[2023-03-15 05:37:30,050] [INFO] DFAST_QC pipeline started.
[2023-03-15 05:37:30,050] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 05:37:30,050] [INFO] DQC Reference Directory: /var/lib/cwl/stg312af320-36f1-48e1-bfe1-c2ffbfaf661d/dqc_reference
[2023-03-15 05:37:31,131] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 05:37:31,131] [INFO] Task started: Prodigal
[2023-03-15 05:37:31,131] [INFO] Running command: cat /var/lib/cwl/stged1f9b29-2669-4211-8424-816c7021e5a5/OceanDNA-b36734.fa | prodigal -d OceanDNA-b36734/cds.fna -a OceanDNA-b36734/protein.faa -g 11 -q > /dev/null
[2023-03-15 05:37:45,566] [INFO] Task succeeded: Prodigal
[2023-03-15 05:37:45,567] [INFO] Task started: HMMsearch
[2023-03-15 05:37:45,567] [INFO] Running command: hmmsearch --tblout OceanDNA-b36734/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg312af320-36f1-48e1-bfe1-c2ffbfaf661d/dqc_reference/reference_markers.hmm OceanDNA-b36734/protein.faa > /dev/null
[2023-03-15 05:37:45,767] [INFO] Task succeeded: HMMsearch
[2023-03-15 05:37:45,768] [INFO] Found 6/6 markers.
[2023-03-15 05:37:45,787] [INFO] Query marker FASTA was written to OceanDNA-b36734/markers.fasta
[2023-03-15 05:37:45,788] [INFO] Task started: Blastn
[2023-03-15 05:37:45,788] [INFO] Running command: blastn -query OceanDNA-b36734/markers.fasta -db /var/lib/cwl/stg312af320-36f1-48e1-bfe1-c2ffbfaf661d/dqc_reference/reference_markers.fasta -out OceanDNA-b36734/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:37:46,355] [INFO] Task succeeded: Blastn
[2023-03-15 05:37:46,356] [INFO] Selected 25 target genomes.
[2023-03-15 05:37:46,356] [INFO] Target genome list was writen to OceanDNA-b36734/target_genomes.txt
[2023-03-15 05:37:46,371] [INFO] Task started: fastANI
[2023-03-15 05:37:46,372] [INFO] Running command: fastANI --query /var/lib/cwl/stged1f9b29-2669-4211-8424-816c7021e5a5/OceanDNA-b36734.fa --refList OceanDNA-b36734/target_genomes.txt --output OceanDNA-b36734/fastani_result.tsv --threads 1
[2023-03-15 05:38:01,404] [INFO] Task succeeded: fastANI
[2023-03-15 05:38:01,404] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg312af320-36f1-48e1-bfe1-c2ffbfaf661d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 05:38:01,404] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg312af320-36f1-48e1-bfe1-c2ffbfaf661d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 05:38:01,404] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 05:38:01,404] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 05:38:01,405] [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 05:38:01,405] [INFO] DFAST Taxonomy check result was written to OceanDNA-b36734/tc_result.tsv
[2023-03-15 05:38:01,405] [INFO] ===== Taxonomy check completed =====
[2023-03-15 05:38:01,405] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 05:38:01,405] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg312af320-36f1-48e1-bfe1-c2ffbfaf661d/dqc_reference/checkm_data
[2023-03-15 05:38:01,408] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 05:38:01,415] [INFO] Task started: CheckM
[2023-03-15 05:38:01,415] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b36734/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b36734/checkm_input OceanDNA-b36734/checkm_result
[2023-03-15 05:38:41,335] [INFO] Task succeeded: CheckM
[2023-03-15 05:38:41,336] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 88.65%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 05:38:41,339] [INFO] ===== Completeness check finished =====
[2023-03-15 05:38:41,339] [INFO] ===== Start GTDB Search =====
[2023-03-15 05:38:41,339] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b36734/markers.fasta)
[2023-03-15 05:38:41,340] [INFO] Task started: Blastn
[2023-03-15 05:38:41,340] [INFO] Running command: blastn -query OceanDNA-b36734/markers.fasta -db /var/lib/cwl/stg312af320-36f1-48e1-bfe1-c2ffbfaf661d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b36734/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:38:42,289] [INFO] Task succeeded: Blastn
[2023-03-15 05:38:42,291] [INFO] Selected 17 target genomes.
[2023-03-15 05:38:42,291] [INFO] Target genome list was writen to OceanDNA-b36734/target_genomes_gtdb.txt
[2023-03-15 05:38:42,309] [INFO] Task started: fastANI
[2023-03-15 05:38:42,310] [INFO] Running command: fastANI --query /var/lib/cwl/stged1f9b29-2669-4211-8424-816c7021e5a5/OceanDNA-b36734.fa --refList OceanDNA-b36734/target_genomes_gtdb.txt --output OceanDNA-b36734/fastani_result_gtdb.tsv --threads 1
[2023-03-15 05:38:52,777] [INFO] Task succeeded: fastANI
[2023-03-15 05:38:52,780] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 05:38:52,780] [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_002725995.1	s__GCA-002726655 sp002725995	99.5053	693	815	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__GCA-002726655	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002726655.1	s__GCA-002726655 sp002726655	83.6969	642	815	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__GCA-002726655	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 05:38:52,780] [INFO] GTDB search result was written to OceanDNA-b36734/result_gtdb.tsv
[2023-03-15 05:38:52,780] [INFO] ===== GTDB Search completed =====
[2023-03-15 05:38:52,781] [INFO] DFAST_QC result json was written to OceanDNA-b36734/dqc_result.json
[2023-03-15 05:38:52,781] [INFO] DFAST_QC completed!
[2023-03-15 05:38:52,781] [INFO] Total running time: 0h1m23s