[2023-03-15 11:54:50,823] [INFO] DFAST_QC pipeline started.
[2023-03-15 11:54:50,824] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 11:54:50,824] [INFO] DQC Reference Directory: /var/lib/cwl/stg00a996c2-1138-4f22-9fed-06475a72f5b6/dqc_reference
[2023-03-15 11:54:51,983] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 11:54:51,984] [INFO] Task started: Prodigal
[2023-03-15 11:54:51,984] [INFO] Running command: cat /var/lib/cwl/stgb9a20bd3-c323-438b-9fc7-ecf1c334998b/OceanDNA-a1079.fa | prodigal -d OceanDNA-a1079/cds.fna -a OceanDNA-a1079/protein.faa -g 11 -q > /dev/null
[2023-03-15 11:54:54,525] [INFO] Task succeeded: Prodigal
[2023-03-15 11:54:54,525] [INFO] Task started: HMMsearch
[2023-03-15 11:54:54,526] [INFO] Running command: hmmsearch --tblout OceanDNA-a1079/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg00a996c2-1138-4f22-9fed-06475a72f5b6/dqc_reference/reference_markers.hmm OceanDNA-a1079/protein.faa > /dev/null
[2023-03-15 11:54:54,719] [INFO] Task succeeded: HMMsearch
[2023-03-15 11:54:54,720] [WARNING] Found 2/6 markers. [/var/lib/cwl/stgb9a20bd3-c323-438b-9fc7-ecf1c334998b/OceanDNA-a1079.fa]
[2023-03-15 11:54:54,726] [INFO] Query marker FASTA was written to OceanDNA-a1079/markers.fasta
[2023-03-15 11:54:54,728] [INFO] Task started: Blastn
[2023-03-15 11:54:54,728] [INFO] Running command: blastn -query OceanDNA-a1079/markers.fasta -db /var/lib/cwl/stg00a996c2-1138-4f22-9fed-06475a72f5b6/dqc_reference/reference_markers.fasta -out OceanDNA-a1079/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:54:55,340] [INFO] Task succeeded: Blastn
[2023-03-15 11:54:55,342] [INFO] Selected 5 target genomes.
[2023-03-15 11:54:55,342] [INFO] Target genome list was writen to OceanDNA-a1079/target_genomes.txt
[2023-03-15 11:54:55,345] [INFO] Task started: fastANI
[2023-03-15 11:54:55,345] [INFO] Running command: fastANI --query /var/lib/cwl/stgb9a20bd3-c323-438b-9fc7-ecf1c334998b/OceanDNA-a1079.fa --refList OceanDNA-a1079/target_genomes.txt --output OceanDNA-a1079/fastani_result.tsv --threads 1
[2023-03-15 11:54:56,627] [INFO] Task succeeded: fastANI
[2023-03-15 11:54:56,627] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg00a996c2-1138-4f22-9fed-06475a72f5b6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 11:54:56,627] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg00a996c2-1138-4f22-9fed-06475a72f5b6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 11:54:56,627] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 11:54:56,628] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 11:54:56,628] [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 11:54:56,628] [INFO] DFAST Taxonomy check result was written to OceanDNA-a1079/tc_result.tsv
[2023-03-15 11:54:56,629] [INFO] ===== Taxonomy check completed =====
[2023-03-15 11:54:56,629] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 11:54:56,629] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg00a996c2-1138-4f22-9fed-06475a72f5b6/dqc_reference/checkm_data
[2023-03-15 11:54:56,677] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 11:54:56,680] [INFO] Task started: CheckM
[2023-03-15 11:54:56,680] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a1079/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a1079/checkm_input OceanDNA-a1079/checkm_result
[2023-03-15 11:55:11,436] [INFO] Task succeeded: CheckM
[2023-03-15 11:55:11,436] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 80.52%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 11:55:11,482] [INFO] ===== Completeness check finished =====
[2023-03-15 11:55:11,482] [INFO] ===== Start GTDB Search =====
[2023-03-15 11:55:11,482] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a1079/markers.fasta)
[2023-03-15 11:55:11,483] [INFO] Task started: Blastn
[2023-03-15 11:55:11,483] [INFO] Running command: blastn -query OceanDNA-a1079/markers.fasta -db /var/lib/cwl/stg00a996c2-1138-4f22-9fed-06475a72f5b6/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a1079/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:55:12,177] [INFO] Task succeeded: Blastn
[2023-03-15 11:55:12,180] [INFO] Selected 9 target genomes.
[2023-03-15 11:55:12,180] [INFO] Target genome list was writen to OceanDNA-a1079/target_genomes_gtdb.txt
[2023-03-15 11:55:12,193] [INFO] Task started: fastANI
[2023-03-15 11:55:12,193] [INFO] Running command: fastANI --query /var/lib/cwl/stgb9a20bd3-c323-438b-9fc7-ecf1c334998b/OceanDNA-a1079.fa --refList OceanDNA-a1079/target_genomes_gtdb.txt --output OceanDNA-a1079/fastani_result_gtdb.tsv --threads 1
[2023-03-15 11:55:13,452] [INFO] Task succeeded: fastANI
[2023-03-15 11:55:13,454] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 11:55:13,454] [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_002688165.1	s__ARS1285 sp002688165	99.3803	93	110	d__Archaea;p__Nanoarchaeota;c__Nanoarchaeia;o__Pacearchaeales;f__GW2011-AR1;g__ARS1285	95.0	95.94	95.94	0.82	0.82	2	conclusive
--------------------------------------------------------------------------------
[2023-03-15 11:55:13,455] [INFO] GTDB search result was written to OceanDNA-a1079/result_gtdb.tsv
[2023-03-15 11:55:13,457] [INFO] ===== GTDB Search completed =====
[2023-03-15 11:55:13,459] [INFO] DFAST_QC result json was written to OceanDNA-a1079/dqc_result.json
[2023-03-15 11:55:13,459] [INFO] DFAST_QC completed!
[2023-03-15 11:55:13,459] [INFO] Total running time: 0h0m23s