[2023-03-17 04:48:53,968] [INFO] DFAST_QC pipeline started.
[2023-03-17 04:48:53,968] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 04:48:53,968] [INFO] DQC Reference Directory: /var/lib/cwl/stge836340b-d761-4ec8-acea-699a066f9014/dqc_reference
[2023-03-17 04:48:55,155] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 04:48:55,155] [INFO] Task started: Prodigal
[2023-03-17 04:48:55,156] [INFO] Running command: cat /var/lib/cwl/stg4daa316f-1675-4d72-bcbe-4e970748cb67/OceanDNA-b26068.fa | prodigal -d OceanDNA-b26068/cds.fna -a OceanDNA-b26068/protein.faa -g 11 -q > /dev/null
[2023-03-17 04:49:01,645] [INFO] Task succeeded: Prodigal
[2023-03-17 04:49:01,645] [INFO] Task started: HMMsearch
[2023-03-17 04:49:01,645] [INFO] Running command: hmmsearch --tblout OceanDNA-b26068/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge836340b-d761-4ec8-acea-699a066f9014/dqc_reference/reference_markers.hmm OceanDNA-b26068/protein.faa > /dev/null
[2023-03-17 04:49:01,805] [INFO] Task succeeded: HMMsearch
[2023-03-17 04:49:01,806] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg4daa316f-1675-4d72-bcbe-4e970748cb67/OceanDNA-b26068.fa]
[2023-03-17 04:49:01,818] [INFO] Query marker FASTA was written to OceanDNA-b26068/markers.fasta
[2023-03-17 04:49:01,819] [INFO] Task started: Blastn
[2023-03-17 04:49:01,819] [INFO] Running command: blastn -query OceanDNA-b26068/markers.fasta -db /var/lib/cwl/stge836340b-d761-4ec8-acea-699a066f9014/dqc_reference/reference_markers.fasta -out OceanDNA-b26068/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 04:49:02,334] [INFO] Task succeeded: Blastn
[2023-03-17 04:49:02,335] [INFO] Selected 17 target genomes.
[2023-03-17 04:49:02,335] [INFO] Target genome list was writen to OceanDNA-b26068/target_genomes.txt
[2023-03-17 04:49:02,344] [INFO] Task started: fastANI
[2023-03-17 04:49:02,344] [INFO] Running command: fastANI --query /var/lib/cwl/stg4daa316f-1675-4d72-bcbe-4e970748cb67/OceanDNA-b26068.fa --refList OceanDNA-b26068/target_genomes.txt --output OceanDNA-b26068/fastani_result.tsv --threads 1
[2023-03-17 04:49:09,665] [INFO] Task succeeded: fastANI
[2023-03-17 04:49:09,666] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge836340b-d761-4ec8-acea-699a066f9014/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 04:49:09,666] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge836340b-d761-4ec8-acea-699a066f9014/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 04:49:09,666] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 04:49:09,666] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 04:49:09,666] [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
--------------------------------------------------------------------------------
[2023-03-17 04:49:09,666] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26068/tc_result.tsv
[2023-03-17 04:49:09,666] [INFO] ===== Taxonomy check completed =====
[2023-03-17 04:49:09,667] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 04:49:09,667] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge836340b-d761-4ec8-acea-699a066f9014/dqc_reference/checkm_data
[2023-03-17 04:49:09,669] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 04:49:09,672] [INFO] Task started: CheckM
[2023-03-17 04:49:09,672] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26068/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26068/checkm_input OceanDNA-b26068/checkm_result
[2023-03-17 04:49:31,251] [INFO] Task succeeded: CheckM
[2023-03-17 04:49:31,251] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 77.77%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 04:49:31,253] [INFO] ===== Completeness check finished =====
[2023-03-17 04:49:31,253] [INFO] ===== Start GTDB Search =====
[2023-03-17 04:49:31,253] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26068/markers.fasta)
[2023-03-17 04:49:31,253] [INFO] Task started: Blastn
[2023-03-17 04:49:31,253] [INFO] Running command: blastn -query OceanDNA-b26068/markers.fasta -db /var/lib/cwl/stge836340b-d761-4ec8-acea-699a066f9014/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26068/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 04:49:32,024] [INFO] Task succeeded: Blastn
[2023-03-17 04:49:32,025] [INFO] Selected 19 target genomes.
[2023-03-17 04:49:32,025] [INFO] Target genome list was writen to OceanDNA-b26068/target_genomes_gtdb.txt
[2023-03-17 04:49:32,382] [INFO] Task started: fastANI
[2023-03-17 04:49:32,382] [INFO] Running command: fastANI --query /var/lib/cwl/stg4daa316f-1675-4d72-bcbe-4e970748cb67/OceanDNA-b26068.fa --refList OceanDNA-b26068/target_genomes_gtdb.txt --output OceanDNA-b26068/fastani_result_gtdb.tsv --threads 1
[2023-03-17 04:49:37,180] [INFO] Task succeeded: fastANI
[2023-03-17 04:49:37,183] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 04:49:37,183] [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_902612965.1	s__GCA-002684695 sp902612965	95.9482	336	384	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__GCA-002684695;g__GCA-002684695	95.0	96.38	96.38	0.79	0.79	2	conclusive
GCA_902539295.1	s__GCA-002684695 sp902539295	94.3398	303	384	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__GCA-002684695;g__GCA-002684695	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002684695.1	s__GCA-002684695 sp002684695	77.2773	122	384	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__GCA-002684695;g__GCA-002684695	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902532475.1	s__GCA-002684695 sp902532475	76.8422	67	384	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__GCA-002684695;g__GCA-002684695	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 04:49:37,183] [INFO] GTDB search result was written to OceanDNA-b26068/result_gtdb.tsv
[2023-03-17 04:49:37,183] [INFO] ===== GTDB Search completed =====
[2023-03-17 04:49:37,184] [INFO] DFAST_QC result json was written to OceanDNA-b26068/dqc_result.json
[2023-03-17 04:49:37,184] [INFO] DFAST_QC completed!
[2023-03-17 04:49:37,184] [INFO] Total running time: 0h0m43s