[2023-03-15 12:06:59,417] [INFO] DFAST_QC pipeline started.
[2023-03-15 12:06:59,424] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 12:06:59,424] [INFO] DQC Reference Directory: /var/lib/cwl/stg852f9da8-52c9-4146-9ab7-d397e71089e5/dqc_reference
[2023-03-15 12:07:00,566] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 12:07:00,567] [INFO] Task started: Prodigal
[2023-03-15 12:07:00,567] [INFO] Running command: cat /var/lib/cwl/stgc4e0e6ee-0a65-4623-b014-6b1acfba962b/OceanDNA-b28313.fa | prodigal -d OceanDNA-b28313/cds.fna -a OceanDNA-b28313/protein.faa -g 11 -q > /dev/null
[2023-03-15 12:07:09,290] [INFO] Task succeeded: Prodigal
[2023-03-15 12:07:09,290] [INFO] Task started: HMMsearch
[2023-03-15 12:07:09,291] [INFO] Running command: hmmsearch --tblout OceanDNA-b28313/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg852f9da8-52c9-4146-9ab7-d397e71089e5/dqc_reference/reference_markers.hmm OceanDNA-b28313/protein.faa > /dev/null
[2023-03-15 12:07:09,476] [INFO] Task succeeded: HMMsearch
[2023-03-15 12:07:09,477] [INFO] Found 6/6 markers.
[2023-03-15 12:07:09,546] [INFO] Query marker FASTA was written to OceanDNA-b28313/markers.fasta
[2023-03-15 12:07:09,547] [INFO] Task started: Blastn
[2023-03-15 12:07:09,547] [INFO] Running command: blastn -query OceanDNA-b28313/markers.fasta -db /var/lib/cwl/stg852f9da8-52c9-4146-9ab7-d397e71089e5/dqc_reference/reference_markers.fasta -out OceanDNA-b28313/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 12:07:10,105] [INFO] Task succeeded: Blastn
[2023-03-15 12:07:10,126] [INFO] Selected 10 target genomes.
[2023-03-15 12:07:10,126] [INFO] Target genome list was writen to OceanDNA-b28313/target_genomes.txt
[2023-03-15 12:07:10,130] [INFO] Task started: fastANI
[2023-03-15 12:07:10,131] [INFO] Running command: fastANI --query /var/lib/cwl/stgc4e0e6ee-0a65-4623-b014-6b1acfba962b/OceanDNA-b28313.fa --refList OceanDNA-b28313/target_genomes.txt --output OceanDNA-b28313/fastani_result.tsv --threads 1
[2023-03-15 12:07:14,596] [INFO] Task succeeded: fastANI
[2023-03-15 12:07:14,596] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg852f9da8-52c9-4146-9ab7-d397e71089e5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 12:07:14,597] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg852f9da8-52c9-4146-9ab7-d397e71089e5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 12:07:14,597] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 12:07:14,597] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 12:07:14,597] [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
--------------------------------------------------------------------------------
[2023-03-15 12:07:14,607] [INFO] DFAST Taxonomy check result was written to OceanDNA-b28313/tc_result.tsv
[2023-03-15 12:07:14,621] [INFO] ===== Taxonomy check completed =====
[2023-03-15 12:07:14,621] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 12:07:14,621] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg852f9da8-52c9-4146-9ab7-d397e71089e5/dqc_reference/checkm_data
[2023-03-15 12:07:14,624] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 12:07:14,628] [INFO] Task started: CheckM
[2023-03-15 12:07:14,628] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b28313/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b28313/checkm_input OceanDNA-b28313/checkm_result
[2023-03-15 12:07:41,318] [INFO] Task succeeded: CheckM
[2023-03-15 12:07:41,319] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.52%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 12:07:41,335] [INFO] ===== Completeness check finished =====
[2023-03-15 12:07:41,335] [INFO] ===== Start GTDB Search =====
[2023-03-15 12:07:41,335] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b28313/markers.fasta)
[2023-03-15 12:07:41,336] [INFO] Task started: Blastn
[2023-03-15 12:07:41,336] [INFO] Running command: blastn -query OceanDNA-b28313/markers.fasta -db /var/lib/cwl/stg852f9da8-52c9-4146-9ab7-d397e71089e5/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b28313/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 12:07:42,238] [INFO] Task succeeded: Blastn
[2023-03-15 12:07:42,269] [INFO] Selected 16 target genomes.
[2023-03-15 12:07:42,269] [INFO] Target genome list was writen to OceanDNA-b28313/target_genomes_gtdb.txt
[2023-03-15 12:07:42,317] [INFO] Task started: fastANI
[2023-03-15 12:07:42,317] [INFO] Running command: fastANI --query /var/lib/cwl/stgc4e0e6ee-0a65-4623-b014-6b1acfba962b/OceanDNA-b28313.fa --refList OceanDNA-b28313/target_genomes_gtdb.txt --output OceanDNA-b28313/fastani_result_gtdb.tsv --threads 1
[2023-03-15 12:07:45,869] [INFO] Task succeeded: fastANI
[2023-03-15 12:07:45,872] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 12:07:45,872] [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_002699695.2	s__CACIIZ01 sp002699695	99.4182	481	546	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CACIIZ01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_014239455.1	s__CACIIZ01 sp014239455	91.1793	240	546	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CACIIZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902599445.1	s__CACIIZ01 sp902599445	80.4701	197	546	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CACIIZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902586855.1	s__CACIIZ01 sp902586855	79.4055	152	546	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CACIIZ01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 12:07:45,887] [INFO] GTDB search result was written to OceanDNA-b28313/result_gtdb.tsv
[2023-03-15 12:07:45,903] [INFO] ===== GTDB Search completed =====
[2023-03-15 12:07:45,917] [INFO] DFAST_QC result json was written to OceanDNA-b28313/dqc_result.json
[2023-03-15 12:07:45,917] [INFO] DFAST_QC completed!
[2023-03-15 12:07:45,917] [INFO] Total running time: 0h0m46s