[2023-03-17 05:16:58,085] [INFO] DFAST_QC pipeline started.
[2023-03-17 05:16:58,085] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 05:16:58,085] [INFO] DQC Reference Directory: /var/lib/cwl/stge7f004aa-1d60-4ad6-9ddc-9b7cc3783472/dqc_reference
[2023-03-17 05:16:59,895] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 05:16:59,895] [INFO] Task started: Prodigal
[2023-03-17 05:16:59,896] [INFO] Running command: cat /var/lib/cwl/stg06e585e9-609c-43dd-b2a1-315777f248f8/OceanDNA-b13985.fa | prodigal -d OceanDNA-b13985/cds.fna -a OceanDNA-b13985/protein.faa -g 11 -q > /dev/null
[2023-03-17 05:17:07,744] [INFO] Task succeeded: Prodigal
[2023-03-17 05:17:07,744] [INFO] Task started: HMMsearch
[2023-03-17 05:17:07,744] [INFO] Running command: hmmsearch --tblout OceanDNA-b13985/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge7f004aa-1d60-4ad6-9ddc-9b7cc3783472/dqc_reference/reference_markers.hmm OceanDNA-b13985/protein.faa > /dev/null
[2023-03-17 05:17:07,899] [INFO] Task succeeded: HMMsearch
[2023-03-17 05:17:07,900] [INFO] Found 6/6 markers.
[2023-03-17 05:17:07,910] [INFO] Query marker FASTA was written to OceanDNA-b13985/markers.fasta
[2023-03-17 05:17:07,910] [INFO] Task started: Blastn
[2023-03-17 05:17:07,910] [INFO] Running command: blastn -query OceanDNA-b13985/markers.fasta -db /var/lib/cwl/stge7f004aa-1d60-4ad6-9ddc-9b7cc3783472/dqc_reference/reference_markers.fasta -out OceanDNA-b13985/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:17:08,414] [INFO] Task succeeded: Blastn
[2023-03-17 05:17:08,415] [INFO] Selected 15 target genomes.
[2023-03-17 05:17:08,415] [INFO] Target genome list was writen to OceanDNA-b13985/target_genomes.txt
[2023-03-17 05:17:08,444] [INFO] Task started: fastANI
[2023-03-17 05:17:08,444] [INFO] Running command: fastANI --query /var/lib/cwl/stg06e585e9-609c-43dd-b2a1-315777f248f8/OceanDNA-b13985.fa --refList OceanDNA-b13985/target_genomes.txt --output OceanDNA-b13985/fastani_result.tsv --threads 1
[2023-03-17 05:17:16,319] [INFO] Task succeeded: fastANI
[2023-03-17 05:17:16,319] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge7f004aa-1d60-4ad6-9ddc-9b7cc3783472/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 05:17:16,319] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge7f004aa-1d60-4ad6-9ddc-9b7cc3783472/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 05:17:16,320] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 05:17:16,320] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 05:17:16,320] [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
--------------------------------------------------------------------------------
[2023-03-17 05:17:16,320] [INFO] DFAST Taxonomy check result was written to OceanDNA-b13985/tc_result.tsv
[2023-03-17 05:17:16,320] [INFO] ===== Taxonomy check completed =====
[2023-03-17 05:17:16,320] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 05:17:16,320] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge7f004aa-1d60-4ad6-9ddc-9b7cc3783472/dqc_reference/checkm_data
[2023-03-17 05:17:16,324] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 05:17:16,327] [INFO] Task started: CheckM
[2023-03-17 05:17:16,327] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b13985/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b13985/checkm_input OceanDNA-b13985/checkm_result
[2023-03-17 05:17:41,035] [INFO] Task succeeded: CheckM
[2023-03-17 05:17:41,035] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.61%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 05:17:41,037] [INFO] ===== Completeness check finished =====
[2023-03-17 05:17:41,038] [INFO] ===== Start GTDB Search =====
[2023-03-17 05:17:41,038] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b13985/markers.fasta)
[2023-03-17 05:17:41,039] [INFO] Task started: Blastn
[2023-03-17 05:17:41,039] [INFO] Running command: blastn -query OceanDNA-b13985/markers.fasta -db /var/lib/cwl/stge7f004aa-1d60-4ad6-9ddc-9b7cc3783472/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b13985/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:17:41,748] [INFO] Task succeeded: Blastn
[2023-03-17 05:17:41,749] [INFO] Selected 17 target genomes.
[2023-03-17 05:17:41,749] [INFO] Target genome list was writen to OceanDNA-b13985/target_genomes_gtdb.txt
[2023-03-17 05:17:42,184] [INFO] Task started: fastANI
[2023-03-17 05:17:42,185] [INFO] Running command: fastANI --query /var/lib/cwl/stg06e585e9-609c-43dd-b2a1-315777f248f8/OceanDNA-b13985.fa --refList OceanDNA-b13985/target_genomes_gtdb.txt --output OceanDNA-b13985/fastani_result_gtdb.tsv --threads 1
[2023-03-17 05:17:49,383] [INFO] Task succeeded: fastANI
[2023-03-17 05:17:49,385] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 05:17:49,385] [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_002717725.1	s__UBA6927 sp002717725	97.2979	315	488	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__SAR202;f__UBA6927;g__UBA6927	95.0	97.61	97.61	0.69	0.69	2	conclusive
--------------------------------------------------------------------------------
[2023-03-17 05:17:49,386] [INFO] GTDB search result was written to OceanDNA-b13985/result_gtdb.tsv
[2023-03-17 05:17:49,386] [INFO] ===== GTDB Search completed =====
[2023-03-17 05:17:49,386] [INFO] DFAST_QC result json was written to OceanDNA-b13985/dqc_result.json
[2023-03-17 05:17:49,386] [INFO] DFAST_QC completed!
[2023-03-17 05:17:49,386] [INFO] Total running time: 0h0m51s