[2023-03-15 14:37:49,314] [INFO] DFAST_QC pipeline started.
[2023-03-15 14:37:49,314] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 14:37:49,314] [INFO] DQC Reference Directory: /var/lib/cwl/stgb3bcffe2-b491-4f0b-886b-cf8a7ef7a648/dqc_reference
[2023-03-15 14:37:50,436] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 14:37:50,436] [INFO] Task started: Prodigal
[2023-03-15 14:37:50,436] [INFO] Running command: cat /var/lib/cwl/stg222fcb6b-5244-47e5-9a0f-0293ccb36943/OceanDNA-b23077.fa | prodigal -d OceanDNA-b23077/cds.fna -a OceanDNA-b23077/protein.faa -g 11 -q > /dev/null
[2023-03-15 14:38:03,323] [INFO] Task succeeded: Prodigal
[2023-03-15 14:38:03,323] [INFO] Task started: HMMsearch
[2023-03-15 14:38:03,323] [INFO] Running command: hmmsearch --tblout OceanDNA-b23077/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb3bcffe2-b491-4f0b-886b-cf8a7ef7a648/dqc_reference/reference_markers.hmm OceanDNA-b23077/protein.faa > /dev/null
[2023-03-15 14:38:03,516] [INFO] Task succeeded: HMMsearch
[2023-03-15 14:38:03,517] [INFO] Found 6/6 markers.
[2023-03-15 14:38:03,533] [INFO] Query marker FASTA was written to OceanDNA-b23077/markers.fasta
[2023-03-15 14:38:03,534] [INFO] Task started: Blastn
[2023-03-15 14:38:03,534] [INFO] Running command: blastn -query OceanDNA-b23077/markers.fasta -db /var/lib/cwl/stgb3bcffe2-b491-4f0b-886b-cf8a7ef7a648/dqc_reference/reference_markers.fasta -out OceanDNA-b23077/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 14:38:04,113] [INFO] Task succeeded: Blastn
[2023-03-15 14:38:04,114] [INFO] Selected 15 target genomes.
[2023-03-15 14:38:04,115] [INFO] Target genome list was writen to OceanDNA-b23077/target_genomes.txt
[2023-03-15 14:38:04,125] [INFO] Task started: fastANI
[2023-03-15 14:38:04,125] [INFO] Running command: fastANI --query /var/lib/cwl/stg222fcb6b-5244-47e5-9a0f-0293ccb36943/OceanDNA-b23077.fa --refList OceanDNA-b23077/target_genomes.txt --output OceanDNA-b23077/fastani_result.tsv --threads 1
[2023-03-15 14:38:14,901] [INFO] Task succeeded: fastANI
[2023-03-15 14:38:14,901] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb3bcffe2-b491-4f0b-886b-cf8a7ef7a648/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 14:38:14,902] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb3bcffe2-b491-4f0b-886b-cf8a7ef7a648/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 14:38:14,902] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 14:38:14,902] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 14:38:14,902] [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 14:38:14,902] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23077/tc_result.tsv
[2023-03-15 14:38:14,902] [INFO] ===== Taxonomy check completed =====
[2023-03-15 14:38:14,903] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 14:38:14,903] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb3bcffe2-b491-4f0b-886b-cf8a7ef7a648/dqc_reference/checkm_data
[2023-03-15 14:38:14,906] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 14:38:15,357] [INFO] Task started: CheckM
[2023-03-15 14:38:15,357] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23077/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23077/checkm_input OceanDNA-b23077/checkm_result
[2023-03-15 14:38:50,928] [INFO] Task succeeded: CheckM
[2023-03-15 14:38:50,929] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 14:38:50,957] [INFO] ===== Completeness check finished =====
[2023-03-15 14:38:50,957] [INFO] ===== Start GTDB Search =====
[2023-03-15 14:38:50,957] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23077/markers.fasta)
[2023-03-15 14:38:50,958] [INFO] Task started: Blastn
[2023-03-15 14:38:50,958] [INFO] Running command: blastn -query OceanDNA-b23077/markers.fasta -db /var/lib/cwl/stgb3bcffe2-b491-4f0b-886b-cf8a7ef7a648/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23077/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 14:38:51,714] [INFO] Task succeeded: Blastn
[2023-03-15 14:38:51,715] [INFO] Selected 16 target genomes.
[2023-03-15 14:38:51,715] [INFO] Target genome list was writen to OceanDNA-b23077/target_genomes_gtdb.txt
[2023-03-15 14:38:51,733] [INFO] Task started: fastANI
[2023-03-15 14:38:51,734] [INFO] Running command: fastANI --query /var/lib/cwl/stg222fcb6b-5244-47e5-9a0f-0293ccb36943/OceanDNA-b23077.fa --refList OceanDNA-b23077/target_genomes_gtdb.txt --output OceanDNA-b23077/fastani_result_gtdb.tsv --threads 1
[2023-03-15 14:38:59,951] [INFO] Task succeeded: fastANI
[2023-03-15 14:38:59,953] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 14:38:59,953] [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_018671175.1	s__JABHIE01 sp018671175	99.8831	646	661	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__UBA1135;g__JABHIE01	95.0	99.89	99.85	0.98	0.97	7	conclusive
--------------------------------------------------------------------------------
[2023-03-15 14:38:59,954] [INFO] GTDB search result was written to OceanDNA-b23077/result_gtdb.tsv
[2023-03-15 14:38:59,957] [INFO] ===== GTDB Search completed =====
[2023-03-15 14:38:59,958] [INFO] DFAST_QC result json was written to OceanDNA-b23077/dqc_result.json
[2023-03-15 14:38:59,958] [INFO] DFAST_QC completed!
[2023-03-15 14:38:59,958] [INFO] Total running time: 0h1m11s