[2023-03-15 13:20:53,689] [INFO] DFAST_QC pipeline started.
[2023-03-15 13:20:53,690] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 13:20:53,690] [INFO] DQC Reference Directory: /var/lib/cwl/stg93237958-5241-4f6e-a834-114b0c6fb8d3/dqc_reference
[2023-03-15 13:20:55,007] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 13:20:55,007] [INFO] Task started: Prodigal
[2023-03-15 13:20:55,007] [INFO] Running command: cat /var/lib/cwl/stgded321fb-5114-44fc-9792-9f1b16affa65/OceanDNA-b5196.fa | prodigal -d OceanDNA-b5196/cds.fna -a OceanDNA-b5196/protein.faa -g 11 -q > /dev/null
[2023-03-15 13:21:01,593] [INFO] Task succeeded: Prodigal
[2023-03-15 13:21:01,593] [INFO] Task started: HMMsearch
[2023-03-15 13:21:01,593] [INFO] Running command: hmmsearch --tblout OceanDNA-b5196/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg93237958-5241-4f6e-a834-114b0c6fb8d3/dqc_reference/reference_markers.hmm OceanDNA-b5196/protein.faa > /dev/null
[2023-03-15 13:21:01,795] [INFO] Task succeeded: HMMsearch
[2023-03-15 13:21:01,796] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgded321fb-5114-44fc-9792-9f1b16affa65/OceanDNA-b5196.fa]
[2023-03-15 13:21:01,809] [INFO] Query marker FASTA was written to OceanDNA-b5196/markers.fasta
[2023-03-15 13:21:01,809] [INFO] Task started: Blastn
[2023-03-15 13:21:01,809] [INFO] Running command: blastn -query OceanDNA-b5196/markers.fasta -db /var/lib/cwl/stg93237958-5241-4f6e-a834-114b0c6fb8d3/dqc_reference/reference_markers.fasta -out OceanDNA-b5196/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:21:02,392] [INFO] Task succeeded: Blastn
[2023-03-15 13:21:02,393] [INFO] Selected 24 target genomes.
[2023-03-15 13:21:02,393] [INFO] Target genome list was writen to OceanDNA-b5196/target_genomes.txt
[2023-03-15 13:21:02,423] [INFO] Task started: fastANI
[2023-03-15 13:21:02,423] [INFO] Running command: fastANI --query /var/lib/cwl/stgded321fb-5114-44fc-9792-9f1b16affa65/OceanDNA-b5196.fa --refList OceanDNA-b5196/target_genomes.txt --output OceanDNA-b5196/fastani_result.tsv --threads 1
[2023-03-15 13:21:15,383] [INFO] Task succeeded: fastANI
[2023-03-15 13:21:15,383] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg93237958-5241-4f6e-a834-114b0c6fb8d3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 13:21:15,383] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg93237958-5241-4f6e-a834-114b0c6fb8d3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 13:21:15,384] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 13:21:15,384] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 13:21:15,384] [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 13:21:15,384] [INFO] DFAST Taxonomy check result was written to OceanDNA-b5196/tc_result.tsv
[2023-03-15 13:21:15,384] [INFO] ===== Taxonomy check completed =====
[2023-03-15 13:21:15,385] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 13:21:15,385] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg93237958-5241-4f6e-a834-114b0c6fb8d3/dqc_reference/checkm_data
[2023-03-15 13:21:15,388] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 13:21:15,391] [INFO] Task started: CheckM
[2023-03-15 13:21:15,391] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b5196/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b5196/checkm_input OceanDNA-b5196/checkm_result
[2023-03-15 13:21:36,807] [INFO] Task succeeded: CheckM
[2023-03-15 13:21:36,808] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 72.22%
Contamintation: 6.48%
Strain heterogeneity: 83.33%
--------------------------------------------------------------------------------
[2023-03-15 13:21:36,817] [INFO] ===== Completeness check finished =====
[2023-03-15 13:21:36,817] [INFO] ===== Start GTDB Search =====
[2023-03-15 13:21:36,818] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b5196/markers.fasta)
[2023-03-15 13:21:36,819] [INFO] Task started: Blastn
[2023-03-15 13:21:36,819] [INFO] Running command: blastn -query OceanDNA-b5196/markers.fasta -db /var/lib/cwl/stg93237958-5241-4f6e-a834-114b0c6fb8d3/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b5196/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:21:37,610] [INFO] Task succeeded: Blastn
[2023-03-15 13:21:37,611] [INFO] Selected 22 target genomes.
[2023-03-15 13:21:37,611] [INFO] Target genome list was writen to OceanDNA-b5196/target_genomes_gtdb.txt
[2023-03-15 13:21:37,638] [INFO] Task started: fastANI
[2023-03-15 13:21:37,638] [INFO] Running command: fastANI --query /var/lib/cwl/stgded321fb-5114-44fc-9792-9f1b16affa65/OceanDNA-b5196.fa --refList OceanDNA-b5196/target_genomes_gtdb.txt --output OceanDNA-b5196/fastani_result_gtdb.tsv --threads 1
[2023-03-15 13:21:45,124] [INFO] Task succeeded: fastANI
[2023-03-15 13:21:45,127] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 13:21:45,127] [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_012960835.1	s__DUAL01 sp012960835	78.5958	90	237	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__DUAL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014381465.1	s__DUAL01 sp014381465	78.0955	110	237	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__DUAL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905478185.1	s__UWMA-0277 sp905478185	77.3481	55	237	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__UWMA-0277	95.0	96.67	96.67	0.88	0.88	2	-
GCA_018647945.1	s__GCA-002697625 sp018647945	76.4846	58	237	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-002697625	95.0	99.64	99.58	0.90	0.90	3	-
--------------------------------------------------------------------------------
[2023-03-15 13:21:45,128] [INFO] GTDB search result was written to OceanDNA-b5196/result_gtdb.tsv
[2023-03-15 13:21:45,128] [INFO] ===== GTDB Search completed =====
[2023-03-15 13:21:45,129] [INFO] DFAST_QC result json was written to OceanDNA-b5196/dqc_result.json
[2023-03-15 13:21:45,129] [INFO] DFAST_QC completed!
[2023-03-15 13:21:45,130] [INFO] Total running time: 0h0m51s