[2023-03-16 04:05:20,415] [INFO] DFAST_QC pipeline started.
[2023-03-16 04:05:20,415] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 04:05:20,415] [INFO] DQC Reference Directory: /var/lib/cwl/stg074b1d94-3600-47f0-a918-8b5f353ad1d8/dqc_reference
[2023-03-16 04:05:22,126] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 04:05:22,126] [INFO] Task started: Prodigal
[2023-03-16 04:05:22,126] [INFO] Running command: cat /var/lib/cwl/stg49294848-db3e-42f9-b639-42847ce54a09/OceanDNA-b24202.fa | prodigal -d OceanDNA-b24202/cds.fna -a OceanDNA-b24202/protein.faa -g 11 -q > /dev/null
[2023-03-16 04:05:26,805] [INFO] Task succeeded: Prodigal
[2023-03-16 04:05:26,806] [INFO] Task started: HMMsearch
[2023-03-16 04:05:26,806] [INFO] Running command: hmmsearch --tblout OceanDNA-b24202/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg074b1d94-3600-47f0-a918-8b5f353ad1d8/dqc_reference/reference_markers.hmm OceanDNA-b24202/protein.faa > /dev/null
[2023-03-16 04:05:26,962] [INFO] Task succeeded: HMMsearch
[2023-03-16 04:05:26,962] [INFO] Found 6/6 markers.
[2023-03-16 04:05:26,969] [INFO] Query marker FASTA was written to OceanDNA-b24202/markers.fasta
[2023-03-16 04:05:26,970] [INFO] Task started: Blastn
[2023-03-16 04:05:26,970] [INFO] Running command: blastn -query OceanDNA-b24202/markers.fasta -db /var/lib/cwl/stg074b1d94-3600-47f0-a918-8b5f353ad1d8/dqc_reference/reference_markers.fasta -out OceanDNA-b24202/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:05:27,577] [INFO] Task succeeded: Blastn
[2023-03-16 04:05:27,578] [INFO] Selected 20 target genomes.
[2023-03-16 04:05:27,578] [INFO] Target genome list was writen to OceanDNA-b24202/target_genomes.txt
[2023-03-16 04:05:27,588] [INFO] Task started: fastANI
[2023-03-16 04:05:27,588] [INFO] Running command: fastANI --query /var/lib/cwl/stg49294848-db3e-42f9-b639-42847ce54a09/OceanDNA-b24202.fa --refList OceanDNA-b24202/target_genomes.txt --output OceanDNA-b24202/fastani_result.tsv --threads 1
[2023-03-16 04:05:33,256] [INFO] Task succeeded: fastANI
[2023-03-16 04:05:33,256] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg074b1d94-3600-47f0-a918-8b5f353ad1d8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 04:05:33,256] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg074b1d94-3600-47f0-a918-8b5f353ad1d8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 04:05:33,257] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 04:05:33,257] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 04:05:33,257] [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 04:05:33,257] [INFO] DFAST Taxonomy check result was written to OceanDNA-b24202/tc_result.tsv
[2023-03-16 04:05:33,257] [INFO] ===== Taxonomy check completed =====
[2023-03-16 04:05:33,257] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 04:05:33,257] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg074b1d94-3600-47f0-a918-8b5f353ad1d8/dqc_reference/checkm_data
[2023-03-16 04:05:33,260] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 04:05:33,262] [INFO] Task started: CheckM
[2023-03-16 04:05:33,262] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b24202/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b24202/checkm_input OceanDNA-b24202/checkm_result
[2023-03-16 04:05:50,918] [INFO] Task succeeded: CheckM
[2023-03-16 04:05:50,918] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 04:05:50,919] [INFO] ===== Completeness check finished =====
[2023-03-16 04:05:50,920] [INFO] ===== Start GTDB Search =====
[2023-03-16 04:05:50,920] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b24202/markers.fasta)
[2023-03-16 04:05:50,920] [INFO] Task started: Blastn
[2023-03-16 04:05:50,920] [INFO] Running command: blastn -query OceanDNA-b24202/markers.fasta -db /var/lib/cwl/stg074b1d94-3600-47f0-a918-8b5f353ad1d8/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b24202/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:05:51,639] [INFO] Task succeeded: Blastn
[2023-03-16 04:05:51,640] [INFO] Selected 16 target genomes.
[2023-03-16 04:05:51,640] [INFO] Target genome list was writen to OceanDNA-b24202/target_genomes_gtdb.txt
[2023-03-16 04:05:51,689] [INFO] Task started: fastANI
[2023-03-16 04:05:51,689] [INFO] Running command: fastANI --query /var/lib/cwl/stg49294848-db3e-42f9-b639-42847ce54a09/OceanDNA-b24202.fa --refList OceanDNA-b24202/target_genomes_gtdb.txt --output OceanDNA-b24202/fastani_result_gtdb.tsv --threads 1
[2023-03-16 04:05:54,703] [INFO] Task succeeded: fastANI
[2023-03-16 04:05:54,707] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 04:05:54,707] [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_902607475.1	s__GCA-002720895 sp902607475	94.1037	180	265	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__GCA-002720895;f__GCA-002720895;g__GCA-002720895	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002711715.1	s__GCA-002720895 sp002711715	86.3667	111	265	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__GCA-002720895;f__GCA-002720895;g__GCA-002720895	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002717245.1	s__GCA-002720895 sp002717245	81.0596	209	265	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__GCA-002720895;f__GCA-002720895;g__GCA-002720895	95.0	99.29	99.29	0.96	0.96	2	-
GCA_002937775.1	s__GCA-002720895 sp002937775	80.6679	163	265	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__GCA-002720895;f__GCA-002720895;g__GCA-002720895	95.0	99.14	99.14	0.75	0.75	2	-
GCA_002720895.1	s__GCA-002720895 sp002720895	80.1157	128	265	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__GCA-002720895;f__GCA-002720895;g__GCA-002720895	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002937815.1	s__PTKQ01 sp002937815	78.2234	52	265	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__GCA-002720895;f__GCA-002720895;g__PTKQ01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 04:05:54,708] [INFO] GTDB search result was written to OceanDNA-b24202/result_gtdb.tsv
[2023-03-16 04:05:54,708] [INFO] ===== GTDB Search completed =====
[2023-03-16 04:05:54,708] [INFO] DFAST_QC result json was written to OceanDNA-b24202/dqc_result.json
[2023-03-16 04:05:54,708] [INFO] DFAST_QC completed!
[2023-03-16 04:05:54,709] [INFO] Total running time: 0h0m34s