[2023-03-14 13:09:10,257] [INFO] DFAST_QC pipeline started.
[2023-03-14 13:09:10,258] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 13:09:10,258] [INFO] DQC Reference Directory: /var/lib/cwl/stg1e70ec8c-8866-4178-9cba-8e1d62d5e607/dqc_reference
[2023-03-14 13:09:11,470] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 13:09:11,470] [INFO] Task started: Prodigal
[2023-03-14 13:09:11,471] [INFO] Running command: cat /var/lib/cwl/stge4b626b1-9e76-4745-afed-f62da658ca7a/OceanDNA-b37083.fa | prodigal -d OceanDNA-b37083/cds.fna -a OceanDNA-b37083/protein.faa -g 11 -q > /dev/null
[2023-03-14 13:09:40,885] [INFO] Task succeeded: Prodigal
[2023-03-14 13:09:40,886] [INFO] Task started: HMMsearch
[2023-03-14 13:09:40,886] [INFO] Running command: hmmsearch --tblout OceanDNA-b37083/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1e70ec8c-8866-4178-9cba-8e1d62d5e607/dqc_reference/reference_markers.hmm OceanDNA-b37083/protein.faa > /dev/null
[2023-03-14 13:09:41,248] [INFO] Task succeeded: HMMsearch
[2023-03-14 13:09:41,249] [INFO] Found 6/6 markers.
[2023-03-14 13:09:41,268] [INFO] Query marker FASTA was written to OceanDNA-b37083/markers.fasta
[2023-03-14 13:09:41,269] [INFO] Task started: Blastn
[2023-03-14 13:09:41,269] [INFO] Running command: blastn -query OceanDNA-b37083/markers.fasta -db /var/lib/cwl/stg1e70ec8c-8866-4178-9cba-8e1d62d5e607/dqc_reference/reference_markers.fasta -out OceanDNA-b37083/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 13:09:41,876] [INFO] Task succeeded: Blastn
[2023-03-14 13:09:41,877] [INFO] Selected 35 target genomes.
[2023-03-14 13:09:41,878] [INFO] Target genome list was writen to OceanDNA-b37083/target_genomes.txt
[2023-03-14 13:09:41,904] [INFO] Task started: fastANI
[2023-03-14 13:09:41,904] [INFO] Running command: fastANI --query /var/lib/cwl/stge4b626b1-9e76-4745-afed-f62da658ca7a/OceanDNA-b37083.fa --refList OceanDNA-b37083/target_genomes.txt --output OceanDNA-b37083/fastani_result.tsv --threads 1
[2023-03-14 13:10:24,801] [INFO] Task succeeded: fastANI
[2023-03-14 13:10:24,802] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1e70ec8c-8866-4178-9cba-8e1d62d5e607/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 13:10:24,802] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1e70ec8c-8866-4178-9cba-8e1d62d5e607/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 13:10:24,802] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 13:10:24,802] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 13:10:24,802] [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
--------------------------------------------------------------------------------
[2023-03-14 13:10:24,802] [INFO] DFAST Taxonomy check result was written to OceanDNA-b37083/tc_result.tsv
[2023-03-14 13:10:24,803] [INFO] ===== Taxonomy check completed =====
[2023-03-14 13:10:24,803] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 13:10:24,803] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1e70ec8c-8866-4178-9cba-8e1d62d5e607/dqc_reference/checkm_data
[2023-03-14 13:10:24,806] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 13:10:24,845] [INFO] Task started: CheckM
[2023-03-14 13:10:24,845] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b37083/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b37083/checkm_input OceanDNA-b37083/checkm_result
[2023-03-14 13:11:08,603] [INFO] Task succeeded: CheckM
[2023-03-14 13:11:08,603] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-14 13:11:08,606] [INFO] ===== Completeness check finished =====
[2023-03-14 13:11:08,606] [INFO] ===== Start GTDB Search =====
[2023-03-14 13:11:08,606] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b37083/markers.fasta)
[2023-03-14 13:11:08,608] [INFO] Task started: Blastn
[2023-03-14 13:11:08,608] [INFO] Running command: blastn -query OceanDNA-b37083/markers.fasta -db /var/lib/cwl/stg1e70ec8c-8866-4178-9cba-8e1d62d5e607/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b37083/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 13:11:09,556] [INFO] Task succeeded: Blastn
[2023-03-14 13:11:09,557] [INFO] Selected 19 target genomes.
[2023-03-14 13:11:09,557] [INFO] Target genome list was writen to OceanDNA-b37083/target_genomes_gtdb.txt
[2023-03-14 13:11:09,571] [INFO] Task started: fastANI
[2023-03-14 13:11:09,571] [INFO] Running command: fastANI --query /var/lib/cwl/stge4b626b1-9e76-4745-afed-f62da658ca7a/OceanDNA-b37083.fa --refList OceanDNA-b37083/target_genomes_gtdb.txt --output OceanDNA-b37083/fastani_result_gtdb.tsv --threads 1
[2023-03-14 13:11:20,191] [INFO] Task succeeded: fastANI
[2023-03-14 13:11:20,194] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 13:11:20,194] [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_905182905.1	s__UBA4421 sp002390555	99.6283	838	967	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA4421	95.0	99.65	99.65	0.88	0.88	2	conclusive
GCA_009886205.1	s__UBA4421 sp009886205	79.3407	450	967	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA4421	95.0	98.44	96.05	0.88	0.79	9	-
GCA_905182095.1	s__UBA4421 sp905182095	78.4675	355	967	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA4421	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002336645.1	s__UBA4421 sp002336645	78.2907	324	967	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA4421	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 13:11:20,195] [INFO] GTDB search result was written to OceanDNA-b37083/result_gtdb.tsv
[2023-03-14 13:11:20,195] [INFO] ===== GTDB Search completed =====
[2023-03-14 13:11:20,195] [INFO] DFAST_QC result json was written to OceanDNA-b37083/dqc_result.json
[2023-03-14 13:11:20,195] [INFO] DFAST_QC completed!
[2023-03-14 13:11:20,195] [INFO] Total running time: 0h2m10s