[2023-03-15 21:01:44,376] [INFO] DFAST_QC pipeline started.
[2023-03-15 21:01:44,376] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 21:01:44,376] [INFO] DQC Reference Directory: /var/lib/cwl/stg3a0026b3-369d-4819-8c15-b091ae2c1451/dqc_reference
[2023-03-15 21:01:45,597] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 21:01:45,597] [INFO] Task started: Prodigal
[2023-03-15 21:01:45,597] [INFO] Running command: cat /var/lib/cwl/stgc2a3bc76-3a70-40e8-b0e1-957b56eeaa7e/OceanDNA-b35396.fa | prodigal -d OceanDNA-b35396/cds.fna -a OceanDNA-b35396/protein.faa -g 11 -q > /dev/null
[2023-03-15 21:02:06,988] [INFO] Task succeeded: Prodigal
[2023-03-15 21:02:06,988] [INFO] Task started: HMMsearch
[2023-03-15 21:02:06,988] [INFO] Running command: hmmsearch --tblout OceanDNA-b35396/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3a0026b3-369d-4819-8c15-b091ae2c1451/dqc_reference/reference_markers.hmm OceanDNA-b35396/protein.faa > /dev/null
[2023-03-15 21:02:07,223] [INFO] Task succeeded: HMMsearch
[2023-03-15 21:02:07,223] [INFO] Found 6/6 markers.
[2023-03-15 21:02:07,248] [INFO] Query marker FASTA was written to OceanDNA-b35396/markers.fasta
[2023-03-15 21:02:07,249] [INFO] Task started: Blastn
[2023-03-15 21:02:07,249] [INFO] Running command: blastn -query OceanDNA-b35396/markers.fasta -db /var/lib/cwl/stg3a0026b3-369d-4819-8c15-b091ae2c1451/dqc_reference/reference_markers.fasta -out OceanDNA-b35396/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:02:07,770] [INFO] Task succeeded: Blastn
[2023-03-15 21:02:07,771] [INFO] Selected 24 target genomes.
[2023-03-15 21:02:07,771] [INFO] Target genome list was writen to OceanDNA-b35396/target_genomes.txt
[2023-03-15 21:02:07,792] [INFO] Task started: fastANI
[2023-03-15 21:02:07,792] [INFO] Running command: fastANI --query /var/lib/cwl/stgc2a3bc76-3a70-40e8-b0e1-957b56eeaa7e/OceanDNA-b35396.fa --refList OceanDNA-b35396/target_genomes.txt --output OceanDNA-b35396/fastani_result.tsv --threads 1
[2023-03-15 21:02:22,743] [INFO] Task succeeded: fastANI
[2023-03-15 21:02:22,743] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3a0026b3-369d-4819-8c15-b091ae2c1451/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 21:02:22,743] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3a0026b3-369d-4819-8c15-b091ae2c1451/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 21:02:22,744] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 21:02:22,744] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 21:02:22,744] [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 21:02:22,744] [INFO] DFAST Taxonomy check result was written to OceanDNA-b35396/tc_result.tsv
[2023-03-15 21:02:22,744] [INFO] ===== Taxonomy check completed =====
[2023-03-15 21:02:22,744] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 21:02:22,744] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3a0026b3-369d-4819-8c15-b091ae2c1451/dqc_reference/checkm_data
[2023-03-15 21:02:22,747] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 21:02:22,753] [INFO] Task started: CheckM
[2023-03-15 21:02:22,753] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b35396/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b35396/checkm_input OceanDNA-b35396/checkm_result
[2023-03-15 21:03:17,097] [INFO] Task succeeded: CheckM
[2023-03-15 21:03:17,098] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.91%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 21:03:17,101] [INFO] ===== Completeness check finished =====
[2023-03-15 21:03:17,101] [INFO] ===== Start GTDB Search =====
[2023-03-15 21:03:17,102] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b35396/markers.fasta)
[2023-03-15 21:03:17,102] [INFO] Task started: Blastn
[2023-03-15 21:03:17,102] [INFO] Running command: blastn -query OceanDNA-b35396/markers.fasta -db /var/lib/cwl/stg3a0026b3-369d-4819-8c15-b091ae2c1451/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b35396/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:03:17,848] [INFO] Task succeeded: Blastn
[2023-03-15 21:03:17,849] [INFO] Selected 26 target genomes.
[2023-03-15 21:03:17,849] [INFO] Target genome list was writen to OceanDNA-b35396/target_genomes_gtdb.txt
[2023-03-15 21:03:18,655] [INFO] Task started: fastANI
[2023-03-15 21:03:18,655] [INFO] Running command: fastANI --query /var/lib/cwl/stgc2a3bc76-3a70-40e8-b0e1-957b56eeaa7e/OceanDNA-b35396.fa --refList OceanDNA-b35396/target_genomes_gtdb.txt --output OceanDNA-b35396/fastani_result_gtdb.tsv --threads 1
[2023-03-15 21:03:33,523] [INFO] Task succeeded: fastANI
[2023-03-15 21:03:33,525] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 21:03:33,526] [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_018669845.1	s__JACNJF01 sp018669845	99.8082	1232	1312	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__GCA-001735895;f__GCA-001735895;g__JACNJF01	95.0	99.85	99.71	0.93	0.91	11	conclusive
GCA_014382695.1	s__JACNJF01 sp014382695	77.0463	133	1312	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__GCA-001735895;f__GCA-001735895;g__JACNJF01	95.0	99.61	99.61	0.86	0.86	2	-
--------------------------------------------------------------------------------
[2023-03-15 21:03:33,526] [INFO] GTDB search result was written to OceanDNA-b35396/result_gtdb.tsv
[2023-03-15 21:03:33,526] [INFO] ===== GTDB Search completed =====
[2023-03-15 21:03:33,526] [INFO] DFAST_QC result json was written to OceanDNA-b35396/dqc_result.json
[2023-03-15 21:03:33,526] [INFO] DFAST_QC completed!
[2023-03-15 21:03:33,526] [INFO] Total running time: 0h1m49s