[2023-03-19 01:50:01,865] [INFO] DFAST_QC pipeline started.
[2023-03-19 01:50:01,865] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 01:50:01,866] [INFO] DQC Reference Directory: /var/lib/cwl/stg28ab41c3-9c14-470a-9a80-60336877678c/dqc_reference
[2023-03-19 01:50:03,564] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 01:50:03,564] [INFO] Task started: Prodigal
[2023-03-19 01:50:03,564] [INFO] Running command: cat /var/lib/cwl/stgbda927e7-12b8-43d4-af02-a3555139e65f/OceanDNA-b31343.fa | prodigal -d OceanDNA-b31343/cds.fna -a OceanDNA-b31343/protein.faa -g 11 -q > /dev/null
[2023-03-19 01:50:12,939] [INFO] Task succeeded: Prodigal
[2023-03-19 01:50:12,939] [INFO] Task started: HMMsearch
[2023-03-19 01:50:12,939] [INFO] Running command: hmmsearch --tblout OceanDNA-b31343/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg28ab41c3-9c14-470a-9a80-60336877678c/dqc_reference/reference_markers.hmm OceanDNA-b31343/protein.faa > /dev/null
[2023-03-19 01:50:13,103] [INFO] Task succeeded: HMMsearch
[2023-03-19 01:50:13,104] [INFO] Found 6/6 markers.
[2023-03-19 01:50:13,114] [INFO] Query marker FASTA was written to OceanDNA-b31343/markers.fasta
[2023-03-19 01:50:13,115] [INFO] Task started: Blastn
[2023-03-19 01:50:13,115] [INFO] Running command: blastn -query OceanDNA-b31343/markers.fasta -db /var/lib/cwl/stg28ab41c3-9c14-470a-9a80-60336877678c/dqc_reference/reference_markers.fasta -out OceanDNA-b31343/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:50:13,626] [INFO] Task succeeded: Blastn
[2023-03-19 01:50:13,627] [INFO] Selected 25 target genomes.
[2023-03-19 01:50:13,627] [INFO] Target genome list was writen to OceanDNA-b31343/target_genomes.txt
[2023-03-19 01:50:13,643] [INFO] Task started: fastANI
[2023-03-19 01:50:13,643] [INFO] Running command: fastANI --query /var/lib/cwl/stgbda927e7-12b8-43d4-af02-a3555139e65f/OceanDNA-b31343.fa --refList OceanDNA-b31343/target_genomes.txt --output OceanDNA-b31343/fastani_result.tsv --threads 1
[2023-03-19 01:50:25,166] [INFO] Task succeeded: fastANI
[2023-03-19 01:50:25,166] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg28ab41c3-9c14-470a-9a80-60336877678c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 01:50:25,167] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg28ab41c3-9c14-470a-9a80-60336877678c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 01:50:25,167] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 01:50:25,167] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 01:50:25,167] [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
--------------------------------------------------------------------------------
[2023-03-19 01:50:25,167] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31343/tc_result.tsv
[2023-03-19 01:50:25,167] [INFO] ===== Taxonomy check completed =====
[2023-03-19 01:50:25,167] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 01:50:25,167] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg28ab41c3-9c14-470a-9a80-60336877678c/dqc_reference/checkm_data
[2023-03-19 01:50:25,170] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 01:50:25,182] [INFO] Task started: CheckM
[2023-03-19 01:50:25,182] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31343/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31343/checkm_input OceanDNA-b31343/checkm_result
[2023-03-19 01:50:53,038] [INFO] Task succeeded: CheckM
[2023-03-19 01:50:53,039] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 01:50:53,071] [INFO] ===== Completeness check finished =====
[2023-03-19 01:50:53,072] [INFO] ===== Start GTDB Search =====
[2023-03-19 01:50:53,072] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31343/markers.fasta)
[2023-03-19 01:50:53,073] [INFO] Task started: Blastn
[2023-03-19 01:50:53,073] [INFO] Running command: blastn -query OceanDNA-b31343/markers.fasta -db /var/lib/cwl/stg28ab41c3-9c14-470a-9a80-60336877678c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31343/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:50:53,804] [INFO] Task succeeded: Blastn
[2023-03-19 01:50:53,805] [INFO] Selected 22 target genomes.
[2023-03-19 01:50:53,805] [INFO] Target genome list was writen to OceanDNA-b31343/target_genomes_gtdb.txt
[2023-03-19 01:50:53,818] [INFO] Task started: fastANI
[2023-03-19 01:50:53,818] [INFO] Running command: fastANI --query /var/lib/cwl/stgbda927e7-12b8-43d4-af02-a3555139e65f/OceanDNA-b31343.fa --refList OceanDNA-b31343/target_genomes_gtdb.txt --output OceanDNA-b31343/fastani_result_gtdb.tsv --threads 1
[2023-03-19 01:50:59,224] [INFO] Task succeeded: fastANI
[2023-03-19 01:50:59,227] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 01:50:59,227] [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_016778745.1	s__JADHOZ01 sp016778745	78.257	164	483	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__UBA1997;g__JADHOZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018969185.1	s__UBA2645 sp018969185	76.2648	52	483	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__UBA1997;g__UBA2645	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 01:50:59,227] [INFO] GTDB search result was written to OceanDNA-b31343/result_gtdb.tsv
[2023-03-19 01:50:59,227] [INFO] ===== GTDB Search completed =====
[2023-03-19 01:50:59,228] [INFO] DFAST_QC result json was written to OceanDNA-b31343/dqc_result.json
[2023-03-19 01:50:59,228] [INFO] DFAST_QC completed!
[2023-03-19 01:50:59,228] [INFO] Total running time: 0h0m57s