[2023-03-16 06:46:39,284] [INFO] DFAST_QC pipeline started.
[2023-03-16 06:46:39,284] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 06:46:39,284] [INFO] DQC Reference Directory: /var/lib/cwl/stg770b6f6c-b7ad-4453-9e1b-f093ca0b01d3/dqc_reference
[2023-03-16 06:46:40,377] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 06:46:40,377] [INFO] Task started: Prodigal
[2023-03-16 06:46:40,377] [INFO] Running command: cat /var/lib/cwl/stg268ae068-0530-4b5a-a8e6-55aa2f278cdb/OceanDNA-b10448.fa | prodigal -d OceanDNA-b10448/cds.fna -a OceanDNA-b10448/protein.faa -g 11 -q > /dev/null
[2023-03-16 06:46:50,786] [INFO] Task succeeded: Prodigal
[2023-03-16 06:46:50,786] [INFO] Task started: HMMsearch
[2023-03-16 06:46:50,786] [INFO] Running command: hmmsearch --tblout OceanDNA-b10448/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg770b6f6c-b7ad-4453-9e1b-f093ca0b01d3/dqc_reference/reference_markers.hmm OceanDNA-b10448/protein.faa > /dev/null
[2023-03-16 06:46:50,934] [INFO] Task succeeded: HMMsearch
[2023-03-16 06:46:50,935] [INFO] Found 6/6 markers.
[2023-03-16 06:46:50,947] [INFO] Query marker FASTA was written to OceanDNA-b10448/markers.fasta
[2023-03-16 06:46:50,948] [INFO] Task started: Blastn
[2023-03-16 06:46:50,948] [INFO] Running command: blastn -query OceanDNA-b10448/markers.fasta -db /var/lib/cwl/stg770b6f6c-b7ad-4453-9e1b-f093ca0b01d3/dqc_reference/reference_markers.fasta -out OceanDNA-b10448/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 06:46:51,483] [INFO] Task succeeded: Blastn
[2023-03-16 06:46:51,484] [INFO] Selected 30 target genomes.
[2023-03-16 06:46:51,484] [INFO] Target genome list was writen to OceanDNA-b10448/target_genomes.txt
[2023-03-16 06:46:51,659] [INFO] Task started: fastANI
[2023-03-16 06:46:51,659] [INFO] Running command: fastANI --query /var/lib/cwl/stg268ae068-0530-4b5a-a8e6-55aa2f278cdb/OceanDNA-b10448.fa --refList OceanDNA-b10448/target_genomes.txt --output OceanDNA-b10448/fastani_result.tsv --threads 1
[2023-03-16 06:47:06,540] [INFO] Task succeeded: fastANI
[2023-03-16 06:47:06,540] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg770b6f6c-b7ad-4453-9e1b-f093ca0b01d3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 06:47:06,540] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg770b6f6c-b7ad-4453-9e1b-f093ca0b01d3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 06:47:06,541] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 06:47:06,541] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 06:47:06,541] [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 06:47:06,541] [INFO] DFAST Taxonomy check result was written to OceanDNA-b10448/tc_result.tsv
[2023-03-16 06:47:06,541] [INFO] ===== Taxonomy check completed =====
[2023-03-16 06:47:06,541] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 06:47:06,541] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg770b6f6c-b7ad-4453-9e1b-f093ca0b01d3/dqc_reference/checkm_data
[2023-03-16 06:47:06,544] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 06:47:06,547] [INFO] Task started: CheckM
[2023-03-16 06:47:06,547] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b10448/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b10448/checkm_input OceanDNA-b10448/checkm_result
[2023-03-16 06:47:36,805] [INFO] Task succeeded: CheckM
[2023-03-16 06:47:36,805] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 88.76%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 06:47:36,807] [INFO] ===== Completeness check finished =====
[2023-03-16 06:47:36,807] [INFO] ===== Start GTDB Search =====
[2023-03-16 06:47:36,807] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b10448/markers.fasta)
[2023-03-16 06:47:36,808] [INFO] Task started: Blastn
[2023-03-16 06:47:36,808] [INFO] Running command: blastn -query OceanDNA-b10448/markers.fasta -db /var/lib/cwl/stg770b6f6c-b7ad-4453-9e1b-f093ca0b01d3/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b10448/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 06:47:37,555] [INFO] Task succeeded: Blastn
[2023-03-16 06:47:37,556] [INFO] Selected 22 target genomes.
[2023-03-16 06:47:37,556] [INFO] Target genome list was writen to OceanDNA-b10448/target_genomes_gtdb.txt
[2023-03-16 06:47:37,678] [INFO] Task started: fastANI
[2023-03-16 06:47:37,678] [INFO] Running command: fastANI --query /var/lib/cwl/stg268ae068-0530-4b5a-a8e6-55aa2f278cdb/OceanDNA-b10448.fa --refList OceanDNA-b10448/target_genomes_gtdb.txt --output OceanDNA-b10448/fastani_result_gtdb.tsv --threads 1
[2023-03-16 06:47:47,711] [INFO] Task succeeded: fastANI
[2023-03-16 06:47:47,714] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 06:47:47,714] [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_011526365.1	s__RFYP01 sp011526365	97.6733	400	420	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__RFYP01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_017852395.1	s__RFYP01 sp017852395	76.2912	66	420	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__RFYP01	95.0	99.71	99.66	0.94	0.93	4	-
--------------------------------------------------------------------------------
[2023-03-16 06:47:47,714] [INFO] GTDB search result was written to OceanDNA-b10448/result_gtdb.tsv
[2023-03-16 06:47:47,714] [INFO] ===== GTDB Search completed =====
[2023-03-16 06:47:47,715] [INFO] DFAST_QC result json was written to OceanDNA-b10448/dqc_result.json
[2023-03-16 06:47:47,715] [INFO] DFAST_QC completed!
[2023-03-16 06:47:47,715] [INFO] Total running time: 0h1m8s