[2023-03-15 14:40:36,524] [INFO] DFAST_QC pipeline started.
[2023-03-15 14:40:36,534] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 14:40:36,534] [INFO] DQC Reference Directory: /var/lib/cwl/stg4587cdd1-b5f8-4731-aea4-47fec9356e6f/dqc_reference
[2023-03-15 14:40:37,641] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 14:40:37,641] [INFO] Task started: Prodigal
[2023-03-15 14:40:37,641] [INFO] Running command: cat /var/lib/cwl/stgcbbf58fd-3381-45e7-b6c6-8cab316143f8/OceanDNA-b213.fa | prodigal -d OceanDNA-b213/cds.fna -a OceanDNA-b213/protein.faa -g 11 -q > /dev/null
[2023-03-15 14:40:48,080] [INFO] Task succeeded: Prodigal
[2023-03-15 14:40:48,080] [INFO] Task started: HMMsearch
[2023-03-15 14:40:48,080] [INFO] Running command: hmmsearch --tblout OceanDNA-b213/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4587cdd1-b5f8-4731-aea4-47fec9356e6f/dqc_reference/reference_markers.hmm OceanDNA-b213/protein.faa > /dev/null
[2023-03-15 14:40:48,248] [INFO] Task succeeded: HMMsearch
[2023-03-15 14:40:48,249] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgcbbf58fd-3381-45e7-b6c6-8cab316143f8/OceanDNA-b213.fa]
[2023-03-15 14:40:48,272] [INFO] Query marker FASTA was written to OceanDNA-b213/markers.fasta
[2023-03-15 14:40:48,273] [INFO] Task started: Blastn
[2023-03-15 14:40:48,273] [INFO] Running command: blastn -query OceanDNA-b213/markers.fasta -db /var/lib/cwl/stg4587cdd1-b5f8-4731-aea4-47fec9356e6f/dqc_reference/reference_markers.fasta -out OceanDNA-b213/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 14:40:48,799] [INFO] Task succeeded: Blastn
[2023-03-15 14:40:48,804] [INFO] Selected 14 target genomes.
[2023-03-15 14:40:48,804] [INFO] Target genome list was writen to OceanDNA-b213/target_genomes.txt
[2023-03-15 14:40:48,812] [INFO] Task started: fastANI
[2023-03-15 14:40:48,812] [INFO] Running command: fastANI --query /var/lib/cwl/stgcbbf58fd-3381-45e7-b6c6-8cab316143f8/OceanDNA-b213.fa --refList OceanDNA-b213/target_genomes.txt --output OceanDNA-b213/fastani_result.tsv --threads 1
[2023-03-15 14:40:59,289] [INFO] Task succeeded: fastANI
[2023-03-15 14:40:59,289] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4587cdd1-b5f8-4731-aea4-47fec9356e6f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 14:40:59,290] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4587cdd1-b5f8-4731-aea4-47fec9356e6f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 14:40:59,290] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 14:40:59,290] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 14:40:59,290] [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 14:40:59,296] [INFO] DFAST Taxonomy check result was written to OceanDNA-b213/tc_result.tsv
[2023-03-15 14:40:59,311] [INFO] ===== Taxonomy check completed =====
[2023-03-15 14:40:59,311] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 14:40:59,311] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4587cdd1-b5f8-4731-aea4-47fec9356e6f/dqc_reference/checkm_data
[2023-03-15 14:40:59,314] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 14:40:59,330] [INFO] Task started: CheckM
[2023-03-15 14:40:59,330] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b213/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b213/checkm_input OceanDNA-b213/checkm_result
[2023-03-15 14:41:29,504] [INFO] Task succeeded: CheckM
[2023-03-15 14:41:29,504] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.15%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 14:41:29,548] [INFO] ===== Completeness check finished =====
[2023-03-15 14:41:29,548] [INFO] ===== Start GTDB Search =====
[2023-03-15 14:41:29,549] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b213/markers.fasta)
[2023-03-15 14:41:29,550] [INFO] Task started: Blastn
[2023-03-15 14:41:29,550] [INFO] Running command: blastn -query OceanDNA-b213/markers.fasta -db /var/lib/cwl/stg4587cdd1-b5f8-4731-aea4-47fec9356e6f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b213/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 14:41:30,342] [INFO] Task succeeded: Blastn
[2023-03-15 14:41:30,345] [INFO] Selected 24 target genomes.
[2023-03-15 14:41:30,345] [INFO] Target genome list was writen to OceanDNA-b213/target_genomes_gtdb.txt
[2023-03-15 14:41:30,363] [INFO] Task started: fastANI
[2023-03-15 14:41:30,363] [INFO] Running command: fastANI --query /var/lib/cwl/stgcbbf58fd-3381-45e7-b6c6-8cab316143f8/OceanDNA-b213.fa --refList OceanDNA-b213/target_genomes_gtdb.txt --output OceanDNA-b213/fastani_result_gtdb.tsv --threads 1
[2023-03-15 14:41:42,969] [INFO] Task succeeded: fastANI
[2023-03-15 14:41:42,970] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 14:41:42,970] [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 14:41:42,978] [INFO] GTDB search result was written to OceanDNA-b213/result_gtdb.tsv
[2023-03-15 14:41:42,981] [INFO] ===== GTDB Search completed =====
[2023-03-15 14:41:42,981] [INFO] DFAST_QC result json was written to OceanDNA-b213/dqc_result.json
[2023-03-15 14:41:42,981] [INFO] DFAST_QC completed!
[2023-03-15 14:41:42,981] [INFO] Total running time: 0h1m6s