[2023-03-16 01:29:15,917] [INFO] DFAST_QC pipeline started.
[2023-03-16 01:29:15,926] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 01:29:15,926] [INFO] DQC Reference Directory: /var/lib/cwl/stg33abab19-c50e-4fe7-97d4-7400d9cc33ba/dqc_reference
[2023-03-16 01:29:18,466] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 01:29:18,468] [INFO] Task started: Prodigal
[2023-03-16 01:29:18,468] [INFO] Running command: cat /var/lib/cwl/stg13a2afb1-a7bd-4ee0-8ad1-b79f3a219d74/OceanDNA-b11506.fa | prodigal -d OceanDNA-b11506/cds.fna -a OceanDNA-b11506/protein.faa -g 11 -q > /dev/null
[2023-03-16 01:29:30,539] [INFO] Task succeeded: Prodigal
[2023-03-16 01:29:30,540] [INFO] Task started: HMMsearch
[2023-03-16 01:29:30,540] [INFO] Running command: hmmsearch --tblout OceanDNA-b11506/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg33abab19-c50e-4fe7-97d4-7400d9cc33ba/dqc_reference/reference_markers.hmm OceanDNA-b11506/protein.faa > /dev/null
[2023-03-16 01:29:30,751] [INFO] Task succeeded: HMMsearch
[2023-03-16 01:29:30,752] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg13a2afb1-a7bd-4ee0-8ad1-b79f3a219d74/OceanDNA-b11506.fa]
[2023-03-16 01:29:30,866] [INFO] Query marker FASTA was written to OceanDNA-b11506/markers.fasta
[2023-03-16 01:29:30,867] [INFO] Task started: Blastn
[2023-03-16 01:29:30,867] [INFO] Running command: blastn -query OceanDNA-b11506/markers.fasta -db /var/lib/cwl/stg33abab19-c50e-4fe7-97d4-7400d9cc33ba/dqc_reference/reference_markers.fasta -out OceanDNA-b11506/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 01:29:31,399] [INFO] Task succeeded: Blastn
[2023-03-16 01:29:31,427] [INFO] Selected 26 target genomes.
[2023-03-16 01:29:31,428] [INFO] Target genome list was writen to OceanDNA-b11506/target_genomes.txt
[2023-03-16 01:29:31,444] [INFO] Task started: fastANI
[2023-03-16 01:29:31,444] [INFO] Running command: fastANI --query /var/lib/cwl/stg13a2afb1-a7bd-4ee0-8ad1-b79f3a219d74/OceanDNA-b11506.fa --refList OceanDNA-b11506/target_genomes.txt --output OceanDNA-b11506/fastani_result.tsv --threads 1
[2023-03-16 01:29:45,467] [INFO] Task succeeded: fastANI
[2023-03-16 01:29:45,467] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg33abab19-c50e-4fe7-97d4-7400d9cc33ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 01:29:45,468] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg33abab19-c50e-4fe7-97d4-7400d9cc33ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 01:29:45,468] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 01:29:45,468] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 01:29:45,468] [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 01:29:45,474] [INFO] DFAST Taxonomy check result was written to OceanDNA-b11506/tc_result.tsv
[2023-03-16 01:29:45,480] [INFO] ===== Taxonomy check completed =====
[2023-03-16 01:29:45,480] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 01:29:45,480] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg33abab19-c50e-4fe7-97d4-7400d9cc33ba/dqc_reference/checkm_data
[2023-03-16 01:29:45,483] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 01:29:45,507] [INFO] Task started: CheckM
[2023-03-16 01:29:45,507] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b11506/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b11506/checkm_input OceanDNA-b11506/checkm_result
[2023-03-16 01:30:20,315] [INFO] Task succeeded: CheckM
[2023-03-16 01:30:20,315] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.52%
Contamintation: 2.60%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 01:30:20,597] [INFO] ===== Completeness check finished =====
[2023-03-16 01:30:20,597] [INFO] ===== Start GTDB Search =====
[2023-03-16 01:30:20,597] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b11506/markers.fasta)
[2023-03-16 01:30:20,598] [INFO] Task started: Blastn
[2023-03-16 01:30:20,598] [INFO] Running command: blastn -query OceanDNA-b11506/markers.fasta -db /var/lib/cwl/stg33abab19-c50e-4fe7-97d4-7400d9cc33ba/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b11506/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 01:30:21,320] [INFO] Task succeeded: Blastn
[2023-03-16 01:30:21,330] [INFO] Selected 28 target genomes.
[2023-03-16 01:30:21,330] [INFO] Target genome list was writen to OceanDNA-b11506/target_genomes_gtdb.txt
[2023-03-16 01:30:22,300] [INFO] Task started: fastANI
[2023-03-16 01:30:22,300] [INFO] Running command: fastANI --query /var/lib/cwl/stg13a2afb1-a7bd-4ee0-8ad1-b79f3a219d74/OceanDNA-b11506.fa --refList OceanDNA-b11506/target_genomes_gtdb.txt --output OceanDNA-b11506/fastani_result_gtdb.tsv --threads 1
[2023-03-16 01:30:35,185] [INFO] Task succeeded: fastANI
[2023-03-16 01:30:35,188] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 01:30:35,188] [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_002722245.1	s__GCA-002722245 sp002722245	79.2919	230	548	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__GCA-002722245;g__GCA-002722245	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002720635.1	s__GCA-002722245 sp002720635	78.4415	96	548	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__GCA-002722245;g__GCA-002722245	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905182585.1	s__GCA-002722245 sp905182585	76.8484	72	548	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__GCA-002722245;g__GCA-002722245	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 01:30:35,193] [INFO] GTDB search result was written to OceanDNA-b11506/result_gtdb.tsv
[2023-03-16 01:30:35,196] [INFO] ===== GTDB Search completed =====
[2023-03-16 01:30:35,200] [INFO] DFAST_QC result json was written to OceanDNA-b11506/dqc_result.json
[2023-03-16 01:30:35,200] [INFO] DFAST_QC completed!
[2023-03-16 01:30:35,200] [INFO] Total running time: 0h1m19s