[2023-03-17 11:52:51,140] [INFO] DFAST_QC pipeline started.
[2023-03-17 11:52:51,144] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 11:52:51,144] [INFO] DQC Reference Directory: /var/lib/cwl/stgd207aead-21f5-4bd8-a83e-df8d296c44ff/dqc_reference
[2023-03-17 11:52:52,827] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 11:52:52,828] [INFO] Task started: Prodigal
[2023-03-17 11:52:52,828] [INFO] Running command: cat /var/lib/cwl/stg568bd45a-8bbd-473c-9876-724f10a0dd44/OceanDNA-b35665.fa | prodigal -d OceanDNA-b35665/cds.fna -a OceanDNA-b35665/protein.faa -g 11 -q > /dev/null
[2023-03-17 11:52:56,796] [INFO] Task succeeded: Prodigal
[2023-03-17 11:52:56,797] [INFO] Task started: HMMsearch
[2023-03-17 11:52:56,797] [INFO] Running command: hmmsearch --tblout OceanDNA-b35665/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd207aead-21f5-4bd8-a83e-df8d296c44ff/dqc_reference/reference_markers.hmm OceanDNA-b35665/protein.faa > /dev/null
[2023-03-17 11:52:57,000] [INFO] Task succeeded: HMMsearch
[2023-03-17 11:52:57,001] [INFO] Found 6/6 markers.
[2023-03-17 11:52:57,040] [INFO] Query marker FASTA was written to OceanDNA-b35665/markers.fasta
[2023-03-17 11:52:57,042] [INFO] Task started: Blastn
[2023-03-17 11:52:57,042] [INFO] Running command: blastn -query OceanDNA-b35665/markers.fasta -db /var/lib/cwl/stgd207aead-21f5-4bd8-a83e-df8d296c44ff/dqc_reference/reference_markers.fasta -out OceanDNA-b35665/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:52:57,806] [INFO] Task succeeded: Blastn
[2023-03-17 11:52:57,830] [INFO] Selected 20 target genomes.
[2023-03-17 11:52:57,830] [INFO] Target genome list was writen to OceanDNA-b35665/target_genomes.txt
[2023-03-17 11:52:57,846] [INFO] Task started: fastANI
[2023-03-17 11:52:57,846] [INFO] Running command: fastANI --query /var/lib/cwl/stg568bd45a-8bbd-473c-9876-724f10a0dd44/OceanDNA-b35665.fa --refList OceanDNA-b35665/target_genomes.txt --output OceanDNA-b35665/fastani_result.tsv --threads 1
[2023-03-17 11:53:07,888] [INFO] Task succeeded: fastANI
[2023-03-17 11:53:07,889] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd207aead-21f5-4bd8-a83e-df8d296c44ff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 11:53:07,889] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd207aead-21f5-4bd8-a83e-df8d296c44ff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 11:53:07,889] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 11:53:07,889] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 11:53:07,889] [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 11:53:07,897] [INFO] DFAST Taxonomy check result was written to OceanDNA-b35665/tc_result.tsv
[2023-03-17 11:53:07,918] [INFO] ===== Taxonomy check completed =====
[2023-03-17 11:53:07,918] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 11:53:07,918] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd207aead-21f5-4bd8-a83e-df8d296c44ff/dqc_reference/checkm_data
[2023-03-17 11:53:07,969] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 11:53:08,123] [INFO] Task started: CheckM
[2023-03-17 11:53:08,123] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b35665/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b35665/checkm_input OceanDNA-b35665/checkm_result
[2023-03-17 11:53:28,772] [INFO] Task succeeded: CheckM
[2023-03-17 11:53:28,772] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 11:53:28,879] [INFO] ===== Completeness check finished =====
[2023-03-17 11:53:28,879] [INFO] ===== Start GTDB Search =====
[2023-03-17 11:53:28,879] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b35665/markers.fasta)
[2023-03-17 11:53:28,881] [INFO] Task started: Blastn
[2023-03-17 11:53:28,881] [INFO] Running command: blastn -query OceanDNA-b35665/markers.fasta -db /var/lib/cwl/stgd207aead-21f5-4bd8-a83e-df8d296c44ff/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b35665/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:53:30,071] [INFO] Task succeeded: Blastn
[2023-03-17 11:53:30,096] [INFO] Selected 28 target genomes.
[2023-03-17 11:53:30,096] [INFO] Target genome list was writen to OceanDNA-b35665/target_genomes_gtdb.txt
[2023-03-17 11:53:30,129] [INFO] Task started: fastANI
[2023-03-17 11:53:30,129] [INFO] Running command: fastANI --query /var/lib/cwl/stg568bd45a-8bbd-473c-9876-724f10a0dd44/OceanDNA-b35665.fa --refList OceanDNA-b35665/target_genomes_gtdb.txt --output OceanDNA-b35665/fastani_result_gtdb.tsv --threads 1
[2023-03-17 11:53:36,820] [INFO] Task succeeded: fastANI
[2023-03-17 11:53:36,823] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 11:53:36,823] [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_902628335.1	s__GCA-2720195 sp902628335	81.9289	147	242	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__GCA-002705445;f__GCA-002716945;g__GCA-2720195	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902632305.1	s__GCA-2720195 sp902632305	76.8866	54	242	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__GCA-002705445;f__GCA-002716945;g__GCA-2720195	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 11:53:36,828] [INFO] GTDB search result was written to OceanDNA-b35665/result_gtdb.tsv
[2023-03-17 11:53:36,838] [INFO] ===== GTDB Search completed =====
[2023-03-17 11:53:36,845] [INFO] DFAST_QC result json was written to OceanDNA-b35665/dqc_result.json
[2023-03-17 11:53:36,845] [INFO] DFAST_QC completed!
[2023-03-17 11:53:36,845] [INFO] Total running time: 0h0m46s