[2023-03-19 01:12:13,951] [INFO] DFAST_QC pipeline started.
[2023-03-19 01:12:13,951] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 01:12:13,951] [INFO] DQC Reference Directory: /var/lib/cwl/stg49a463cb-1bf1-428e-9f33-3e1b0fa8606a/dqc_reference
[2023-03-19 01:12:15,733] [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/stg724d056b-5f0d-48ae-8ebe-311637e7ed17/OceanDNA-b12508.fa | prodigal -d OceanDNA-b12508/cds.fna -a OceanDNA-b12508/protein.faa -g 11 -q > /dev/null
[2023-03-19 01:12:38,432] [INFO] Task succeeded: Prodigal
[2023-03-19 01:12:38,432] [INFO] Task started: HMMsearch
[2023-03-19 01:12:38,432] [INFO] Running command: hmmsearch --tblout OceanDNA-b12508/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg49a463cb-1bf1-428e-9f33-3e1b0fa8606a/dqc_reference/reference_markers.hmm OceanDNA-b12508/protein.faa > /dev/null
[2023-03-19 01:12:38,628] [INFO] Task succeeded: HMMsearch
[2023-03-19 01:12:38,629] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg724d056b-5f0d-48ae-8ebe-311637e7ed17/OceanDNA-b12508.fa]
[2023-03-19 01:12:38,648] [INFO] Query marker FASTA was written to OceanDNA-b12508/markers.fasta
[2023-03-19 01:12:38,649] [INFO] Task started: Blastn
[2023-03-19 01:12:38,649] [INFO] Running command: blastn -query OceanDNA-b12508/markers.fasta -db /var/lib/cwl/stg49a463cb-1bf1-428e-9f33-3e1b0fa8606a/dqc_reference/reference_markers.fasta -out OceanDNA-b12508/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:12:39,166] [INFO] Task succeeded: Blastn
[2023-03-19 01:12:39,167] [INFO] Selected 21 target genomes.
[2023-03-19 01:12:39,167] [INFO] Target genome list was writen to OceanDNA-b12508/target_genomes.txt
[2023-03-19 01:12:39,183] [INFO] Task started: fastANI
[2023-03-19 01:12:39,183] [INFO] Running command: fastANI --query /var/lib/cwl/stg724d056b-5f0d-48ae-8ebe-311637e7ed17/OceanDNA-b12508.fa --refList OceanDNA-b12508/target_genomes.txt --output OceanDNA-b12508/fastani_result.tsv --threads 1
[2023-03-19 01:12:52,293] [INFO] Task succeeded: fastANI
[2023-03-19 01:12:52,294] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg49a463cb-1bf1-428e-9f33-3e1b0fa8606a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 01:12:52,294] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg49a463cb-1bf1-428e-9f33-3e1b0fa8606a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 01:12:52,294] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 01:12:52,294] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 01:12:52,294] [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 01:12:52,294] [INFO] DFAST Taxonomy check result was written to OceanDNA-b12508/tc_result.tsv
[2023-03-19 01:12:52,294] [INFO] ===== Taxonomy check completed =====
[2023-03-19 01:12:52,294] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 01:12:52,295] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg49a463cb-1bf1-428e-9f33-3e1b0fa8606a/dqc_reference/checkm_data
[2023-03-19 01:12:52,298] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 01:12:52,302] [INFO] Task started: CheckM
[2023-03-19 01:12:52,302] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b12508/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b12508/checkm_input OceanDNA-b12508/checkm_result
[2023-03-19 01:13:49,981] [INFO] Task succeeded: CheckM
[2023-03-19 01:13:49,981] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 88.89%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 01:13:50,175] [INFO] ===== Completeness check finished =====
[2023-03-19 01:13:50,176] [INFO] ===== Start GTDB Search =====
[2023-03-19 01:13:50,176] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b12508/markers.fasta)
[2023-03-19 01:13:50,177] [INFO] Task started: Blastn
[2023-03-19 01:13:50,177] [INFO] Running command: blastn -query OceanDNA-b12508/markers.fasta -db /var/lib/cwl/stg49a463cb-1bf1-428e-9f33-3e1b0fa8606a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b12508/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:13:50,864] [INFO] Task succeeded: Blastn
[2023-03-19 01:13:50,865] [INFO] Selected 26 target genomes.
[2023-03-19 01:13:50,865] [INFO] Target genome list was writen to OceanDNA-b12508/target_genomes_gtdb.txt
[2023-03-19 01:13:50,923] [INFO] Task started: fastANI
[2023-03-19 01:13:50,923] [INFO] Running command: fastANI --query /var/lib/cwl/stg724d056b-5f0d-48ae-8ebe-311637e7ed17/OceanDNA-b12508.fa --refList OceanDNA-b12508/target_genomes_gtdb.txt --output OceanDNA-b12508/fastani_result_gtdb.tsv --threads 1
[2023-03-19 01:14:04,464] [INFO] Task succeeded: fastANI
[2023-03-19 01:14:04,467] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 01:14:04,468] [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_003456455.1	s__UBA10329 sp003456455	78.4883	187	997	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA10329;g__UBA10329	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018402015.1	s__UBA10329 sp018402015	77.591	184	997	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA10329;g__UBA10329	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016124845.1	s__UBA10329 sp016124845	76.579	154	997	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA10329;g__UBA10329	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 01:14:04,468] [INFO] GTDB search result was written to OceanDNA-b12508/result_gtdb.tsv
[2023-03-19 01:14:04,468] [INFO] ===== GTDB Search completed =====
[2023-03-19 01:14:04,469] [INFO] DFAST_QC result json was written to OceanDNA-b12508/dqc_result.json
[2023-03-19 01:14:04,469] [INFO] DFAST_QC completed!
[2023-03-19 01:14:04,469] [INFO] Total running time: 0h1m51s