[2023-03-17 03:29:19,761] [INFO] DFAST_QC pipeline started.
[2023-03-17 03:29:19,762] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 03:29:19,762] [INFO] DQC Reference Directory: /var/lib/cwl/stg33a4be8d-e694-440d-9ebc-47cb529ccc4b/dqc_reference
[2023-03-17 03:29:21,321] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 03:29:21,321] [INFO] Task started: Prodigal
[2023-03-17 03:29:21,322] [INFO] Running command: cat /var/lib/cwl/stg2beb18e5-7038-4df4-8f3b-3ca666c411c8/OceanDNA-b9058.fa | prodigal -d OceanDNA-b9058/cds.fna -a OceanDNA-b9058/protein.faa -g 11 -q > /dev/null
[2023-03-17 03:29:28,172] [INFO] Task succeeded: Prodigal
[2023-03-17 03:29:28,172] [INFO] Task started: HMMsearch
[2023-03-17 03:29:28,172] [INFO] Running command: hmmsearch --tblout OceanDNA-b9058/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg33a4be8d-e694-440d-9ebc-47cb529ccc4b/dqc_reference/reference_markers.hmm OceanDNA-b9058/protein.faa > /dev/null
[2023-03-17 03:29:28,329] [INFO] Task succeeded: HMMsearch
[2023-03-17 03:29:28,329] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg2beb18e5-7038-4df4-8f3b-3ca666c411c8/OceanDNA-b9058.fa]
[2023-03-17 03:29:28,340] [INFO] Query marker FASTA was written to OceanDNA-b9058/markers.fasta
[2023-03-17 03:29:28,340] [INFO] Task started: Blastn
[2023-03-17 03:29:28,340] [INFO] Running command: blastn -query OceanDNA-b9058/markers.fasta -db /var/lib/cwl/stg33a4be8d-e694-440d-9ebc-47cb529ccc4b/dqc_reference/reference_markers.fasta -out OceanDNA-b9058/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 03:29:29,201] [INFO] Task succeeded: Blastn
[2023-03-17 03:29:29,202] [INFO] Selected 25 target genomes.
[2023-03-17 03:29:29,202] [INFO] Target genome list was writen to OceanDNA-b9058/target_genomes.txt
[2023-03-17 03:29:29,214] [INFO] Task started: fastANI
[2023-03-17 03:29:29,215] [INFO] Running command: fastANI --query /var/lib/cwl/stg2beb18e5-7038-4df4-8f3b-3ca666c411c8/OceanDNA-b9058.fa --refList OceanDNA-b9058/target_genomes.txt --output OceanDNA-b9058/fastani_result.tsv --threads 1
[2023-03-17 03:29:43,712] [INFO] Task succeeded: fastANI
[2023-03-17 03:29:43,712] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg33a4be8d-e694-440d-9ebc-47cb529ccc4b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 03:29:43,712] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg33a4be8d-e694-440d-9ebc-47cb529ccc4b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 03:29:43,713] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 03:29:43,713] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 03:29:43,713] [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 03:29:43,713] [INFO] DFAST Taxonomy check result was written to OceanDNA-b9058/tc_result.tsv
[2023-03-17 03:29:43,713] [INFO] ===== Taxonomy check completed =====
[2023-03-17 03:29:43,713] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 03:29:43,713] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg33a4be8d-e694-440d-9ebc-47cb529ccc4b/dqc_reference/checkm_data
[2023-03-17 03:29:43,716] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 03:29:43,719] [INFO] Task started: CheckM
[2023-03-17 03:29:43,719] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b9058/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b9058/checkm_input OceanDNA-b9058/checkm_result
[2023-03-17 03:30:06,271] [INFO] Task succeeded: CheckM
[2023-03-17 03:30:06,271] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 1.04%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 03:30:06,273] [INFO] ===== Completeness check finished =====
[2023-03-17 03:30:06,273] [INFO] ===== Start GTDB Search =====
[2023-03-17 03:30:06,273] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b9058/markers.fasta)
[2023-03-17 03:30:06,273] [INFO] Task started: Blastn
[2023-03-17 03:30:06,273] [INFO] Running command: blastn -query OceanDNA-b9058/markers.fasta -db /var/lib/cwl/stg33a4be8d-e694-440d-9ebc-47cb529ccc4b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b9058/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 03:30:06,919] [INFO] Task succeeded: Blastn
[2023-03-17 03:30:06,920] [INFO] Selected 21 target genomes.
[2023-03-17 03:30:06,920] [INFO] Target genome list was writen to OceanDNA-b9058/target_genomes_gtdb.txt
[2023-03-17 03:30:06,943] [INFO] Task started: fastANI
[2023-03-17 03:30:06,943] [INFO] Running command: fastANI --query /var/lib/cwl/stg2beb18e5-7038-4df4-8f3b-3ca666c411c8/OceanDNA-b9058.fa --refList OceanDNA-b9058/target_genomes_gtdb.txt --output OceanDNA-b9058/fastani_result_gtdb.tsv --threads 1
[2023-03-17 03:30:13,710] [INFO] Task succeeded: fastANI
[2023-03-17 03:30:13,715] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 03:30:13,740] [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_902517245.1	s__MS024-2A sp902517245	95.9656	249	352	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902512755.1	s__MS024-2A sp902512755	82.6087	173	352	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002169865.1	s__MS024-2A sp002169865	79.1152	84	352	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905480425.1	s__MS024-2A sp905480425	76.6917	81	352	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	95.11	95.11	0.87	0.87	2	-
GCA_002714815.1	s__MS024-2A sp002714815	76.5735	97	352	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905182305.1	s__MS024-2A sp905182305	76.5478	76	352	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002719315.1	s__GCA-2719315 sp002719315	76.0209	57	352	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-2719315	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 03:30:13,740] [INFO] GTDB search result was written to OceanDNA-b9058/result_gtdb.tsv
[2023-03-17 03:30:13,740] [INFO] ===== GTDB Search completed =====
[2023-03-17 03:30:13,741] [INFO] DFAST_QC result json was written to OceanDNA-b9058/dqc_result.json
[2023-03-17 03:30:13,741] [INFO] DFAST_QC completed!
[2023-03-17 03:30:13,741] [INFO] Total running time: 0h0m54s