[2023-03-16 21:45:13,528] [INFO] DFAST_QC pipeline started.
[2023-03-16 21:45:13,529] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 21:45:13,529] [INFO] DQC Reference Directory: /var/lib/cwl/stga29b1c17-0157-4e1f-bf99-d6535fcb796c/dqc_reference
[2023-03-16 21:45:15,325] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 21:45:15,327] [INFO] Task started: Prodigal
[2023-03-16 21:45:15,327] [INFO] Running command: cat /var/lib/cwl/stge530c76e-07a1-410d-ad66-e2b1fc57b99e/OceanDNA-b33070.fa | prodigal -d OceanDNA-b33070/cds.fna -a OceanDNA-b33070/protein.faa -g 11 -q > /dev/null
[2023-03-16 21:45:33,242] [INFO] Task succeeded: Prodigal
[2023-03-16 21:45:33,242] [INFO] Task started: HMMsearch
[2023-03-16 21:45:33,242] [INFO] Running command: hmmsearch --tblout OceanDNA-b33070/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga29b1c17-0157-4e1f-bf99-d6535fcb796c/dqc_reference/reference_markers.hmm OceanDNA-b33070/protein.faa > /dev/null
[2023-03-16 21:45:33,443] [INFO] Task succeeded: HMMsearch
[2023-03-16 21:45:33,443] [INFO] Found 6/6 markers.
[2023-03-16 21:45:33,462] [INFO] Query marker FASTA was written to OceanDNA-b33070/markers.fasta
[2023-03-16 21:45:33,462] [INFO] Task started: Blastn
[2023-03-16 21:45:33,462] [INFO] Running command: blastn -query OceanDNA-b33070/markers.fasta -db /var/lib/cwl/stga29b1c17-0157-4e1f-bf99-d6535fcb796c/dqc_reference/reference_markers.fasta -out OceanDNA-b33070/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 21:45:34,033] [INFO] Task succeeded: Blastn
[2023-03-16 21:45:34,034] [INFO] Selected 24 target genomes.
[2023-03-16 21:45:34,034] [INFO] Target genome list was writen to OceanDNA-b33070/target_genomes.txt
[2023-03-16 21:45:34,049] [INFO] Task started: fastANI
[2023-03-16 21:45:34,050] [INFO] Running command: fastANI --query /var/lib/cwl/stge530c76e-07a1-410d-ad66-e2b1fc57b99e/OceanDNA-b33070.fa --refList OceanDNA-b33070/target_genomes.txt --output OceanDNA-b33070/fastani_result.tsv --threads 1
[2023-03-16 21:45:51,337] [INFO] Task succeeded: fastANI
[2023-03-16 21:45:51,337] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga29b1c17-0157-4e1f-bf99-d6535fcb796c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 21:45:51,337] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga29b1c17-0157-4e1f-bf99-d6535fcb796c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 21:45:51,337] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 21:45:51,337] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 21:45:51,338] [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
--------------------------------------------------------------------------------
[2023-03-16 21:45:51,338] [INFO] DFAST Taxonomy check result was written to OceanDNA-b33070/tc_result.tsv
[2023-03-16 21:45:51,338] [INFO] ===== Taxonomy check completed =====
[2023-03-16 21:45:51,338] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 21:45:51,338] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga29b1c17-0157-4e1f-bf99-d6535fcb796c/dqc_reference/checkm_data
[2023-03-16 21:45:51,341] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 21:45:51,347] [INFO] Task started: CheckM
[2023-03-16 21:45:51,347] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b33070/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b33070/checkm_input OceanDNA-b33070/checkm_result
[2023-03-16 21:46:37,499] [INFO] Task succeeded: CheckM
[2023-03-16 21:46:37,500] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 21:46:37,502] [INFO] ===== Completeness check finished =====
[2023-03-16 21:46:37,502] [INFO] ===== Start GTDB Search =====
[2023-03-16 21:46:37,502] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b33070/markers.fasta)
[2023-03-16 21:46:37,502] [INFO] Task started: Blastn
[2023-03-16 21:46:37,502] [INFO] Running command: blastn -query OceanDNA-b33070/markers.fasta -db /var/lib/cwl/stga29b1c17-0157-4e1f-bf99-d6535fcb796c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b33070/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 21:46:38,400] [INFO] Task succeeded: Blastn
[2023-03-16 21:46:38,401] [INFO] Selected 21 target genomes.
[2023-03-16 21:46:38,401] [INFO] Target genome list was writen to OceanDNA-b33070/target_genomes_gtdb.txt
[2023-03-16 21:46:38,480] [INFO] Task started: fastANI
[2023-03-16 21:46:38,480] [INFO] Running command: fastANI --query /var/lib/cwl/stge530c76e-07a1-410d-ad66-e2b1fc57b99e/OceanDNA-b33070.fa --refList OceanDNA-b33070/target_genomes_gtdb.txt --output OceanDNA-b33070/fastani_result_gtdb.tsv --threads 1
[2023-03-16 21:46:50,147] [INFO] Task succeeded: fastANI
[2023-03-16 21:46:50,150] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 21:46:50,150] [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_002724395.1	s__GCA-002724395 sp002724395	99.8565	983	999	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA8366;f__UBA8366;g__GCA-002724395	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002715005.1	s__GCA-002724395 sp002715005	92.9677	951	999	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA8366;f__UBA8366;g__GCA-002724395	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002722095.1	s__UBA8366 sp002722095	75.898	84	999	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA8366;f__UBA8366;g__UBA8366	95.0	99.86	99.86	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2023-03-16 21:46:50,150] [INFO] GTDB search result was written to OceanDNA-b33070/result_gtdb.tsv
[2023-03-16 21:46:50,150] [INFO] ===== GTDB Search completed =====
[2023-03-16 21:46:50,151] [INFO] DFAST_QC result json was written to OceanDNA-b33070/dqc_result.json
[2023-03-16 21:46:50,151] [INFO] DFAST_QC completed!
[2023-03-16 21:46:50,151] [INFO] Total running time: 0h1m37s