[2023-03-18 20:40:39,433] [INFO] DFAST_QC pipeline started.
[2023-03-18 20:40:39,433] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 20:40:39,433] [INFO] DQC Reference Directory: /var/lib/cwl/stgc62ae460-ee88-4067-ae52-a4d131005664/dqc_reference
[2023-03-18 20:40:41,205] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 20:40:41,206] [INFO] Task started: Prodigal
[2023-03-18 20:40:41,206] [INFO] Running command: cat /var/lib/cwl/stg7a65e49e-43c3-4c3c-bd8f-2a6aea59ea45/OceanDNA-b15980.fa | prodigal -d OceanDNA-b15980/cds.fna -a OceanDNA-b15980/protein.faa -g 11 -q > /dev/null
[2023-03-18 20:40:50,915] [INFO] Task succeeded: Prodigal
[2023-03-18 20:40:50,915] [INFO] Task started: HMMsearch
[2023-03-18 20:40:50,915] [INFO] Running command: hmmsearch --tblout OceanDNA-b15980/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc62ae460-ee88-4067-ae52-a4d131005664/dqc_reference/reference_markers.hmm OceanDNA-b15980/protein.faa > /dev/null
[2023-03-18 20:40:51,065] [INFO] Task succeeded: HMMsearch
[2023-03-18 20:40:51,066] [INFO] Found 6/6 markers.
[2023-03-18 20:40:51,080] [INFO] Query marker FASTA was written to OceanDNA-b15980/markers.fasta
[2023-03-18 20:40:51,080] [INFO] Task started: Blastn
[2023-03-18 20:40:51,080] [INFO] Running command: blastn -query OceanDNA-b15980/markers.fasta -db /var/lib/cwl/stgc62ae460-ee88-4067-ae52-a4d131005664/dqc_reference/reference_markers.fasta -out OceanDNA-b15980/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 20:40:51,668] [INFO] Task succeeded: Blastn
[2023-03-18 20:40:51,669] [INFO] Selected 17 target genomes.
[2023-03-18 20:40:51,669] [INFO] Target genome list was writen to OceanDNA-b15980/target_genomes.txt
[2023-03-18 20:40:51,678] [INFO] Task started: fastANI
[2023-03-18 20:40:51,678] [INFO] Running command: fastANI --query /var/lib/cwl/stg7a65e49e-43c3-4c3c-bd8f-2a6aea59ea45/OceanDNA-b15980.fa --refList OceanDNA-b15980/target_genomes.txt --output OceanDNA-b15980/fastani_result.tsv --threads 1
[2023-03-18 20:41:04,072] [INFO] Task succeeded: fastANI
[2023-03-18 20:41:04,072] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc62ae460-ee88-4067-ae52-a4d131005664/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 20:41:04,073] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc62ae460-ee88-4067-ae52-a4d131005664/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 20:41:04,076] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 20:41:04,076] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 20:41:04,076] [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
Streptomyces brasiliensis	strain=JCM 3086	GCA_014647875.1	1954	1954	type	True	74.7366	54	520	95	below_threshold
Frankia torreyi	strain=CpI1	GCA_000948395.1	1856	1856	type	True	74.5925	50	520	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 20:41:04,076] [INFO] DFAST Taxonomy check result was written to OceanDNA-b15980/tc_result.tsv
[2023-03-18 20:41:04,076] [INFO] ===== Taxonomy check completed =====
[2023-03-18 20:41:04,076] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 20:41:04,076] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc62ae460-ee88-4067-ae52-a4d131005664/dqc_reference/checkm_data
[2023-03-18 20:41:04,077] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 20:41:04,080] [INFO] Task started: CheckM
[2023-03-18 20:41:04,081] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b15980/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b15980/checkm_input OceanDNA-b15980/checkm_result
[2023-03-18 20:41:31,909] [INFO] Task succeeded: CheckM
[2023-03-18 20:41:31,909] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 54.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 20:41:31,911] [INFO] ===== Completeness check finished =====
[2023-03-18 20:41:31,911] [INFO] ===== Start GTDB Search =====
[2023-03-18 20:41:31,911] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b15980/markers.fasta)
[2023-03-18 20:41:31,912] [INFO] Task started: Blastn
[2023-03-18 20:41:31,912] [INFO] Running command: blastn -query OceanDNA-b15980/markers.fasta -db /var/lib/cwl/stgc62ae460-ee88-4067-ae52-a4d131005664/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b15980/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 20:41:32,825] [INFO] Task succeeded: Blastn
[2023-03-18 20:41:32,825] [INFO] Selected 22 target genomes.
[2023-03-18 20:41:32,826] [INFO] Target genome list was writen to OceanDNA-b15980/target_genomes_gtdb.txt
[2023-03-18 20:41:32,885] [INFO] Task started: fastANI
[2023-03-18 20:41:32,885] [INFO] Running command: fastANI --query /var/lib/cwl/stg7a65e49e-43c3-4c3c-bd8f-2a6aea59ea45/OceanDNA-b15980.fa --refList OceanDNA-b15980/target_genomes_gtdb.txt --output OceanDNA-b15980/fastani_result_gtdb.tsv --threads 1
[2023-03-18 20:41:46,147] [INFO] Task succeeded: fastANI
[2023-03-18 20:41:46,150] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 20:41:46,150] [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
GCF_014647875.1	s__Streptomyces brasiliensis	74.7366	54	520	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018982965.1	s__Streptomyces sp018982965	74.6699	50	520	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 20:41:46,150] [INFO] GTDB search result was written to OceanDNA-b15980/result_gtdb.tsv
[2023-03-18 20:41:46,150] [INFO] ===== GTDB Search completed =====
[2023-03-18 20:41:46,151] [INFO] DFAST_QC result json was written to OceanDNA-b15980/dqc_result.json
[2023-03-18 20:41:46,151] [INFO] DFAST_QC completed!
[2023-03-18 20:41:46,151] [INFO] Total running time: 0h1m7s