[2023-03-19 01:12:13,940] [INFO] DFAST_QC pipeline started.
[2023-03-19 01:12:13,940] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 01:12:13,941] [INFO] DQC Reference Directory: /var/lib/cwl/stge6eee8ef-f3c7-4105-8330-21bab856d745/dqc_reference
[2023-03-19 01:12:15,732] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 01:12:15,733] [INFO] Task started: Prodigal
[2023-03-19 01:12:15,733] [INFO] Running command: cat /var/lib/cwl/stgd3cffc21-7e4f-4649-a0b1-516a58aa547c/OceanDNA-b30622.fa | prodigal -d OceanDNA-b30622/cds.fna -a OceanDNA-b30622/protein.faa -g 11 -q > /dev/null
[2023-03-19 01:12:24,403] [INFO] Task succeeded: Prodigal
[2023-03-19 01:12:24,403] [INFO] Task started: HMMsearch
[2023-03-19 01:12:24,403] [INFO] Running command: hmmsearch --tblout OceanDNA-b30622/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge6eee8ef-f3c7-4105-8330-21bab856d745/dqc_reference/reference_markers.hmm OceanDNA-b30622/protein.faa > /dev/null
[2023-03-19 01:12:24,556] [INFO] Task succeeded: HMMsearch
[2023-03-19 01:12:24,557] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgd3cffc21-7e4f-4649-a0b1-516a58aa547c/OceanDNA-b30622.fa]
[2023-03-19 01:12:24,570] [INFO] Query marker FASTA was written to OceanDNA-b30622/markers.fasta
[2023-03-19 01:12:24,571] [INFO] Task started: Blastn
[2023-03-19 01:12:24,571] [INFO] Running command: blastn -query OceanDNA-b30622/markers.fasta -db /var/lib/cwl/stge6eee8ef-f3c7-4105-8330-21bab856d745/dqc_reference/reference_markers.fasta -out OceanDNA-b30622/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:12:25,008] [INFO] Task succeeded: Blastn
[2023-03-19 01:12:25,008] [INFO] Selected 12 target genomes.
[2023-03-19 01:12:25,009] [INFO] Target genome list was writen to OceanDNA-b30622/target_genomes.txt
[2023-03-19 01:12:25,018] [INFO] Task started: fastANI
[2023-03-19 01:12:25,018] [INFO] Running command: fastANI --query /var/lib/cwl/stgd3cffc21-7e4f-4649-a0b1-516a58aa547c/OceanDNA-b30622.fa --refList OceanDNA-b30622/target_genomes.txt --output OceanDNA-b30622/fastani_result.tsv --threads 1
[2023-03-19 01:12:32,157] [INFO] Task succeeded: fastANI
[2023-03-19 01:12:32,158] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge6eee8ef-f3c7-4105-8330-21bab856d745/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 01:12:32,158] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge6eee8ef-f3c7-4105-8330-21bab856d745/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 01:12:32,158] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 01:12:32,158] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 01:12:32,158] [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
--------------------------------------------------------------------------------
[2023-03-19 01:12:32,158] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30622/tc_result.tsv
[2023-03-19 01:12:32,158] [INFO] ===== Taxonomy check completed =====
[2023-03-19 01:12:32,158] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 01:12:32,159] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge6eee8ef-f3c7-4105-8330-21bab856d745/dqc_reference/checkm_data
[2023-03-19 01:12:32,162] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 01:12:32,165] [INFO] Task started: CheckM
[2023-03-19 01:12:32,165] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30622/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30622/checkm_input OceanDNA-b30622/checkm_result
[2023-03-19 01:12:58,740] [INFO] Task succeeded: CheckM
[2023-03-19 01:12:58,741] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 73.40%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 01:12:58,743] [INFO] ===== Completeness check finished =====
[2023-03-19 01:12:58,743] [INFO] ===== Start GTDB Search =====
[2023-03-19 01:12:58,743] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30622/markers.fasta)
[2023-03-19 01:12:58,744] [INFO] Task started: Blastn
[2023-03-19 01:12:58,745] [INFO] Running command: blastn -query OceanDNA-b30622/markers.fasta -db /var/lib/cwl/stge6eee8ef-f3c7-4105-8330-21bab856d745/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30622/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:12:59,182] [INFO] Task succeeded: Blastn
[2023-03-19 01:12:59,183] [INFO] Selected 15 target genomes.
[2023-03-19 01:12:59,183] [INFO] Target genome list was writen to OceanDNA-b30622/target_genomes_gtdb.txt
[2023-03-19 01:12:59,196] [INFO] Task started: fastANI
[2023-03-19 01:12:59,196] [INFO] Running command: fastANI --query /var/lib/cwl/stgd3cffc21-7e4f-4649-a0b1-516a58aa547c/OceanDNA-b30622.fa --refList OceanDNA-b30622/target_genomes_gtdb.txt --output OceanDNA-b30622/fastani_result_gtdb.tsv --threads 1
[2023-03-19 01:13:07,766] [INFO] Task succeeded: fastANI
[2023-03-19 01:13:07,769] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 01:13:07,769] [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_003447515.1	s__Amylibacter sp003447515	80.2327	196	472	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amylibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018607905.1	s__Amylibacter sp002387535	76.8384	111	472	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amylibacter	95.0	99.84	99.84	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2023-03-19 01:13:07,770] [INFO] GTDB search result was written to OceanDNA-b30622/result_gtdb.tsv
[2023-03-19 01:13:07,770] [INFO] ===== GTDB Search completed =====
[2023-03-19 01:13:07,770] [INFO] DFAST_QC result json was written to OceanDNA-b30622/dqc_result.json
[2023-03-19 01:13:07,771] [INFO] DFAST_QC completed!
[2023-03-19 01:13:07,771] [INFO] Total running time: 0h0m54s