtdb.tsv --threads 1
[2023-03-18 08:59:48,367] [INFO] Task succeeded: fastANI
[2023-03-18 08:59:48,367] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 08:59:48,368] [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
--------------------------------------------------------------------------------
[2023-03-18 08:59:48,369] [INFO] GTDB search result was written to OceanDNA-b54/result_gtdb.tsv
[2023-03-18 08:59:48,371] [INFO] ===== GTDB Search completed =====
[2023-03-18 08:59:48,373] [INFO] DFAST_QC result json was written to OceanDNA-b54/dqc_result.json
[2023-03-18 08:59:48,373] [INFO] DFAST_QC completed!
[2023-03-18 08:59:48,373] [INFO] Total running time: 0h0m45s