[2023-03-19 05:19:33,800] [INFO] DFAST_QC pipeline started.
[2023-03-19 05:19:33,801] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 05:19:33,801] [INFO] DQC Reference Directory: /var/lib/cwl/stg441e3ca6-8873-4a5e-a3a9-505c7a8e949f/dqc_reference
[2023-03-19 05:19:35,397] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 05:19:35,398] [INFO] Task started: Prodigal
[2023-03-19 05:19:35,398] [INFO] Running command: cat /var/lib/cwl/stg4c2afcb7-2837-4792-a4c7-bb1b0949ab4c/OceanDNA-b40237.fa | prodigal -d OceanDNA-b40237/cds.fna -a OceanDNA-b40237/protein.faa -g 11 -q > /dev/null
[2023-03-19 05:19:47,219] [INFO] Task succeeded: Prodigal
[2023-03-19 05:19:47,220] [INFO] Task started: HMMsearch
[2023-03-19 05:19:47,220] [INFO] Running command: hmmsearch --tblout OceanDNA-b40237/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg441e3ca6-8873-4a5e-a3a9-505c7a8e949f/dqc_reference/reference_markers.hmm OceanDNA-b40237/protein.faa > /dev/null
[2023-03-19 05:19:47,460] [INFO] Task succeeded: HMMsearch
[2023-03-19 05:19:47,461] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg4c2afcb7-2837-4792-a4c7-bb1b0949ab4c/OceanDNA-b40237.fa]
[2023-03-19 05:19:47,477] [INFO] Query marker FASTA was written to OceanDNA-b40237/markers.fasta
[2023-03-19 05:19:47,477] [INFO] Task started: Blastn
[2023-03-19 05:19:47,477] [INFO] Running command: blastn -query OceanDNA-b40237/markers.fasta -db /var/lib/cwl/stg441e3ca6-8873-4a5e-a3a9-505c7a8e949f/dqc_reference/reference_markers.fasta -out OceanDNA-b40237/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 05:19:48,008] [INFO] Task succeeded: Blastn
[2023-03-19 05:19:48,009] [INFO] Selected 35 target genomes.
[2023-03-19 05:19:48,009] [INFO] Target genome list was writen to OceanDNA-b40237/target_genomes.txt
[2023-03-19 05:19:48,029] [INFO] Task started: fastANI
[2023-03-19 05:19:48,029] [INFO] Running command: fastANI --query /var/lib/cwl/stg4c2afcb7-2837-4792-a4c7-bb1b0949ab4c/OceanDNA-b40237.fa --refList OceanDNA-b40237/target_genomes.txt --output OceanDNA-b40237/fastani_result.tsv --threads 1
[2023-03-19 05:20:09,804] [INFO] Task succeeded: fastANI
[2023-03-19 05:20:09,804] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg441e3ca6-8873-4a5e-a3a9-505c7a8e949f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 05:20:09,804] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg441e3ca6-8873-4a5e-a3a9-505c7a8e949f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 05:20:09,804] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 05:20:09,804] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 05:20:09,804] [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 05:20:09,805] [INFO] DFAST Taxonomy check result was written to OceanDNA-b40237/tc_result.tsv
[2023-03-19 05:20:09,805] [INFO] ===== Taxonomy check completed =====
[2023-03-19 05:20:09,805] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 05:20:09,805] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg441e3ca6-8873-4a5e-a3a9-505c7a8e949f/dqc_reference/checkm_data
[2023-03-19 05:20:09,807] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 05:20:09,910] [INFO] Task started: CheckM
[2023-03-19 05:20:09,910] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b40237/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b40237/checkm_input OceanDNA-b40237/checkm_result
[2023-03-19 05:20:43,636] [INFO] Task succeeded: CheckM
[2023-03-19 05:20:43,636] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 77.08%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 05:20:43,638] [INFO] ===== Completeness check finished =====
[2023-03-19 05:20:43,638] [INFO] ===== Start GTDB Search =====
[2023-03-19 05:20:43,638] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b40237/markers.fasta)
[2023-03-19 05:20:43,638] [INFO] Task started: Blastn
[2023-03-19 05:20:43,638] [INFO] Running command: blastn -query OceanDNA-b40237/markers.fasta -db /var/lib/cwl/stg441e3ca6-8873-4a5e-a3a9-505c7a8e949f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b40237/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 05:20:44,354] [INFO] Task succeeded: Blastn
[2023-03-19 05:20:44,355] [INFO] Selected 29 target genomes.
[2023-03-19 05:20:44,355] [INFO] Target genome list was writen to OceanDNA-b40237/target_genomes_gtdb.txt
[2023-03-19 05:20:44,442] [INFO] Task started: fastANI
[2023-03-19 05:20:44,442] [INFO] Running command: fastANI --query /var/lib/cwl/stg4c2afcb7-2837-4792-a4c7-bb1b0949ab4c/OceanDNA-b40237.fa --refList OceanDNA-b40237/target_genomes_gtdb.txt --output OceanDNA-b40237/fastani_result_gtdb.tsv --threads 1
[2023-03-19 05:21:01,635] [INFO] Task succeeded: fastANI
[2023-03-19 05:21:01,637] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 05:21:01,637] [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_018698975.1	s__RFVC01 sp018698975	90.9633	590	681	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__RFVC01	95.0	99.67	99.67	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2023-03-19 05:21:01,637] [INFO] GTDB search result was written to OceanDNA-b40237/result_gtdb.tsv
[2023-03-19 05:21:01,637] [INFO] ===== GTDB Search completed =====
[2023-03-19 05:21:01,638] [INFO] DFAST_QC result json was written to OceanDNA-b40237/dqc_result.json
[2023-03-19 05:21:01,638] [INFO] DFAST_QC completed!
[2023-03-19 05:21:01,638] [INFO] Total running time: 0h1m28s