[2023-03-17 23:10:23,691] [INFO] DFAST_QC pipeline started.
[2023-03-17 23:10:23,692] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 23:10:23,693] [INFO] DQC Reference Directory: /var/lib/cwl/stg10caa5b2-ec41-4b67-8405-da3e4fcc9b76/dqc_reference
[2023-03-17 23:10:24,819] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 23:10:24,819] [INFO] Task started: Prodigal
[2023-03-17 23:10:24,819] [INFO] Running command: cat /var/lib/cwl/stg9d3d6053-1534-42f2-b5a2-9168005f3774/OceanDNA-b17126.fa | prodigal -d OceanDNA-b17126/cds.fna -a OceanDNA-b17126/protein.faa -g 11 -q > /dev/null
[2023-03-17 23:10:39,366] [INFO] Task succeeded: Prodigal
[2023-03-17 23:10:39,366] [INFO] Task started: HMMsearch
[2023-03-17 23:10:39,366] [INFO] Running command: hmmsearch --tblout OceanDNA-b17126/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg10caa5b2-ec41-4b67-8405-da3e4fcc9b76/dqc_reference/reference_markers.hmm OceanDNA-b17126/protein.faa > /dev/null
[2023-03-17 23:10:39,569] [INFO] Task succeeded: HMMsearch
[2023-03-17 23:10:39,569] [INFO] Found 6/6 markers.
[2023-03-17 23:10:39,587] [INFO] Query marker FASTA was written to OceanDNA-b17126/markers.fasta
[2023-03-17 23:10:39,588] [INFO] Task started: Blastn
[2023-03-17 23:10:39,588] [INFO] Running command: blastn -query OceanDNA-b17126/markers.fasta -db /var/lib/cwl/stg10caa5b2-ec41-4b67-8405-da3e4fcc9b76/dqc_reference/reference_markers.fasta -out OceanDNA-b17126/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:10:40,109] [INFO] Task succeeded: Blastn
[2023-03-17 23:10:40,110] [INFO] Selected 23 target genomes.
[2023-03-17 23:10:40,110] [INFO] Target genome list was writen to OceanDNA-b17126/target_genomes.txt
[2023-03-17 23:10:40,120] [INFO] Task started: fastANI
[2023-03-17 23:10:40,120] [INFO] Running command: fastANI --query /var/lib/cwl/stg9d3d6053-1534-42f2-b5a2-9168005f3774/OceanDNA-b17126.fa --refList OceanDNA-b17126/target_genomes.txt --output OceanDNA-b17126/fastani_result.tsv --threads 1
[2023-03-17 23:10:56,003] [INFO] Task succeeded: fastANI
[2023-03-17 23:10:56,003] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg10caa5b2-ec41-4b67-8405-da3e4fcc9b76/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 23:10:56,004] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg10caa5b2-ec41-4b67-8405-da3e4fcc9b76/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 23:10:56,004] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 23:10:56,004] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 23:10:56,004] [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 23:10:56,004] [INFO] DFAST Taxonomy check result was written to OceanDNA-b17126/tc_result.tsv
[2023-03-17 23:10:56,004] [INFO] ===== Taxonomy check completed =====
[2023-03-17 23:10:56,004] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 23:10:56,004] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg10caa5b2-ec41-4b67-8405-da3e4fcc9b76/dqc_reference/checkm_data
[2023-03-17 23:10:56,008] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 23:10:56,013] [INFO] Task started: CheckM
[2023-03-17 23:10:56,013] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b17126/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b17126/checkm_input OceanDNA-b17126/checkm_result
[2023-03-17 23:11:35,530] [INFO] Task succeeded: CheckM
[2023-03-17 23:11:35,531] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 23:11:35,535] [INFO] ===== Completeness check finished =====
[2023-03-17 23:11:35,535] [INFO] ===== Start GTDB Search =====
[2023-03-17 23:11:35,535] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b17126/markers.fasta)
[2023-03-17 23:11:35,536] [INFO] Task started: Blastn
[2023-03-17 23:11:35,536] [INFO] Running command: blastn -query OceanDNA-b17126/markers.fasta -db /var/lib/cwl/stg10caa5b2-ec41-4b67-8405-da3e4fcc9b76/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b17126/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:11:36,264] [INFO] Task succeeded: Blastn
[2023-03-17 23:11:36,265] [INFO] Selected 18 target genomes.
[2023-03-17 23:11:36,265] [INFO] Target genome list was writen to OceanDNA-b17126/target_genomes_gtdb.txt
[2023-03-17 23:11:36,280] [INFO] Task started: fastANI
[2023-03-17 23:11:36,280] [INFO] Running command: fastANI --query /var/lib/cwl/stg9d3d6053-1534-42f2-b5a2-9168005f3774/OceanDNA-b17126.fa --refList OceanDNA-b17126/target_genomes_gtdb.txt --output OceanDNA-b17126/fastani_result_gtdb.tsv --threads 1
[2023-03-17 23:11:47,502] [INFO] Task succeeded: fastANI
[2023-03-17 23:11:47,504] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 23:11:47,504] [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_002328165.1	s__UBA2156 sp002328165	98.157	752	829	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__UBA2156;g__UBA2156	95.0	99.97	99.94	0.96	0.93	4	conclusive
GCA_011049715.1	s__UBA2156 sp011049715	92.0575	623	829	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__UBA2156;g__UBA2156	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 23:11:47,504] [INFO] GTDB search result was written to OceanDNA-b17126/result_gtdb.tsv
[2023-03-17 23:11:47,505] [INFO] ===== GTDB Search completed =====
[2023-03-17 23:11:47,505] [INFO] DFAST_QC result json was written to OceanDNA-b17126/dqc_result.json
[2023-03-17 23:11:47,505] [INFO] DFAST_QC completed!
[2023-03-17 23:11:47,505] [INFO] Total running time: 0h1m24s