[2023-03-16 10:46:24,055] [INFO] DFAST_QC pipeline started.
[2023-03-16 10:46:24,055] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 10:46:24,055] [INFO] DQC Reference Directory: /var/lib/cwl/stg97c3a555-5b38-49c5-8ac1-57188c85c028/dqc_reference
[2023-03-16 10:46:25,192] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 10:46:25,193] [INFO] Task started: Prodigal
[2023-03-16 10:46:25,193] [INFO] Running command: cat /var/lib/cwl/stg47ef0785-b226-40f4-a9e1-a17760a64dba/OceanDNA-b45645.fa | prodigal -d OceanDNA-b45645/cds.fna -a OceanDNA-b45645/protein.faa -g 11 -q > /dev/null
[2023-03-16 10:46:33,675] [INFO] Task succeeded: Prodigal
[2023-03-16 10:46:33,675] [INFO] Task started: HMMsearch
[2023-03-16 10:46:33,675] [INFO] Running command: hmmsearch --tblout OceanDNA-b45645/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg97c3a555-5b38-49c5-8ac1-57188c85c028/dqc_reference/reference_markers.hmm OceanDNA-b45645/protein.faa > /dev/null
[2023-03-16 10:46:33,817] [INFO] Task succeeded: HMMsearch
[2023-03-16 10:46:33,818] [INFO] Found 6/6 markers.
[2023-03-16 10:46:33,832] [INFO] Query marker FASTA was written to OceanDNA-b45645/markers.fasta
[2023-03-16 10:46:33,833] [INFO] Task started: Blastn
[2023-03-16 10:46:33,833] [INFO] Running command: blastn -query OceanDNA-b45645/markers.fasta -db /var/lib/cwl/stg97c3a555-5b38-49c5-8ac1-57188c85c028/dqc_reference/reference_markers.fasta -out OceanDNA-b45645/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:46:34,333] [INFO] Task succeeded: Blastn
[2023-03-16 10:46:34,334] [INFO] Selected 12 target genomes.
[2023-03-16 10:46:34,334] [INFO] Target genome list was writen to OceanDNA-b45645/target_genomes.txt
[2023-03-16 10:46:34,384] [INFO] Task started: fastANI
[2023-03-16 10:46:34,384] [INFO] Running command: fastANI --query /var/lib/cwl/stg47ef0785-b226-40f4-a9e1-a17760a64dba/OceanDNA-b45645.fa --refList OceanDNA-b45645/target_genomes.txt --output OceanDNA-b45645/fastani_result.tsv --threads 1
[2023-03-16 10:46:41,452] [INFO] Task succeeded: fastANI
[2023-03-16 10:46:41,453] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg97c3a555-5b38-49c5-8ac1-57188c85c028/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 10:46:41,453] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg97c3a555-5b38-49c5-8ac1-57188c85c028/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 10:46:41,453] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 10:46:41,453] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 10:46:41,453] [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
--------------------------------------------------------------------------------
[2023-03-16 10:46:41,453] [INFO] DFAST Taxonomy check result was written to OceanDNA-b45645/tc_result.tsv
[2023-03-16 10:46:41,453] [INFO] ===== Taxonomy check completed =====
[2023-03-16 10:46:41,454] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 10:46:41,454] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg97c3a555-5b38-49c5-8ac1-57188c85c028/dqc_reference/checkm_data
[2023-03-16 10:46:41,456] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 10:46:41,562] [INFO] Task started: CheckM
[2023-03-16 10:46:41,562] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b45645/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b45645/checkm_input OceanDNA-b45645/checkm_result
[2023-03-16 10:47:22,410] [INFO] Task succeeded: CheckM
[2023-03-16 10:47:22,410] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.04%
Contamintation: 1.04%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-16 10:47:22,412] [INFO] ===== Completeness check finished =====
[2023-03-16 10:47:22,412] [INFO] ===== Start GTDB Search =====
[2023-03-16 10:47:22,413] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b45645/markers.fasta)
[2023-03-16 10:47:22,413] [INFO] Task started: Blastn
[2023-03-16 10:47:22,414] [INFO] Running command: blastn -query OceanDNA-b45645/markers.fasta -db /var/lib/cwl/stg97c3a555-5b38-49c5-8ac1-57188c85c028/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b45645/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:47:23,167] [INFO] Task succeeded: Blastn
[2023-03-16 10:47:23,168] [INFO] Selected 22 target genomes.
[2023-03-16 10:47:23,168] [INFO] Target genome list was writen to OceanDNA-b45645/target_genomes_gtdb.txt
[2023-03-16 10:47:23,186] [INFO] Task started: fastANI
[2023-03-16 10:47:23,187] [INFO] Running command: fastANI --query /var/lib/cwl/stg47ef0785-b226-40f4-a9e1-a17760a64dba/OceanDNA-b45645.fa --refList OceanDNA-b45645/target_genomes_gtdb.txt --output OceanDNA-b45645/fastani_result_gtdb.tsv --threads 1
[2023-03-16 10:47:36,189] [INFO] Task succeeded: fastANI
[2023-03-16 10:47:36,191] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 10:47:36,191] [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_002726435.1	s__MB11C04 sp002726435	93.3997	78	138	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__MB11C04	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 10:47:36,192] [INFO] GTDB search result was written to OceanDNA-b45645/result_gtdb.tsv
[2023-03-16 10:47:36,192] [INFO] ===== GTDB Search completed =====
[2023-03-16 10:47:36,193] [INFO] DFAST_QC result json was written to OceanDNA-b45645/dqc_result.json
[2023-03-16 10:47:36,193] [INFO] DFAST_QC completed!
[2023-03-16 10:47:36,193] [INFO] Total running time: 0h1m12s