[2023-03-18 21:15:29,380] [INFO] DFAST_QC pipeline started.
[2023-03-18 21:15:29,380] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 21:15:29,380] [INFO] DQC Reference Directory: /var/lib/cwl/stg2116046d-b250-4831-a99f-37d7593033b9/dqc_reference
[2023-03-18 21:15:31,045] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 21:15:31,046] [INFO] Task started: Prodigal
[2023-03-18 21:15:31,046] [INFO] Running command: cat /var/lib/cwl/stgf4623500-09d6-45b8-8584-1454aa9976d2/OceanDNA-b32626.fa | prodigal -d OceanDNA-b32626/cds.fna -a OceanDNA-b32626/protein.faa -g 11 -q > /dev/null
[2023-03-18 21:15:37,229] [INFO] Task succeeded: Prodigal
[2023-03-18 21:15:37,230] [INFO] Task started: HMMsearch
[2023-03-18 21:15:37,230] [INFO] Running command: hmmsearch --tblout OceanDNA-b32626/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2116046d-b250-4831-a99f-37d7593033b9/dqc_reference/reference_markers.hmm OceanDNA-b32626/protein.faa > /dev/null
[2023-03-18 21:15:37,365] [INFO] Task succeeded: HMMsearch
[2023-03-18 21:15:37,366] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgf4623500-09d6-45b8-8584-1454aa9976d2/OceanDNA-b32626.fa]
[2023-03-18 21:15:37,378] [INFO] Query marker FASTA was written to OceanDNA-b32626/markers.fasta
[2023-03-18 21:15:37,380] [INFO] Task started: Blastn
[2023-03-18 21:15:37,380] [INFO] Running command: blastn -query OceanDNA-b32626/markers.fasta -db /var/lib/cwl/stg2116046d-b250-4831-a99f-37d7593033b9/dqc_reference/reference_markers.fasta -out OceanDNA-b32626/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:15:37,824] [INFO] Task succeeded: Blastn
[2023-03-18 21:15:37,826] [INFO] Selected 11 target genomes.
[2023-03-18 21:15:37,826] [INFO] Target genome list was writen to OceanDNA-b32626/target_genomes.txt
[2023-03-18 21:15:37,833] [INFO] Task started: fastANI
[2023-03-18 21:15:37,833] [INFO] Running command: fastANI --query /var/lib/cwl/stgf4623500-09d6-45b8-8584-1454aa9976d2/OceanDNA-b32626.fa --refList OceanDNA-b32626/target_genomes.txt --output OceanDNA-b32626/fastani_result.tsv --threads 1
[2023-03-18 21:15:43,053] [INFO] Task succeeded: fastANI
[2023-03-18 21:15:43,053] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2116046d-b250-4831-a99f-37d7593033b9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 21:15:43,054] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2116046d-b250-4831-a99f-37d7593033b9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 21:15:43,054] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 21:15:43,054] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 21:15:43,054] [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
--------------------------------------------------------------------------------
[2023-03-18 21:15:43,055] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32626/tc_result.tsv
[2023-03-18 21:15:43,055] [INFO] ===== Taxonomy check completed =====
[2023-03-18 21:15:43,056] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 21:15:43,056] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2116046d-b250-4831-a99f-37d7593033b9/dqc_reference/checkm_data
[2023-03-18 21:15:43,059] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 21:15:43,064] [INFO] Task started: CheckM
[2023-03-18 21:15:43,064] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32626/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32626/checkm_input OceanDNA-b32626/checkm_result
[2023-03-18 21:16:04,200] [INFO] Task succeeded: CheckM
[2023-03-18 21:16:04,200] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.03%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 21:16:04,213] [INFO] ===== Completeness check finished =====
[2023-03-18 21:16:04,213] [INFO] ===== Start GTDB Search =====
[2023-03-18 21:16:04,213] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32626/markers.fasta)
[2023-03-18 21:16:04,215] [INFO] Task started: Blastn
[2023-03-18 21:16:04,215] [INFO] Running command: blastn -query OceanDNA-b32626/markers.fasta -db /var/lib/cwl/stg2116046d-b250-4831-a99f-37d7593033b9/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32626/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:16:04,649] [INFO] Task succeeded: Blastn
[2023-03-18 21:16:04,650] [INFO] Selected 11 target genomes.
[2023-03-18 21:16:04,650] [INFO] Target genome list was writen to OceanDNA-b32626/target_genomes_gtdb.txt
[2023-03-18 21:16:04,665] [INFO] Task started: fastANI
[2023-03-18 21:16:04,665] [INFO] Running command: fastANI --query /var/lib/cwl/stgf4623500-09d6-45b8-8584-1454aa9976d2/OceanDNA-b32626.fa --refList OceanDNA-b32626/target_genomes_gtdb.txt --output OceanDNA-b32626/fastani_result_gtdb.tsv --threads 1
[2023-03-18 21:16:07,693] [INFO] Task succeeded: fastANI
[2023-03-18 21:16:07,696] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 21:16:07,696] [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_002937495.1	s__UBA12223 sp002937495	80.0516	158	411	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA1280;f__UBA12223;g__UBA12223	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003450915.1	s__UBA12223 sp003450915	78.8533	148	411	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA1280;f__UBA12223;g__UBA12223	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 21:16:07,696] [INFO] GTDB search result was written to OceanDNA-b32626/result_gtdb.tsv
[2023-03-18 21:16:07,696] [INFO] ===== GTDB Search completed =====
[2023-03-18 21:16:07,697] [INFO] DFAST_QC result json was written to OceanDNA-b32626/dqc_result.json
[2023-03-18 21:16:07,697] [INFO] DFAST_QC completed!
[2023-03-18 21:16:07,697] [INFO] Total running time: 0h0m38s