[2023-03-18 23:47:14,094] [INFO] DFAST_QC pipeline started.
[2023-03-18 23:47:14,094] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 23:47:14,094] [INFO] DQC Reference Directory: /var/lib/cwl/stg99905db1-b835-4780-87f0-a18e6fb9388d/dqc_reference
[2023-03-18 23:47:15,194] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 23:47:15,195] [INFO] Task started: Prodigal
[2023-03-18 23:47:15,195] [INFO] Running command: cat /var/lib/cwl/stgfdd9e583-10e6-431a-9bbb-6b02e483db41/OceanDNA-b46198.fa | prodigal -d OceanDNA-b46198/cds.fna -a OceanDNA-b46198/protein.faa -g 11 -q > /dev/null
[2023-03-18 23:47:28,790] [INFO] Task succeeded: Prodigal
[2023-03-18 23:47:28,791] [INFO] Task started: HMMsearch
[2023-03-18 23:47:28,791] [INFO] Running command: hmmsearch --tblout OceanDNA-b46198/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg99905db1-b835-4780-87f0-a18e6fb9388d/dqc_reference/reference_markers.hmm OceanDNA-b46198/protein.faa > /dev/null
[2023-03-18 23:47:28,960] [INFO] Task succeeded: HMMsearch
[2023-03-18 23:47:28,961] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgfdd9e583-10e6-431a-9bbb-6b02e483db41/OceanDNA-b46198.fa]
[2023-03-18 23:47:28,974] [INFO] Query marker FASTA was written to OceanDNA-b46198/markers.fasta
[2023-03-18 23:47:28,976] [INFO] Task started: Blastn
[2023-03-18 23:47:28,976] [INFO] Running command: blastn -query OceanDNA-b46198/markers.fasta -db /var/lib/cwl/stg99905db1-b835-4780-87f0-a18e6fb9388d/dqc_reference/reference_markers.fasta -out OceanDNA-b46198/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:47:29,538] [INFO] Task succeeded: Blastn
[2023-03-18 23:47:29,539] [INFO] Selected 10 target genomes.
[2023-03-18 23:47:29,539] [INFO] Target genome list was writen to OceanDNA-b46198/target_genomes.txt
[2023-03-18 23:47:29,545] [INFO] Task started: fastANI
[2023-03-18 23:47:29,545] [INFO] Running command: fastANI --query /var/lib/cwl/stgfdd9e583-10e6-431a-9bbb-6b02e483db41/OceanDNA-b46198.fa --refList OceanDNA-b46198/target_genomes.txt --output OceanDNA-b46198/fastani_result.tsv --threads 1
[2023-03-18 23:47:35,782] [INFO] Task succeeded: fastANI
[2023-03-18 23:47:35,782] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg99905db1-b835-4780-87f0-a18e6fb9388d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 23:47:35,782] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg99905db1-b835-4780-87f0-a18e6fb9388d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 23:47:35,782] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 23:47:35,782] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 23:47:35,783] [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
--------------------------------------------------------------------------------
[2023-03-18 23:47:35,783] [INFO] DFAST Taxonomy check result was written to OceanDNA-b46198/tc_result.tsv
[2023-03-18 23:47:35,783] [INFO] ===== Taxonomy check completed =====
[2023-03-18 23:47:35,783] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 23:47:35,783] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg99905db1-b835-4780-87f0-a18e6fb9388d/dqc_reference/checkm_data
[2023-03-18 23:47:35,786] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 23:47:35,789] [INFO] Task started: CheckM
[2023-03-18 23:47:35,789] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b46198/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b46198/checkm_input OceanDNA-b46198/checkm_result
[2023-03-18 23:48:12,616] [INFO] Task succeeded: CheckM
[2023-03-18 23:48:12,617] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 23:48:12,619] [INFO] ===== Completeness check finished =====
[2023-03-18 23:48:12,619] [INFO] ===== Start GTDB Search =====
[2023-03-18 23:48:12,619] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b46198/markers.fasta)
[2023-03-18 23:48:12,620] [INFO] Task started: Blastn
[2023-03-18 23:48:12,620] [INFO] Running command: blastn -query OceanDNA-b46198/markers.fasta -db /var/lib/cwl/stg99905db1-b835-4780-87f0-a18e6fb9388d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b46198/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:48:13,600] [INFO] Task succeeded: Blastn
[2023-03-18 23:48:13,601] [INFO] Selected 21 target genomes.
[2023-03-18 23:48:13,601] [INFO] Target genome list was writen to OceanDNA-b46198/target_genomes_gtdb.txt
[2023-03-18 23:48:13,613] [INFO] Task started: fastANI
[2023-03-18 23:48:13,613] [INFO] Running command: fastANI --query /var/lib/cwl/stgfdd9e583-10e6-431a-9bbb-6b02e483db41/OceanDNA-b46198.fa --refList OceanDNA-b46198/target_genomes_gtdb.txt --output OceanDNA-b46198/fastani_result_gtdb.tsv --threads 1
[2023-03-18 23:48:23,522] [INFO] Task succeeded: fastANI
[2023-03-18 23:48:23,524] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 23:48:23,524] [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_003226295.1	s__Moanabacter tarae	99.9971	784	795	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__UBA2987;g__Moanabacter	95.0	99.99	99.99	1.00	1.00	2	conclusive
--------------------------------------------------------------------------------
[2023-03-18 23:48:23,524] [INFO] GTDB search result was written to OceanDNA-b46198/result_gtdb.tsv
[2023-03-18 23:48:23,524] [INFO] ===== GTDB Search completed =====
[2023-03-18 23:48:23,524] [INFO] DFAST_QC result json was written to OceanDNA-b46198/dqc_result.json
[2023-03-18 23:48:23,525] [INFO] DFAST_QC completed!
[2023-03-18 23:48:23,525] [INFO] Total running time: 0h1m9s