[2023-03-17 11:57:19,286] [INFO] DFAST_QC pipeline started.
[2023-03-17 11:57:19,286] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 11:57:19,286] [INFO] DQC Reference Directory: /var/lib/cwl/stg75a88b8f-4aab-401d-8da4-0fd2776aeb21/dqc_reference
[2023-03-17 11:57:20,888] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 11:57:20,888] [INFO] Task started: Prodigal
[2023-03-17 11:57:20,888] [INFO] Running command: cat /var/lib/cwl/stg3476f18a-5e48-423d-81e9-fe83cb9d5b5f/OceanDNA-b39211.fa | prodigal -d OceanDNA-b39211/cds.fna -a OceanDNA-b39211/protein.faa -g 11 -q > /dev/null
[2023-03-17 11:57:26,525] [INFO] Task succeeded: Prodigal
[2023-03-17 11:57:26,525] [INFO] Task started: HMMsearch
[2023-03-17 11:57:26,526] [INFO] Running command: hmmsearch --tblout OceanDNA-b39211/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg75a88b8f-4aab-401d-8da4-0fd2776aeb21/dqc_reference/reference_markers.hmm OceanDNA-b39211/protein.faa > /dev/null
[2023-03-17 11:57:26,786] [INFO] Task succeeded: HMMsearch
[2023-03-17 11:57:26,786] [INFO] Found 6/6 markers.
[2023-03-17 11:57:26,798] [INFO] Query marker FASTA was written to OceanDNA-b39211/markers.fasta
[2023-03-17 11:57:26,800] [INFO] Task started: Blastn
[2023-03-17 11:57:26,800] [INFO] Running command: blastn -query OceanDNA-b39211/markers.fasta -db /var/lib/cwl/stg75a88b8f-4aab-401d-8da4-0fd2776aeb21/dqc_reference/reference_markers.fasta -out OceanDNA-b39211/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:57:29,523] [INFO] Task succeeded: Blastn
[2023-03-17 11:57:29,524] [INFO] Selected 15 target genomes.
[2023-03-17 11:57:29,524] [INFO] Target genome list was writen to OceanDNA-b39211/target_genomes.txt
[2023-03-17 11:57:29,547] [INFO] Task started: fastANI
[2023-03-17 11:57:29,547] [INFO] Running command: fastANI --query /var/lib/cwl/stg3476f18a-5e48-423d-81e9-fe83cb9d5b5f/OceanDNA-b39211.fa --refList OceanDNA-b39211/target_genomes.txt --output OceanDNA-b39211/fastani_result.tsv --threads 1
[2023-03-17 11:57:35,594] [INFO] Task succeeded: fastANI
[2023-03-17 11:57:35,594] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg75a88b8f-4aab-401d-8da4-0fd2776aeb21/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 11:57:35,594] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg75a88b8f-4aab-401d-8da4-0fd2776aeb21/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 11:57:35,595] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 11:57:35,595] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 11:57:35,595] [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 11:57:35,595] [INFO] DFAST Taxonomy check result was written to OceanDNA-b39211/tc_result.tsv
[2023-03-17 11:57:35,595] [INFO] ===== Taxonomy check completed =====
[2023-03-17 11:57:35,595] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 11:57:35,595] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg75a88b8f-4aab-401d-8da4-0fd2776aeb21/dqc_reference/checkm_data
[2023-03-17 11:57:35,598] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 11:57:35,600] [INFO] Task started: CheckM
[2023-03-17 11:57:35,601] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b39211/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b39211/checkm_input OceanDNA-b39211/checkm_result
[2023-03-17 11:57:55,725] [INFO] Task succeeded: CheckM
[2023-03-17 11:57:55,725] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 82.64%
Contamintation: 5.15%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 11:57:55,727] [INFO] ===== Completeness check finished =====
[2023-03-17 11:57:55,727] [INFO] ===== Start GTDB Search =====
[2023-03-17 11:57:55,727] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b39211/markers.fasta)
[2023-03-17 11:57:55,727] [INFO] Task started: Blastn
[2023-03-17 11:57:55,727] [INFO] Running command: blastn -query OceanDNA-b39211/markers.fasta -db /var/lib/cwl/stg75a88b8f-4aab-401d-8da4-0fd2776aeb21/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b39211/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:57:56,511] [INFO] Task succeeded: Blastn
[2023-03-17 11:57:56,512] [INFO] Selected 28 target genomes.
[2023-03-17 11:57:56,512] [INFO] Target genome list was writen to OceanDNA-b39211/target_genomes_gtdb.txt
[2023-03-17 11:57:56,760] [INFO] Task started: fastANI
[2023-03-17 11:57:56,760] [INFO] Running command: fastANI --query /var/lib/cwl/stg3476f18a-5e48-423d-81e9-fe83cb9d5b5f/OceanDNA-b39211.fa --refList OceanDNA-b39211/target_genomes_gtdb.txt --output OceanDNA-b39211/fastani_result_gtdb.tsv --threads 1
[2023-03-17 11:58:08,137] [INFO] Task succeeded: fastANI
[2023-03-17 11:58:08,139] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 11:58:08,139] [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_902527245.1	s__AAA300-D14 sp002715065	97.6337	277	299	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__AAA300-D14	95.0	97.38	96.11	0.85	0.80	14	conclusive
--------------------------------------------------------------------------------
[2023-03-17 11:58:08,139] [INFO] GTDB search result was written to OceanDNA-b39211/result_gtdb.tsv
[2023-03-17 11:58:08,139] [INFO] ===== GTDB Search completed =====
[2023-03-17 11:58:08,139] [INFO] DFAST_QC result json was written to OceanDNA-b39211/dqc_result.json
[2023-03-17 11:58:08,139] [INFO] DFAST_QC completed!
[2023-03-17 11:58:08,140] [INFO] Total running time: 0h0m49s