[2023-03-15 21:48:07,258] [INFO] DFAST_QC pipeline started.
[2023-03-15 21:48:07,259] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 21:48:07,259] [INFO] DQC Reference Directory: /var/lib/cwl/stgfc9ab083-89a5-47b6-8227-71857e1b69fe/dqc_reference
[2023-03-15 21:48:08,883] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 21:48:08,883] [INFO] Task started: Prodigal
[2023-03-15 21:48:08,883] [INFO] Running command: cat /var/lib/cwl/stgdb2fba8b-953f-4db0-a0d1-c89bfc21233a/OceanDNA-b33090.fa | prodigal -d OceanDNA-b33090/cds.fna -a OceanDNA-b33090/protein.faa -g 11 -q > /dev/null
[2023-03-15 21:48:26,619] [INFO] Task succeeded: Prodigal
[2023-03-15 21:48:26,619] [INFO] Task started: HMMsearch
[2023-03-15 21:48:26,619] [INFO] Running command: hmmsearch --tblout OceanDNA-b33090/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfc9ab083-89a5-47b6-8227-71857e1b69fe/dqc_reference/reference_markers.hmm OceanDNA-b33090/protein.faa > /dev/null
[2023-03-15 21:48:26,821] [INFO] Task succeeded: HMMsearch
[2023-03-15 21:48:26,822] [INFO] Found 6/6 markers.
[2023-03-15 21:48:26,848] [INFO] Query marker FASTA was written to OceanDNA-b33090/markers.fasta
[2023-03-15 21:48:26,848] [INFO] Task started: Blastn
[2023-03-15 21:48:26,848] [INFO] Running command: blastn -query OceanDNA-b33090/markers.fasta -db /var/lib/cwl/stgfc9ab083-89a5-47b6-8227-71857e1b69fe/dqc_reference/reference_markers.fasta -out OceanDNA-b33090/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:48:27,468] [INFO] Task succeeded: Blastn
[2023-03-15 21:48:27,469] [INFO] Selected 28 target genomes.
[2023-03-15 21:48:27,469] [INFO] Target genome list was writen to OceanDNA-b33090/target_genomes.txt
[2023-03-15 21:48:27,488] [INFO] Task started: fastANI
[2023-03-15 21:48:27,488] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb2fba8b-953f-4db0-a0d1-c89bfc21233a/OceanDNA-b33090.fa --refList OceanDNA-b33090/target_genomes.txt --output OceanDNA-b33090/fastani_result.tsv --threads 1
[2023-03-15 21:48:46,696] [INFO] Task succeeded: fastANI
[2023-03-15 21:48:46,697] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfc9ab083-89a5-47b6-8227-71857e1b69fe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 21:48:46,697] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfc9ab083-89a5-47b6-8227-71857e1b69fe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 21:48:46,697] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 21:48:46,697] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 21:48:46,697] [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 21:48:46,698] [INFO] DFAST Taxonomy check result was written to OceanDNA-b33090/tc_result.tsv
[2023-03-15 21:48:46,698] [INFO] ===== Taxonomy check completed =====
[2023-03-15 21:48:46,698] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 21:48:46,698] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfc9ab083-89a5-47b6-8227-71857e1b69fe/dqc_reference/checkm_data
[2023-03-15 21:48:46,701] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 21:48:46,706] [INFO] Task started: CheckM
[2023-03-15 21:48:46,706] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b33090/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b33090/checkm_input OceanDNA-b33090/checkm_result
[2023-03-15 21:49:32,887] [INFO] Task succeeded: CheckM
[2023-03-15 21:49:32,887] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.03%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 21:49:32,890] [INFO] ===== Completeness check finished =====
[2023-03-15 21:49:32,890] [INFO] ===== Start GTDB Search =====
[2023-03-15 21:49:32,890] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b33090/markers.fasta)
[2023-03-15 21:49:32,890] [INFO] Task started: Blastn
[2023-03-15 21:49:32,890] [INFO] Running command: blastn -query OceanDNA-b33090/markers.fasta -db /var/lib/cwl/stgfc9ab083-89a5-47b6-8227-71857e1b69fe/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b33090/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:49:34,001] [INFO] Task succeeded: Blastn
[2023-03-15 21:49:34,002] [INFO] Selected 23 target genomes.
[2023-03-15 21:49:34,002] [INFO] Target genome list was writen to OceanDNA-b33090/target_genomes_gtdb.txt
[2023-03-15 21:49:34,174] [INFO] Task started: fastANI
[2023-03-15 21:49:34,174] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb2fba8b-953f-4db0-a0d1-c89bfc21233a/OceanDNA-b33090.fa --refList OceanDNA-b33090/target_genomes_gtdb.txt --output OceanDNA-b33090/fastani_result_gtdb.tsv --threads 1
[2023-03-15 21:49:49,713] [INFO] Task succeeded: fastANI
[2023-03-15 21:49:49,717] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 21:49:49,717] [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_018665505.1	s__UBA6544 sp018665505	92.2799	654	902	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA8366;f__UBA8366;g__UBA6544	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002716125.1	s__UBA6544 sp002716125	77.0907	237	902	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA8366;f__UBA8366;g__UBA6544	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002434595.1	s__UBA6544 sp002434595	76.2171	95	902	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA8366;f__UBA8366;g__UBA6544	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012103325.1	s__GCA-2717185 sp012103325	75.7006	53	902	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA8366;f__GCA-2717185;g__GCA-2717185	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 21:49:49,717] [INFO] GTDB search result was written to OceanDNA-b33090/result_gtdb.tsv
[2023-03-15 21:49:49,717] [INFO] ===== GTDB Search completed =====
[2023-03-15 21:49:49,718] [INFO] DFAST_QC result json was written to OceanDNA-b33090/dqc_result.json
[2023-03-15 21:49:49,718] [INFO] DFAST_QC completed!
[2023-03-15 21:49:49,718] [INFO] Total running time: 0h1m42s