[2023-03-16 00:50:05,234] [INFO] DFAST_QC pipeline started.
[2023-03-16 00:50:05,240] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 00:50:05,241] [INFO] DQC Reference Directory: /var/lib/cwl/stgb45ac8cc-ebdb-4108-9eee-27012b9e1cd9/dqc_reference
[2023-03-16 00:50:06,326] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 00:50:06,327] [INFO] Task started: Prodigal
[2023-03-16 00:50:06,327] [INFO] Running command: cat /var/lib/cwl/stg7c5aa9c1-8a3f-4106-ac92-b7d3e71f6ab8/OceanDNA-b31318.fa | prodigal -d OceanDNA-b31318/cds.fna -a OceanDNA-b31318/protein.faa -g 11 -q > /dev/null
[2023-03-16 00:50:11,027] [INFO] Task succeeded: Prodigal
[2023-03-16 00:50:11,027] [INFO] Task started: HMMsearch
[2023-03-16 00:50:11,027] [INFO] Running command: hmmsearch --tblout OceanDNA-b31318/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb45ac8cc-ebdb-4108-9eee-27012b9e1cd9/dqc_reference/reference_markers.hmm OceanDNA-b31318/protein.faa > /dev/null
[2023-03-16 00:50:11,189] [INFO] Task succeeded: HMMsearch
[2023-03-16 00:50:11,190] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg7c5aa9c1-8a3f-4106-ac92-b7d3e71f6ab8/OceanDNA-b31318.fa]
[2023-03-16 00:50:11,205] [INFO] Query marker FASTA was written to OceanDNA-b31318/markers.fasta
[2023-03-16 00:50:11,207] [INFO] Task started: Blastn
[2023-03-16 00:50:11,207] [INFO] Running command: blastn -query OceanDNA-b31318/markers.fasta -db /var/lib/cwl/stgb45ac8cc-ebdb-4108-9eee-27012b9e1cd9/dqc_reference/reference_markers.fasta -out OceanDNA-b31318/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 00:50:11,769] [INFO] Task succeeded: Blastn
[2023-03-16 00:50:11,780] [INFO] Selected 13 target genomes.
[2023-03-16 00:50:11,781] [INFO] Target genome list was writen to OceanDNA-b31318/target_genomes.txt
[2023-03-16 00:50:11,788] [INFO] Task started: fastANI
[2023-03-16 00:50:11,788] [INFO] Running command: fastANI --query /var/lib/cwl/stg7c5aa9c1-8a3f-4106-ac92-b7d3e71f6ab8/OceanDNA-b31318.fa --refList OceanDNA-b31318/target_genomes.txt --output OceanDNA-b31318/fastani_result.tsv --threads 1
[2023-03-16 00:50:17,362] [INFO] Task succeeded: fastANI
[2023-03-16 00:50:17,362] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb45ac8cc-ebdb-4108-9eee-27012b9e1cd9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 00:50:17,363] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb45ac8cc-ebdb-4108-9eee-27012b9e1cd9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 00:50:17,363] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 00:50:17,363] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 00:50:17,363] [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 00:50:17,365] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31318/tc_result.tsv
[2023-03-16 00:50:17,367] [INFO] ===== Taxonomy check completed =====
[2023-03-16 00:50:17,367] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 00:50:17,368] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb45ac8cc-ebdb-4108-9eee-27012b9e1cd9/dqc_reference/checkm_data
[2023-03-16 00:50:17,378] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 00:50:17,391] [INFO] Task started: CheckM
[2023-03-16 00:50:17,391] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31318/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31318/checkm_input OceanDNA-b31318/checkm_result
[2023-03-16 00:50:37,831] [INFO] Task succeeded: CheckM
[2023-03-16 00:50:37,832] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 82.58%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 00:50:37,940] [INFO] ===== Completeness check finished =====
[2023-03-16 00:50:37,940] [INFO] ===== Start GTDB Search =====
[2023-03-16 00:50:37,941] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31318/markers.fasta)
[2023-03-16 00:50:37,943] [INFO] Task started: Blastn
[2023-03-16 00:50:37,943] [INFO] Running command: blastn -query OceanDNA-b31318/markers.fasta -db /var/lib/cwl/stgb45ac8cc-ebdb-4108-9eee-27012b9e1cd9/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31318/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 00:50:39,001] [INFO] Task succeeded: Blastn
[2023-03-16 00:50:39,006] [INFO] Selected 16 target genomes.
[2023-03-16 00:50:39,006] [INFO] Target genome list was writen to OceanDNA-b31318/target_genomes_gtdb.txt
[2023-03-16 00:50:39,021] [INFO] Task started: fastANI
[2023-03-16 00:50:39,021] [INFO] Running command: fastANI --query /var/lib/cwl/stg7c5aa9c1-8a3f-4106-ac92-b7d3e71f6ab8/OceanDNA-b31318.fa --refList OceanDNA-b31318/target_genomes_gtdb.txt --output OceanDNA-b31318/fastani_result_gtdb.tsv --threads 1
[2023-03-16 00:50:42,610] [INFO] Task succeeded: fastANI
[2023-03-16 00:50:42,613] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 00:50:42,613] [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_018659145.1	s__JADHOX01 sp018659145	99.7192	198	205	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__JABIRX01;g__JADHOX01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018659605.1	s__JADHOX01 sp018659605	79.3163	95	205	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__JABIRX01;g__JADHOX01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 00:50:42,626] [INFO] GTDB search result was written to OceanDNA-b31318/result_gtdb.tsv
[2023-03-16 00:50:42,646] [INFO] ===== GTDB Search completed =====
[2023-03-16 00:50:42,659] [INFO] DFAST_QC result json was written to OceanDNA-b31318/dqc_result.json
[2023-03-16 00:50:42,659] [INFO] DFAST_QC completed!
[2023-03-16 00:50:42,660] [INFO] Total running time: 0h0m37s