[2023-03-17 23:08:31,960] [INFO] DFAST_QC pipeline started.
[2023-03-17 23:08:31,961] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 23:08:31,962] [INFO] DQC Reference Directory: /var/lib/cwl/stg2e8f35b7-ee3d-41e2-87c4-a1464d16e144/dqc_reference
[2023-03-17 23:08:33,187] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 23:08:33,187] [INFO] Task started: Prodigal
[2023-03-17 23:08:33,187] [INFO] Running command: cat /var/lib/cwl/stg19c659c9-b899-4081-a108-ffbaa000d1b0/OceanDNA-b3609.fa | prodigal -d OceanDNA-b3609/cds.fna -a OceanDNA-b3609/protein.faa -g 11 -q > /dev/null
[2023-03-17 23:08:53,651] [INFO] Task succeeded: Prodigal
[2023-03-17 23:08:53,652] [INFO] Task started: HMMsearch
[2023-03-17 23:08:53,652] [INFO] Running command: hmmsearch --tblout OceanDNA-b3609/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2e8f35b7-ee3d-41e2-87c4-a1464d16e144/dqc_reference/reference_markers.hmm OceanDNA-b3609/protein.faa > /dev/null
[2023-03-17 23:08:53,867] [INFO] Task succeeded: HMMsearch
[2023-03-17 23:08:53,867] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg19c659c9-b899-4081-a108-ffbaa000d1b0/OceanDNA-b3609.fa]
[2023-03-17 23:08:53,899] [INFO] Query marker FASTA was written to OceanDNA-b3609/markers.fasta
[2023-03-17 23:08:53,900] [INFO] Task started: Blastn
[2023-03-17 23:08:53,900] [INFO] Running command: blastn -query OceanDNA-b3609/markers.fasta -db /var/lib/cwl/stg2e8f35b7-ee3d-41e2-87c4-a1464d16e144/dqc_reference/reference_markers.fasta -out OceanDNA-b3609/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:08:54,396] [INFO] Task succeeded: Blastn
[2023-03-17 23:08:54,398] [INFO] Selected 12 target genomes.
[2023-03-17 23:08:54,398] [INFO] Target genome list was writen to OceanDNA-b3609/target_genomes.txt
[2023-03-17 23:08:54,406] [INFO] Task started: fastANI
[2023-03-17 23:08:54,406] [INFO] Running command: fastANI --query /var/lib/cwl/stg19c659c9-b899-4081-a108-ffbaa000d1b0/OceanDNA-b3609.fa --refList OceanDNA-b3609/target_genomes.txt --output OceanDNA-b3609/fastani_result.tsv --threads 1
[2023-03-17 23:09:02,844] [INFO] Task succeeded: fastANI
[2023-03-17 23:09:02,845] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2e8f35b7-ee3d-41e2-87c4-a1464d16e144/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 23:09:02,845] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2e8f35b7-ee3d-41e2-87c4-a1464d16e144/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 23:09:02,846] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 23:09:02,846] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 23:09:02,846] [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
--------------------------------------------------------------------------------
[2023-03-17 23:09:02,848] [INFO] DFAST Taxonomy check result was written to OceanDNA-b3609/tc_result.tsv
[2023-03-17 23:09:02,849] [INFO] ===== Taxonomy check completed =====
[2023-03-17 23:09:02,849] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 23:09:02,849] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2e8f35b7-ee3d-41e2-87c4-a1464d16e144/dqc_reference/checkm_data
[2023-03-17 23:09:02,853] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 23:09:02,942] [INFO] Task started: CheckM
[2023-03-17 23:09:02,942] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b3609/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b3609/checkm_input OceanDNA-b3609/checkm_result
[2023-03-17 23:09:55,850] [INFO] Task succeeded: CheckM
[2023-03-17 23:09:55,851] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 73.86%
Contamintation: 4.55%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-17 23:09:55,889] [INFO] ===== Completeness check finished =====
[2023-03-17 23:09:55,890] [INFO] ===== Start GTDB Search =====
[2023-03-17 23:09:55,890] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b3609/markers.fasta)
[2023-03-17 23:09:55,891] [INFO] Task started: Blastn
[2023-03-17 23:09:55,891] [INFO] Running command: blastn -query OceanDNA-b3609/markers.fasta -db /var/lib/cwl/stg2e8f35b7-ee3d-41e2-87c4-a1464d16e144/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b3609/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:09:56,552] [INFO] Task succeeded: Blastn
[2023-03-17 23:09:56,555] [INFO] Selected 12 target genomes.
[2023-03-17 23:09:56,555] [INFO] Target genome list was writen to OceanDNA-b3609/target_genomes_gtdb.txt
[2023-03-17 23:09:56,562] [INFO] Task started: fastANI
[2023-03-17 23:09:56,562] [INFO] Running command: fastANI --query /var/lib/cwl/stg19c659c9-b899-4081-a108-ffbaa000d1b0/OceanDNA-b3609.fa --refList OceanDNA-b3609/target_genomes_gtdb.txt --output OceanDNA-b3609/fastani_result_gtdb.tsv --threads 1
[2023-03-17 23:10:03,946] [INFO] Task succeeded: fastANI
[2023-03-17 23:10:03,947] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 23:10:03,947] [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
--------------------------------------------------------------------------------
[2023-03-17 23:10:03,949] [INFO] GTDB search result was written to OceanDNA-b3609/result_gtdb.tsv
[2023-03-17 23:10:03,951] [INFO] ===== GTDB Search completed =====
[2023-03-17 23:10:03,954] [INFO] DFAST_QC result json was written to OceanDNA-b3609/dqc_result.json
[2023-03-17 23:10:03,954] [INFO] DFAST_QC completed!
[2023-03-17 23:10:03,954] [INFO] Total running time: 0h1m32s