[2023-03-16 06:31:19,181] [INFO] DFAST_QC pipeline started.
[2023-03-16 06:31:19,181] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 06:31:19,181] [INFO] DQC Reference Directory: /var/lib/cwl/stgd6c8e03c-359e-4bef-8939-68bca6ce1ec3/dqc_reference
[2023-03-16 06:31:20,281] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 06:31:20,281] [INFO] Task started: Prodigal
[2023-03-16 06:31:20,281] [INFO] Running command: cat /var/lib/cwl/stgc8d10af4-3a82-42d4-9525-e16e81b1d928/OceanDNA-b45323.fa | prodigal -d OceanDNA-b45323/cds.fna -a OceanDNA-b45323/protein.faa -g 11 -q > /dev/null
[2023-03-16 06:31:23,257] [INFO] Task succeeded: Prodigal
[2023-03-16 06:31:23,257] [INFO] Task started: HMMsearch
[2023-03-16 06:31:23,257] [INFO] Running command: hmmsearch --tblout OceanDNA-b45323/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd6c8e03c-359e-4bef-8939-68bca6ce1ec3/dqc_reference/reference_markers.hmm OceanDNA-b45323/protein.faa > /dev/null
[2023-03-16 06:31:23,403] [INFO] Task succeeded: HMMsearch
[2023-03-16 06:31:23,404] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgc8d10af4-3a82-42d4-9525-e16e81b1d928/OceanDNA-b45323.fa]
[2023-03-16 06:31:23,413] [INFO] Query marker FASTA was written to OceanDNA-b45323/markers.fasta
[2023-03-16 06:31:23,413] [INFO] Task started: Blastn
[2023-03-16 06:31:23,413] [INFO] Running command: blastn -query OceanDNA-b45323/markers.fasta -db /var/lib/cwl/stgd6c8e03c-359e-4bef-8939-68bca6ce1ec3/dqc_reference/reference_markers.fasta -out OceanDNA-b45323/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 06:31:23,908] [INFO] Task succeeded: Blastn
[2023-03-16 06:31:23,910] [INFO] Selected 14 target genomes.
[2023-03-16 06:31:23,910] [INFO] Target genome list was writen to OceanDNA-b45323/target_genomes.txt
[2023-03-16 06:31:23,920] [INFO] Task started: fastANI
[2023-03-16 06:31:23,920] [INFO] Running command: fastANI --query /var/lib/cwl/stgc8d10af4-3a82-42d4-9525-e16e81b1d928/OceanDNA-b45323.fa --refList OceanDNA-b45323/target_genomes.txt --output OceanDNA-b45323/fastani_result.tsv --threads 1
[2023-03-16 06:31:29,298] [INFO] Task succeeded: fastANI
[2023-03-16 06:31:29,298] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd6c8e03c-359e-4bef-8939-68bca6ce1ec3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 06:31:29,298] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd6c8e03c-359e-4bef-8939-68bca6ce1ec3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 06:31:29,299] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 06:31:29,299] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 06:31:29,299] [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 06:31:29,300] [INFO] DFAST Taxonomy check result was written to OceanDNA-b45323/tc_result.tsv
[2023-03-16 06:31:29,301] [INFO] ===== Taxonomy check completed =====
[2023-03-16 06:31:29,301] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 06:31:29,301] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd6c8e03c-359e-4bef-8939-68bca6ce1ec3/dqc_reference/checkm_data
[2023-03-16 06:31:29,304] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 06:31:29,307] [INFO] Task started: CheckM
[2023-03-16 06:31:29,307] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b45323/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b45323/checkm_input OceanDNA-b45323/checkm_result
[2023-03-16 06:31:43,842] [INFO] Task succeeded: CheckM
[2023-03-16 06:31:43,842] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.27%
Contamintation: 2.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 06:31:43,849] [INFO] ===== Completeness check finished =====
[2023-03-16 06:31:43,849] [INFO] ===== Start GTDB Search =====
[2023-03-16 06:31:43,849] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b45323/markers.fasta)
[2023-03-16 06:31:43,850] [INFO] Task started: Blastn
[2023-03-16 06:31:43,850] [INFO] Running command: blastn -query OceanDNA-b45323/markers.fasta -db /var/lib/cwl/stgd6c8e03c-359e-4bef-8939-68bca6ce1ec3/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b45323/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 06:31:44,554] [INFO] Task succeeded: Blastn
[2023-03-16 06:31:44,556] [INFO] Selected 24 target genomes.
[2023-03-16 06:31:44,556] [INFO] Target genome list was writen to OceanDNA-b45323/target_genomes_gtdb.txt
[2023-03-16 06:31:44,607] [INFO] Task started: fastANI
[2023-03-16 06:31:44,607] [INFO] Running command: fastANI --query /var/lib/cwl/stgc8d10af4-3a82-42d4-9525-e16e81b1d928/OceanDNA-b45323.fa --refList OceanDNA-b45323/target_genomes_gtdb.txt --output OceanDNA-b45323/fastani_result_gtdb.tsv --threads 1
[2023-03-16 06:31:50,895] [INFO] Task succeeded: fastANI
[2023-03-16 06:31:50,897] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 06:31:50,897] [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_002712105.1	s__GCA-2712105 sp002712105	76.5003	50	191	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__Kiritimatiellales;f__Pontiellaceae;g__GCA-2712105	95.0	97.04	97.04	0.84	0.84	2	-
--------------------------------------------------------------------------------
[2023-03-16 06:31:50,899] [INFO] GTDB search result was written to OceanDNA-b45323/result_gtdb.tsv
[2023-03-16 06:31:50,901] [INFO] ===== GTDB Search completed =====
[2023-03-16 06:31:50,903] [INFO] DFAST_QC result json was written to OceanDNA-b45323/dqc_result.json
[2023-03-16 06:31:50,903] [INFO] DFAST_QC completed!
[2023-03-16 06:31:50,903] [INFO] Total running time: 0h0m32s