[2023-03-17 00:36:57,825] [INFO] DFAST_QC pipeline started.
[2023-03-17 00:36:57,826] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 00:36:57,826] [INFO] DQC Reference Directory: /var/lib/cwl/stg9b73258f-8804-4d13-897a-a6aa23c2fd46/dqc_reference
[2023-03-17 00:36:59,972] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 00:36:59,972] [INFO] Task started: Prodigal
[2023-03-17 00:36:59,973] [INFO] Running command: cat /var/lib/cwl/stg46f46832-1df3-4cb1-b597-4fcd8d1eb898/OceanDNA-b6506.fa | prodigal -d OceanDNA-b6506/cds.fna -a OceanDNA-b6506/protein.faa -g 11 -q > /dev/null
[2023-03-17 00:37:10,948] [INFO] Task succeeded: Prodigal
[2023-03-17 00:37:10,948] [INFO] Task started: HMMsearch
[2023-03-17 00:37:10,949] [INFO] Running command: hmmsearch --tblout OceanDNA-b6506/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9b73258f-8804-4d13-897a-a6aa23c2fd46/dqc_reference/reference_markers.hmm OceanDNA-b6506/protein.faa > /dev/null
[2023-03-17 00:37:11,129] [INFO] Task succeeded: HMMsearch
[2023-03-17 00:37:11,130] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg46f46832-1df3-4cb1-b597-4fcd8d1eb898/OceanDNA-b6506.fa]
[2023-03-17 00:37:11,147] [INFO] Query marker FASTA was written to OceanDNA-b6506/markers.fasta
[2023-03-17 00:37:11,148] [INFO] Task started: Blastn
[2023-03-17 00:37:11,148] [INFO] Running command: blastn -query OceanDNA-b6506/markers.fasta -db /var/lib/cwl/stg9b73258f-8804-4d13-897a-a6aa23c2fd46/dqc_reference/reference_markers.fasta -out OceanDNA-b6506/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 00:37:11,597] [INFO] Task succeeded: Blastn
[2023-03-17 00:37:11,597] [INFO] Selected 20 target genomes.
[2023-03-17 00:37:11,598] [INFO] Target genome list was writen to OceanDNA-b6506/target_genomes.txt
[2023-03-17 00:37:11,609] [INFO] Task started: fastANI
[2023-03-17 00:37:11,610] [INFO] Running command: fastANI --query /var/lib/cwl/stg46f46832-1df3-4cb1-b597-4fcd8d1eb898/OceanDNA-b6506.fa --refList OceanDNA-b6506/target_genomes.txt --output OceanDNA-b6506/fastani_result.tsv --threads 1
[2023-03-17 00:37:24,094] [INFO] Task succeeded: fastANI
[2023-03-17 00:37:24,094] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9b73258f-8804-4d13-897a-a6aa23c2fd46/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 00:37:24,095] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9b73258f-8804-4d13-897a-a6aa23c2fd46/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 00:37:24,098] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 00:37:24,098] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 00:37:24,098] [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
Aquimarina agarivorans	strain=HQM9	GCA_000218485.2	980584	980584	type	True	76.8283	83	425	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 00:37:24,098] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6506/tc_result.tsv
[2023-03-17 00:37:24,098] [INFO] ===== Taxonomy check completed =====
[2023-03-17 00:37:24,098] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 00:37:24,098] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9b73258f-8804-4d13-897a-a6aa23c2fd46/dqc_reference/checkm_data
[2023-03-17 00:37:24,099] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 00:37:24,103] [INFO] Task started: CheckM
[2023-03-17 00:37:24,103] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6506/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6506/checkm_input OceanDNA-b6506/checkm_result
[2023-03-17 00:37:55,614] [INFO] Task succeeded: CheckM
[2023-03-17 00:37:55,614] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 33.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 00:37:55,616] [INFO] ===== Completeness check finished =====
[2023-03-17 00:37:55,616] [INFO] ===== Start GTDB Search =====
[2023-03-17 00:37:55,617] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6506/markers.fasta)
[2023-03-17 00:37:55,618] [INFO] Task started: Blastn
[2023-03-17 00:37:55,618] [INFO] Running command: blastn -query OceanDNA-b6506/markers.fasta -db /var/lib/cwl/stg9b73258f-8804-4d13-897a-a6aa23c2fd46/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6506/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 00:37:56,079] [INFO] Task succeeded: Blastn
[2023-03-17 00:37:56,080] [INFO] Selected 19 target genomes.
[2023-03-17 00:37:56,080] [INFO] Target genome list was writen to OceanDNA-b6506/target_genomes_gtdb.txt
[2023-03-17 00:37:56,526] [INFO] Task started: fastANI
[2023-03-17 00:37:56,526] [INFO] Running command: fastANI --query /var/lib/cwl/stg46f46832-1df3-4cb1-b597-4fcd8d1eb898/OceanDNA-b6506.fa --refList OceanDNA-b6506/target_genomes_gtdb.txt --output OceanDNA-b6506/fastani_result_gtdb.tsv --threads 1
[2023-03-17 00:38:08,930] [INFO] Task succeeded: fastANI
[2023-03-17 00:38:08,932] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 00:38:08,933] [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_000218485.1	s__Aquimarina agarivorans	76.8302	83	425	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 00:38:08,933] [INFO] GTDB search result was written to OceanDNA-b6506/result_gtdb.tsv
[2023-03-17 00:38:08,933] [INFO] ===== GTDB Search completed =====
[2023-03-17 00:38:08,935] [INFO] DFAST_QC result json was written to OceanDNA-b6506/dqc_result.json
[2023-03-17 00:38:08,935] [INFO] DFAST_QC completed!
[2023-03-17 00:38:08,935] [INFO] Total running time: 0h1m11s