[2023-03-15 14:43:58,298] [INFO] DFAST_QC pipeline started.
[2023-03-15 14:43:58,301] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 14:43:58,301] [INFO] DQC Reference Directory: /var/lib/cwl/stg2f213cec-99fb-488e-9254-78db31be0910/dqc_reference
[2023-03-15 14:43:59,397] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 14:43:59,398] [INFO] Task started: Prodigal
[2023-03-15 14:43:59,398] [INFO] Running command: cat /var/lib/cwl/stg8b667521-d358-456c-bfe0-e8554662ab04/OceanDNA-b13854.fa | prodigal -d OceanDNA-b13854/cds.fna -a OceanDNA-b13854/protein.faa -g 11 -q > /dev/null
[2023-03-15 14:44:05,833] [INFO] Task succeeded: Prodigal
[2023-03-15 14:44:05,834] [INFO] Task started: HMMsearch
[2023-03-15 14:44:05,834] [INFO] Running command: hmmsearch --tblout OceanDNA-b13854/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2f213cec-99fb-488e-9254-78db31be0910/dqc_reference/reference_markers.hmm OceanDNA-b13854/protein.faa > /dev/null
[2023-03-15 14:44:06,002] [INFO] Task succeeded: HMMsearch
[2023-03-15 14:44:06,002] [INFO] Found 6/6 markers.
[2023-03-15 14:44:06,045] [INFO] Query marker FASTA was written to OceanDNA-b13854/markers.fasta
[2023-03-15 14:44:06,046] [INFO] Task started: Blastn
[2023-03-15 14:44:06,046] [INFO] Running command: blastn -query OceanDNA-b13854/markers.fasta -db /var/lib/cwl/stg2f213cec-99fb-488e-9254-78db31be0910/dqc_reference/reference_markers.fasta -out OceanDNA-b13854/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 14:44:06,590] [INFO] Task succeeded: Blastn
[2023-03-15 14:44:06,599] [INFO] Selected 10 target genomes.
[2023-03-15 14:44:06,599] [INFO] Target genome list was writen to OceanDNA-b13854/target_genomes.txt
[2023-03-15 14:44:06,605] [INFO] Task started: fastANI
[2023-03-15 14:44:06,605] [INFO] Running command: fastANI --query /var/lib/cwl/stg8b667521-d358-456c-bfe0-e8554662ab04/OceanDNA-b13854.fa --refList OceanDNA-b13854/target_genomes.txt --output OceanDNA-b13854/fastani_result.tsv --threads 1
[2023-03-15 14:44:11,892] [INFO] Task succeeded: fastANI
[2023-03-15 14:44:11,892] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2f213cec-99fb-488e-9254-78db31be0910/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 14:44:11,892] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2f213cec-99fb-488e-9254-78db31be0910/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 14:44:11,893] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 14:44:11,893] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 14:44:11,893] [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 14:44:11,895] [INFO] DFAST Taxonomy check result was written to OceanDNA-b13854/tc_result.tsv
[2023-03-15 14:44:11,899] [INFO] ===== Taxonomy check completed =====
[2023-03-15 14:44:11,899] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 14:44:11,899] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2f213cec-99fb-488e-9254-78db31be0910/dqc_reference/checkm_data
[2023-03-15 14:44:11,954] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 14:44:11,959] [INFO] Task started: CheckM
[2023-03-15 14:44:11,960] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b13854/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b13854/checkm_input OceanDNA-b13854/checkm_result
[2023-03-15 14:44:35,687] [INFO] Task succeeded: CheckM
[2023-03-15 14:44:35,688] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 14:44:35,758] [INFO] ===== Completeness check finished =====
[2023-03-15 14:44:35,758] [INFO] ===== Start GTDB Search =====
[2023-03-15 14:44:35,758] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b13854/markers.fasta)
[2023-03-15 14:44:35,760] [INFO] Task started: Blastn
[2023-03-15 14:44:35,760] [INFO] Running command: blastn -query OceanDNA-b13854/markers.fasta -db /var/lib/cwl/stg2f213cec-99fb-488e-9254-78db31be0910/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b13854/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 14:44:36,729] [INFO] Task succeeded: Blastn
[2023-03-15 14:44:36,737] [INFO] Selected 14 target genomes.
[2023-03-15 14:44:36,737] [INFO] Target genome list was writen to OceanDNA-b13854/target_genomes_gtdb.txt
[2023-03-15 14:44:36,855] [INFO] Task started: fastANI
[2023-03-15 14:44:36,855] [INFO] Running command: fastANI --query /var/lib/cwl/stg8b667521-d358-456c-bfe0-e8554662ab04/OceanDNA-b13854.fa --refList OceanDNA-b13854/target_genomes_gtdb.txt --output OceanDNA-b13854/fastani_result_gtdb.tsv --threads 1
[2023-03-15 14:44:42,562] [INFO] Task succeeded: fastANI
[2023-03-15 14:44:42,564] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 14:44:42,564] [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_002722455.1	s__GCA-2722455 sp002722455	99.6939	353	425	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__SAR202;f__GCA-2722455;g__GCA-2722455	95.0	99.91	99.91	0.79	0.79	2	conclusive
--------------------------------------------------------------------------------
[2023-03-15 14:44:42,566] [INFO] GTDB search result was written to OceanDNA-b13854/result_gtdb.tsv
[2023-03-15 14:44:42,571] [INFO] ===== GTDB Search completed =====
[2023-03-15 14:44:42,574] [INFO] DFAST_QC result json was written to OceanDNA-b13854/dqc_result.json
[2023-03-15 14:44:42,574] [INFO] DFAST_QC completed!
[2023-03-15 14:44:42,574] [INFO] Total running time: 0h0m44s