[2023-03-16 01:03:15,439] [INFO] DFAST_QC pipeline started.
[2023-03-16 01:03:15,439] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 01:03:15,439] [INFO] DQC Reference Directory: /var/lib/cwl/stge9577fa7-8789-4843-aa5c-d0283a3a92e9/dqc_reference
[2023-03-16 01:03:16,616] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 01:03:16,616] [INFO] Task started: Prodigal
[2023-03-16 01:03:16,616] [INFO] Running command: cat /var/lib/cwl/stgbf62a7e0-e001-4f8a-aca3-85ee408c1de1/OceanDNA-b33581.fa | prodigal -d OceanDNA-b33581/cds.fna -a OceanDNA-b33581/protein.faa -g 11 -q > /dev/null
[2023-03-16 01:03:21,054] [INFO] Task succeeded: Prodigal
[2023-03-16 01:03:21,054] [INFO] Task started: HMMsearch
[2023-03-16 01:03:21,054] [INFO] Running command: hmmsearch --tblout OceanDNA-b33581/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge9577fa7-8789-4843-aa5c-d0283a3a92e9/dqc_reference/reference_markers.hmm OceanDNA-b33581/protein.faa > /dev/null
[2023-03-16 01:03:21,212] [INFO] Task succeeded: HMMsearch
[2023-03-16 01:03:21,212] [INFO] Found 6/6 markers.
[2023-03-16 01:03:21,223] [INFO] Query marker FASTA was written to OceanDNA-b33581/markers.fasta
[2023-03-16 01:03:21,224] [INFO] Task started: Blastn
[2023-03-16 01:03:21,224] [INFO] Running command: blastn -query OceanDNA-b33581/markers.fasta -db /var/lib/cwl/stge9577fa7-8789-4843-aa5c-d0283a3a92e9/dqc_reference/reference_markers.fasta -out OceanDNA-b33581/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 01:03:21,720] [INFO] Task succeeded: Blastn
[2023-03-16 01:03:21,721] [INFO] Selected 20 target genomes.
[2023-03-16 01:03:21,721] [INFO] Target genome list was writen to OceanDNA-b33581/target_genomes.txt
[2023-03-16 01:03:21,738] [INFO] Task started: fastANI
[2023-03-16 01:03:21,738] [INFO] Running command: fastANI --query /var/lib/cwl/stgbf62a7e0-e001-4f8a-aca3-85ee408c1de1/OceanDNA-b33581.fa --refList OceanDNA-b33581/target_genomes.txt --output OceanDNA-b33581/fastani_result.tsv --threads 1
[2023-03-16 01:03:30,898] [INFO] Task succeeded: fastANI
[2023-03-16 01:03:30,898] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge9577fa7-8789-4843-aa5c-d0283a3a92e9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 01:03:30,899] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge9577fa7-8789-4843-aa5c-d0283a3a92e9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 01:03:30,899] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 01:03:30,899] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 01:03:30,899] [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 01:03:30,899] [INFO] DFAST Taxonomy check result was written to OceanDNA-b33581/tc_result.tsv
[2023-03-16 01:03:30,899] [INFO] ===== Taxonomy check completed =====
[2023-03-16 01:03:30,899] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 01:03:30,899] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge9577fa7-8789-4843-aa5c-d0283a3a92e9/dqc_reference/checkm_data
[2023-03-16 01:03:30,902] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 01:03:30,905] [INFO] Task started: CheckM
[2023-03-16 01:03:30,905] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b33581/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b33581/checkm_input OceanDNA-b33581/checkm_result
[2023-03-16 01:03:48,417] [INFO] Task succeeded: CheckM
[2023-03-16 01:03:48,417] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.78%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 01:03:48,419] [INFO] ===== Completeness check finished =====
[2023-03-16 01:03:48,420] [INFO] ===== Start GTDB Search =====
[2023-03-16 01:03:48,420] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b33581/markers.fasta)
[2023-03-16 01:03:48,421] [INFO] Task started: Blastn
[2023-03-16 01:03:48,421] [INFO] Running command: blastn -query OceanDNA-b33581/markers.fasta -db /var/lib/cwl/stge9577fa7-8789-4843-aa5c-d0283a3a92e9/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b33581/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 01:03:49,116] [INFO] Task succeeded: Blastn
[2023-03-16 01:03:49,117] [INFO] Selected 21 target genomes.
[2023-03-16 01:03:49,117] [INFO] Target genome list was writen to OceanDNA-b33581/target_genomes_gtdb.txt
[2023-03-16 01:03:50,152] [INFO] Task started: fastANI
[2023-03-16 01:03:50,152] [INFO] Running command: fastANI --query /var/lib/cwl/stgbf62a7e0-e001-4f8a-aca3-85ee408c1de1/OceanDNA-b33581.fa --refList OceanDNA-b33581/target_genomes_gtdb.txt --output OceanDNA-b33581/fastani_result_gtdb.tsv --threads 1
[2023-03-16 01:03:57,864] [INFO] Task succeeded: fastANI
[2023-03-16 01:03:57,867] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 01:03:57,867] [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_004214155.1	s__UBA7377 sp004214155	99.0155	256	267	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae_A;g__UBA7377	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902586195.1	s__UBA7377 sp902586195	88.9126	169	267	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae_A;g__UBA7377	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 01:03:57,867] [INFO] GTDB search result was written to OceanDNA-b33581/result_gtdb.tsv
[2023-03-16 01:03:57,867] [INFO] ===== GTDB Search completed =====
[2023-03-16 01:03:57,868] [INFO] DFAST_QC result json was written to OceanDNA-b33581/dqc_result.json
[2023-03-16 01:03:57,868] [INFO] DFAST_QC completed!
[2023-03-16 01:03:57,868] [INFO] Total running time: 0h0m42s