[2023-03-15 21:48:06,743] [INFO] DFAST_QC pipeline started.
[2023-03-15 21:48:06,743] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 21:48:06,743] [INFO] DQC Reference Directory: /var/lib/cwl/stg77e1543a-7f8c-4c10-90ea-5ea5d56504d4/dqc_reference
[2023-03-15 21:48:07,859] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 21:48:07,859] [INFO] Task started: Prodigal
[2023-03-15 21:48:07,859] [INFO] Running command: cat /var/lib/cwl/stg716acb64-57f7-46ba-9ed9-2477dc29ff60/OceanDNA-b661.fa | prodigal -d OceanDNA-b661/cds.fna -a OceanDNA-b661/protein.faa -g 11 -q > /dev/null
[2023-03-15 21:48:13,717] [INFO] Task succeeded: Prodigal
[2023-03-15 21:48:13,718] [INFO] Task started: HMMsearch
[2023-03-15 21:48:13,718] [INFO] Running command: hmmsearch --tblout OceanDNA-b661/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg77e1543a-7f8c-4c10-90ea-5ea5d56504d4/dqc_reference/reference_markers.hmm OceanDNA-b661/protein.faa > /dev/null
[2023-03-15 21:48:13,852] [INFO] Task succeeded: HMMsearch
[2023-03-15 21:48:13,852] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg716acb64-57f7-46ba-9ed9-2477dc29ff60/OceanDNA-b661.fa]
[2023-03-15 21:48:13,862] [INFO] Query marker FASTA was written to OceanDNA-b661/markers.fasta
[2023-03-15 21:48:13,863] [INFO] Task started: Blastn
[2023-03-15 21:48:13,864] [INFO] Running command: blastn -query OceanDNA-b661/markers.fasta -db /var/lib/cwl/stg77e1543a-7f8c-4c10-90ea-5ea5d56504d4/dqc_reference/reference_markers.fasta -out OceanDNA-b661/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:48:14,292] [INFO] Task succeeded: Blastn
[2023-03-15 21:48:14,293] [INFO] Selected 7 target genomes.
[2023-03-15 21:48:14,293] [INFO] Target genome list was writen to OceanDNA-b661/target_genomes.txt
[2023-03-15 21:48:14,297] [INFO] Task started: fastANI
[2023-03-15 21:48:14,297] [INFO] Running command: fastANI --query /var/lib/cwl/stg716acb64-57f7-46ba-9ed9-2477dc29ff60/OceanDNA-b661.fa --refList OceanDNA-b661/target_genomes.txt --output OceanDNA-b661/fastani_result.tsv --threads 1
[2023-03-15 21:48:17,870] [INFO] Task succeeded: fastANI
[2023-03-15 21:48:17,870] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg77e1543a-7f8c-4c10-90ea-5ea5d56504d4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 21:48:17,871] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg77e1543a-7f8c-4c10-90ea-5ea5d56504d4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 21:48:17,871] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 21:48:17,871] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 21:48:17,871] [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 21:48:17,871] [INFO] DFAST Taxonomy check result was written to OceanDNA-b661/tc_result.tsv
[2023-03-15 21:48:17,871] [INFO] ===== Taxonomy check completed =====
[2023-03-15 21:48:17,871] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 21:48:17,872] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg77e1543a-7f8c-4c10-90ea-5ea5d56504d4/dqc_reference/checkm_data
[2023-03-15 21:48:17,875] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 21:48:18,084] [INFO] Task started: CheckM
[2023-03-15 21:48:18,084] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b661/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b661/checkm_input OceanDNA-b661/checkm_result
[2023-03-15 21:48:38,387] [INFO] Task succeeded: CheckM
[2023-03-15 21:48:38,387] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.52%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 21:48:38,391] [INFO] ===== Completeness check finished =====
[2023-03-15 21:48:38,391] [INFO] ===== Start GTDB Search =====
[2023-03-15 21:48:38,391] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b661/markers.fasta)
[2023-03-15 21:48:38,392] [INFO] Task started: Blastn
[2023-03-15 21:48:38,393] [INFO] Running command: blastn -query OceanDNA-b661/markers.fasta -db /var/lib/cwl/stg77e1543a-7f8c-4c10-90ea-5ea5d56504d4/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b661/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:48:38,824] [INFO] Task succeeded: Blastn
[2023-03-15 21:48:38,825] [INFO] Selected 13 target genomes.
[2023-03-15 21:48:38,825] [INFO] Target genome list was writen to OceanDNA-b661/target_genomes_gtdb.txt
[2023-03-15 21:48:38,961] [INFO] Task started: fastANI
[2023-03-15 21:48:38,961] [INFO] Running command: fastANI --query /var/lib/cwl/stg716acb64-57f7-46ba-9ed9-2477dc29ff60/OceanDNA-b661.fa --refList OceanDNA-b661/target_genomes_gtdb.txt --output OceanDNA-b661/fastani_result_gtdb.tsv --threads 1
[2023-03-15 21:48:43,450] [INFO] Task succeeded: fastANI
[2023-03-15 21:48:43,450] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 21:48:43,450] [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 21:48:43,452] [INFO] GTDB search result was written to OceanDNA-b661/result_gtdb.tsv
[2023-03-15 21:48:43,454] [INFO] ===== GTDB Search completed =====
[2023-03-15 21:48:43,455] [INFO] DFAST_QC result json was written to OceanDNA-b661/dqc_result.json
[2023-03-15 21:48:43,456] [INFO] DFAST_QC completed!
[2023-03-15 21:48:43,456] [INFO] Total running time: 0h0m37s