[2023-03-16 19:17:07,329] [INFO] DFAST_QC pipeline started.
[2023-03-16 19:17:07,330] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 19:17:07,330] [INFO] DQC Reference Directory: /var/lib/cwl/stg50495aa9-c134-404d-bf1c-a12c5d5f20de/dqc_reference
[2023-03-16 19:17:08,446] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 19:17:08,446] [INFO] Task started: Prodigal
[2023-03-16 19:17:08,446] [INFO] Running command: cat /var/lib/cwl/stg84f1dadc-ebb7-44d3-9389-e3fe0d9744c9/OceanDNA-b12595.fa | prodigal -d OceanDNA-b12595/cds.fna -a OceanDNA-b12595/protein.faa -g 11 -q > /dev/null
[2023-03-16 19:17:19,537] [INFO] Task succeeded: Prodigal
[2023-03-16 19:17:19,537] [INFO] Task started: HMMsearch
[2023-03-16 19:17:19,537] [INFO] Running command: hmmsearch --tblout OceanDNA-b12595/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg50495aa9-c134-404d-bf1c-a12c5d5f20de/dqc_reference/reference_markers.hmm OceanDNA-b12595/protein.faa > /dev/null
[2023-03-16 19:17:19,696] [INFO] Task succeeded: HMMsearch
[2023-03-16 19:17:19,697] [INFO] Found 6/6 markers.
[2023-03-16 19:17:19,708] [INFO] Query marker FASTA was written to OceanDNA-b12595/markers.fasta
[2023-03-16 19:17:19,710] [INFO] Task started: Blastn
[2023-03-16 19:17:19,710] [INFO] Running command: blastn -query OceanDNA-b12595/markers.fasta -db /var/lib/cwl/stg50495aa9-c134-404d-bf1c-a12c5d5f20de/dqc_reference/reference_markers.fasta -out OceanDNA-b12595/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 19:17:20,295] [INFO] Task succeeded: Blastn
[2023-03-16 19:17:20,296] [INFO] Selected 26 target genomes.
[2023-03-16 19:17:20,297] [INFO] Target genome list was writen to OceanDNA-b12595/target_genomes.txt
[2023-03-16 19:17:20,305] [INFO] Task started: fastANI
[2023-03-16 19:17:20,305] [INFO] Running command: fastANI --query /var/lib/cwl/stg84f1dadc-ebb7-44d3-9389-e3fe0d9744c9/OceanDNA-b12595.fa --refList OceanDNA-b12595/target_genomes.txt --output OceanDNA-b12595/fastani_result.tsv --threads 1
[2023-03-16 19:17:43,688] [INFO] Task succeeded: fastANI
[2023-03-16 19:17:43,688] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg50495aa9-c134-404d-bf1c-a12c5d5f20de/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 19:17:43,688] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg50495aa9-c134-404d-bf1c-a12c5d5f20de/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 19:17:43,688] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 19:17:43,689] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 19:17:43,689] [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 19:17:43,689] [INFO] DFAST Taxonomy check result was written to OceanDNA-b12595/tc_result.tsv
[2023-03-16 19:17:43,690] [INFO] ===== Taxonomy check completed =====
[2023-03-16 19:17:43,690] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 19:17:43,690] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg50495aa9-c134-404d-bf1c-a12c5d5f20de/dqc_reference/checkm_data
[2023-03-16 19:17:43,700] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 19:17:43,738] [INFO] Task started: CheckM
[2023-03-16 19:17:43,738] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b12595/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b12595/checkm_input OceanDNA-b12595/checkm_result
[2023-03-16 19:18:25,892] [INFO] Task succeeded: CheckM
[2023-03-16 19:18:25,892] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 19:18:25,895] [INFO] ===== Completeness check finished =====
[2023-03-16 19:18:25,895] [INFO] ===== Start GTDB Search =====
[2023-03-16 19:18:25,895] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b12595/markers.fasta)
[2023-03-16 19:18:25,898] [INFO] Task started: Blastn
[2023-03-16 19:18:25,898] [INFO] Running command: blastn -query OceanDNA-b12595/markers.fasta -db /var/lib/cwl/stg50495aa9-c134-404d-bf1c-a12c5d5f20de/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b12595/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 19:18:27,203] [INFO] Task succeeded: Blastn
[2023-03-16 19:18:27,205] [INFO] Selected 28 target genomes.
[2023-03-16 19:18:27,205] [INFO] Target genome list was writen to OceanDNA-b12595/target_genomes_gtdb.txt
[2023-03-16 19:18:27,219] [INFO] Task started: fastANI
[2023-03-16 19:18:27,219] [INFO] Running command: fastANI --query /var/lib/cwl/stg84f1dadc-ebb7-44d3-9389-e3fe0d9744c9/OceanDNA-b12595.fa --refList OceanDNA-b12595/target_genomes_gtdb.txt --output OceanDNA-b12595/fastani_result_gtdb.tsv --threads 1
[2023-03-16 19:18:40,453] [INFO] Task succeeded: fastANI
[2023-03-16 19:18:40,456] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 19:18:40,456] [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_002478765.1	s__UBA7430 sp002478765	78.8133	197	533	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA7430;g__UBA7430	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002457305.1	s__MED-G21 sp002457305	77.9779	89	533	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA7430;g__MED-G21	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002685115.1	s__UBA6772 sp002685115	77.3174	50	533	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA7430;g__UBA6772	95.0	96.61	96.05	0.74	0.59	4	-
--------------------------------------------------------------------------------
[2023-03-16 19:18:40,458] [INFO] GTDB search result was written to OceanDNA-b12595/result_gtdb.tsv
[2023-03-16 19:18:40,458] [INFO] ===== GTDB Search completed =====
[2023-03-16 19:18:40,459] [INFO] DFAST_QC result json was written to OceanDNA-b12595/dqc_result.json
[2023-03-16 19:18:40,459] [INFO] DFAST_QC completed!
[2023-03-16 19:18:40,459] [INFO] Total running time: 0h1m33s