[2023-03-15 03:56:21,767] [INFO] DFAST_QC pipeline started.
[2023-03-15 03:56:21,767] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 03:56:21,767] [INFO] DQC Reference Directory: /var/lib/cwl/stg0eed71b1-7569-4285-bd0c-783ea6936c54/dqc_reference
[2023-03-15 03:56:23,409] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 03:56:23,409] [INFO] Task started: Prodigal
[2023-03-15 03:56:23,409] [INFO] Running command: cat /var/lib/cwl/stg49ccafcf-4ebd-4e51-9753-02cf7a165c78/OceanDNA-b43678.fa | prodigal -d OceanDNA-b43678/cds.fna -a OceanDNA-b43678/protein.faa -g 11 -q > /dev/null
[2023-03-15 03:56:37,910] [INFO] Task succeeded: Prodigal
[2023-03-15 03:56:37,911] [INFO] Task started: HMMsearch
[2023-03-15 03:56:37,911] [INFO] Running command: hmmsearch --tblout OceanDNA-b43678/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0eed71b1-7569-4285-bd0c-783ea6936c54/dqc_reference/reference_markers.hmm OceanDNA-b43678/protein.faa > /dev/null
[2023-03-15 03:56:38,139] [INFO] Task succeeded: HMMsearch
[2023-03-15 03:56:38,139] [INFO] Found 6/6 markers.
[2023-03-15 03:56:38,155] [INFO] Query marker FASTA was written to OceanDNA-b43678/markers.fasta
[2023-03-15 03:56:38,155] [INFO] Task started: Blastn
[2023-03-15 03:56:38,155] [INFO] Running command: blastn -query OceanDNA-b43678/markers.fasta -db /var/lib/cwl/stg0eed71b1-7569-4285-bd0c-783ea6936c54/dqc_reference/reference_markers.fasta -out OceanDNA-b43678/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 03:56:38,735] [INFO] Task succeeded: Blastn
[2023-03-15 03:56:38,736] [INFO] Selected 32 target genomes.
[2023-03-15 03:56:38,737] [INFO] Target genome list was writen to OceanDNA-b43678/target_genomes.txt
[2023-03-15 03:56:38,756] [INFO] Task started: fastANI
[2023-03-15 03:56:38,756] [INFO] Running command: fastANI --query /var/lib/cwl/stg49ccafcf-4ebd-4e51-9753-02cf7a165c78/OceanDNA-b43678.fa --refList OceanDNA-b43678/target_genomes.txt --output OceanDNA-b43678/fastani_result.tsv --threads 1
[2023-03-15 03:56:57,110] [INFO] Task succeeded: fastANI
[2023-03-15 03:56:57,110] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0eed71b1-7569-4285-bd0c-783ea6936c54/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 03:56:57,111] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0eed71b1-7569-4285-bd0c-783ea6936c54/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 03:56:57,111] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 03:56:57,111] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 03:56:57,111] [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 03:56:57,111] [INFO] DFAST Taxonomy check result was written to OceanDNA-b43678/tc_result.tsv
[2023-03-15 03:56:57,111] [INFO] ===== Taxonomy check completed =====
[2023-03-15 03:56:57,111] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 03:56:57,111] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0eed71b1-7569-4285-bd0c-783ea6936c54/dqc_reference/checkm_data
[2023-03-15 03:56:57,114] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 03:56:57,189] [INFO] Task started: CheckM
[2023-03-15 03:56:57,189] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b43678/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b43678/checkm_input OceanDNA-b43678/checkm_result
[2023-03-15 03:57:36,394] [INFO] Task succeeded: CheckM
[2023-03-15 03:57:36,394] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 03:57:36,397] [INFO] ===== Completeness check finished =====
[2023-03-15 03:57:36,397] [INFO] ===== Start GTDB Search =====
[2023-03-15 03:57:36,398] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b43678/markers.fasta)
[2023-03-15 03:57:36,399] [INFO] Task started: Blastn
[2023-03-15 03:57:36,399] [INFO] Running command: blastn -query OceanDNA-b43678/markers.fasta -db /var/lib/cwl/stg0eed71b1-7569-4285-bd0c-783ea6936c54/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b43678/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 03:57:37,341] [INFO] Task succeeded: Blastn
[2023-03-15 03:57:37,342] [INFO] Selected 24 target genomes.
[2023-03-15 03:57:37,342] [INFO] Target genome list was writen to OceanDNA-b43678/target_genomes_gtdb.txt
[2023-03-15 03:57:37,371] [INFO] Task started: fastANI
[2023-03-15 03:57:37,371] [INFO] Running command: fastANI --query /var/lib/cwl/stg49ccafcf-4ebd-4e51-9753-02cf7a165c78/OceanDNA-b43678.fa --refList OceanDNA-b43678/target_genomes_gtdb.txt --output OceanDNA-b43678/fastani_result_gtdb.tsv --threads 1
[2023-03-15 03:57:49,499] [INFO] Task succeeded: fastANI
[2023-03-15 03:57:49,502] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 03:57:49,502] [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_002714255.1	s__UBA11791 sp002714255	97.5322	472	778	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Arenicellales;f__UBA868;g__UBA11791	95.0	98.20	98.17	0.64	0.59	4	conclusive
GCA_012960345.1	s__UBA11791 sp012960345	93.7957	661	778	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Arenicellales;f__UBA868;g__UBA11791	95.0	99.31	99.31	0.83	0.83	2	-
GCA_905612355.1	s__UBA11791 sp905612355	93.3285	375	778	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Arenicellales;f__UBA868;g__UBA11791	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 03:57:49,503] [INFO] GTDB search result was written to OceanDNA-b43678/result_gtdb.tsv
[2023-03-15 03:57:49,503] [INFO] ===== GTDB Search completed =====
[2023-03-15 03:57:49,503] [INFO] DFAST_QC result json was written to OceanDNA-b43678/dqc_result.json
[2023-03-15 03:57:49,503] [INFO] DFAST_QC completed!
[2023-03-15 03:57:49,503] [INFO] Total running time: 0h1m28s