[2023-03-14 14:31:44,399] [INFO] DFAST_QC pipeline started.
[2023-03-14 14:31:44,399] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 14:31:44,399] [INFO] DQC Reference Directory: /var/lib/cwl/stga9145698-196f-4e5b-aa8c-8cc15e88b593/dqc_reference
[2023-03-14 14:31:45,739] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 14:31:45,739] [INFO] Task started: Prodigal
[2023-03-14 14:31:45,740] [INFO] Running command: cat /var/lib/cwl/stg8da4fd85-00bd-40ee-a3f0-4df4e0e822ca/OceanDNA-b35372.fa | prodigal -d OceanDNA-b35372/cds.fna -a OceanDNA-b35372/protein.faa -g 11 -q > /dev/null
[2023-03-14 14:31:57,349] [INFO] Task succeeded: Prodigal
[2023-03-14 14:31:57,350] [INFO] Task started: HMMsearch
[2023-03-14 14:31:57,350] [INFO] Running command: hmmsearch --tblout OceanDNA-b35372/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga9145698-196f-4e5b-aa8c-8cc15e88b593/dqc_reference/reference_markers.hmm OceanDNA-b35372/protein.faa > /dev/null
[2023-03-14 14:31:57,523] [INFO] Task succeeded: HMMsearch
[2023-03-14 14:31:57,523] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg8da4fd85-00bd-40ee-a3f0-4df4e0e822ca/OceanDNA-b35372.fa]
[2023-03-14 14:31:57,540] [INFO] Query marker FASTA was written to OceanDNA-b35372/markers.fasta
[2023-03-14 14:31:57,542] [INFO] Task started: Blastn
[2023-03-14 14:31:57,542] [INFO] Running command: blastn -query OceanDNA-b35372/markers.fasta -db /var/lib/cwl/stga9145698-196f-4e5b-aa8c-8cc15e88b593/dqc_reference/reference_markers.fasta -out OceanDNA-b35372/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 14:31:58,103] [INFO] Task succeeded: Blastn
[2023-03-14 14:31:58,104] [INFO] Selected 23 target genomes.
[2023-03-14 14:31:58,104] [INFO] Target genome list was writen to OceanDNA-b35372/target_genomes.txt
[2023-03-14 14:31:58,139] [INFO] Task started: fastANI
[2023-03-14 14:31:58,139] [INFO] Running command: fastANI --query /var/lib/cwl/stg8da4fd85-00bd-40ee-a3f0-4df4e0e822ca/OceanDNA-b35372.fa --refList OceanDNA-b35372/target_genomes.txt --output OceanDNA-b35372/fastani_result.tsv --threads 1
[2023-03-14 14:32:12,228] [INFO] Task succeeded: fastANI
[2023-03-14 14:32:12,228] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga9145698-196f-4e5b-aa8c-8cc15e88b593/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 14:32:12,228] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga9145698-196f-4e5b-aa8c-8cc15e88b593/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 14:32:12,228] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 14:32:12,228] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 14:32:12,228] [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 14:32:12,229] [INFO] DFAST Taxonomy check result was written to OceanDNA-b35372/tc_result.tsv
[2023-03-14 14:32:12,229] [INFO] ===== Taxonomy check completed =====
[2023-03-14 14:32:12,229] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 14:32:12,229] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga9145698-196f-4e5b-aa8c-8cc15e88b593/dqc_reference/checkm_data
[2023-03-14 14:32:12,282] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 14:32:12,287] [INFO] Task started: CheckM
[2023-03-14 14:32:12,287] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b35372/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b35372/checkm_input OceanDNA-b35372/checkm_result
[2023-03-14 14:32:59,724] [INFO] Task succeeded: CheckM
[2023-03-14 14:32:59,724] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 50.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 14:32:59,726] [INFO] ===== Completeness check finished =====
[2023-03-14 14:32:59,727] [INFO] ===== Start GTDB Search =====
[2023-03-14 14:32:59,727] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b35372/markers.fasta)
[2023-03-14 14:32:59,728] [INFO] Task started: Blastn
[2023-03-14 14:32:59,728] [INFO] Running command: blastn -query OceanDNA-b35372/markers.fasta -db /var/lib/cwl/stga9145698-196f-4e5b-aa8c-8cc15e88b593/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b35372/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 14:33:00,569] [INFO] Task succeeded: Blastn
[2023-03-14 14:33:00,570] [INFO] Selected 25 target genomes.
[2023-03-14 14:33:00,570] [INFO] Target genome list was writen to OceanDNA-b35372/target_genomes_gtdb.txt
[2023-03-14 14:33:00,676] [INFO] Task started: fastANI
[2023-03-14 14:33:00,676] [INFO] Running command: fastANI --query /var/lib/cwl/stg8da4fd85-00bd-40ee-a3f0-4df4e0e822ca/OceanDNA-b35372.fa --refList OceanDNA-b35372/target_genomes_gtdb.txt --output OceanDNA-b35372/fastani_result_gtdb.tsv --threads 1
[2023-03-14 14:33:23,311] [INFO] Task succeeded: fastANI
[2023-03-14 14:33:23,314] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 14:33:23,314] [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_014382695.1	s__JACNJF01 sp014382695	77.2355	100	674	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__GCA-001735895;f__GCA-001735895;g__JACNJF01	95.0	99.61	99.61	0.86	0.86	2	-
GCA_018669845.1	s__JACNJF01 sp018669845	76.5898	85	674	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__GCA-001735895;f__GCA-001735895;g__JACNJF01	95.0	99.85	99.71	0.93	0.91	11	-
--------------------------------------------------------------------------------
[2023-03-14 14:33:23,314] [INFO] GTDB search result was written to OceanDNA-b35372/result_gtdb.tsv
[2023-03-14 14:33:23,314] [INFO] ===== GTDB Search completed =====
[2023-03-14 14:33:23,315] [INFO] DFAST_QC result json was written to OceanDNA-b35372/dqc_result.json
[2023-03-14 14:33:23,315] [INFO] DFAST_QC completed!
[2023-03-14 14:33:23,315] [INFO] Total running time: 0h1m39s