[2023-03-19 02:40:15,840] [INFO] DFAST_QC pipeline started.
[2023-03-19 02:40:15,840] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 02:40:15,840] [INFO] DQC Reference Directory: /var/lib/cwl/stg9ec241dd-305c-4e91-9fca-6e4f7af1f1db/dqc_reference
[2023-03-19 02:40:17,559] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 02:40:17,563] [INFO] Task started: Prodigal
[2023-03-19 02:40:17,563] [INFO] Running command: cat /var/lib/cwl/stg2c225077-558d-477c-894a-1b8b6538cbcc/OceanDNA-b46204.fa | prodigal -d OceanDNA-b46204/cds.fna -a OceanDNA-b46204/protein.faa -g 11 -q > /dev/null
[2023-03-19 02:40:45,417] [INFO] Task succeeded: Prodigal
[2023-03-19 02:40:45,418] [INFO] Task started: HMMsearch
[2023-03-19 02:40:45,418] [INFO] Running command: hmmsearch --tblout OceanDNA-b46204/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9ec241dd-305c-4e91-9fca-6e4f7af1f1db/dqc_reference/reference_markers.hmm OceanDNA-b46204/protein.faa > /dev/null
[2023-03-19 02:40:45,619] [INFO] Task succeeded: HMMsearch
[2023-03-19 02:40:45,619] [INFO] Found 6/6 markers.
[2023-03-19 02:40:45,646] [INFO] Query marker FASTA was written to OceanDNA-b46204/markers.fasta
[2023-03-19 02:40:45,648] [INFO] Task started: Blastn
[2023-03-19 02:40:45,648] [INFO] Running command: blastn -query OceanDNA-b46204/markers.fasta -db /var/lib/cwl/stg9ec241dd-305c-4e91-9fca-6e4f7af1f1db/dqc_reference/reference_markers.fasta -out OceanDNA-b46204/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:40:46,193] [INFO] Task succeeded: Blastn
[2023-03-19 02:40:46,195] [INFO] Selected 11 target genomes.
[2023-03-19 02:40:46,195] [INFO] Target genome list was writen to OceanDNA-b46204/target_genomes.txt
[2023-03-19 02:40:46,202] [INFO] Task started: fastANI
[2023-03-19 02:40:46,203] [INFO] Running command: fastANI --query /var/lib/cwl/stg2c225077-558d-477c-894a-1b8b6538cbcc/OceanDNA-b46204.fa --refList OceanDNA-b46204/target_genomes.txt --output OceanDNA-b46204/fastani_result.tsv --threads 1
[2023-03-19 02:40:53,666] [INFO] Task succeeded: fastANI
[2023-03-19 02:40:53,666] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9ec241dd-305c-4e91-9fca-6e4f7af1f1db/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 02:40:53,666] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9ec241dd-305c-4e91-9fca-6e4f7af1f1db/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 02:40:53,666] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 02:40:53,666] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 02:40:53,667] [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
--------------------------------------------------------------------------------
[2023-03-19 02:40:53,667] [INFO] DFAST Taxonomy check result was written to OceanDNA-b46204/tc_result.tsv
[2023-03-19 02:40:53,668] [INFO] ===== Taxonomy check completed =====
[2023-03-19 02:40:53,668] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 02:40:53,669] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9ec241dd-305c-4e91-9fca-6e4f7af1f1db/dqc_reference/checkm_data
[2023-03-19 02:40:53,671] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 02:40:53,681] [INFO] Task started: CheckM
[2023-03-19 02:40:53,681] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b46204/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b46204/checkm_input OceanDNA-b46204/checkm_result
[2023-03-19 02:42:04,488] [INFO] Task succeeded: CheckM
[2023-03-19 02:42:04,488] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.76%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-19 02:42:04,524] [INFO] ===== Completeness check finished =====
[2023-03-19 02:42:04,524] [INFO] ===== Start GTDB Search =====
[2023-03-19 02:42:04,524] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b46204/markers.fasta)
[2023-03-19 02:42:04,525] [INFO] Task started: Blastn
[2023-03-19 02:42:04,525] [INFO] Running command: blastn -query OceanDNA-b46204/markers.fasta -db /var/lib/cwl/stg9ec241dd-305c-4e91-9fca-6e4f7af1f1db/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b46204/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:42:05,588] [INFO] Task succeeded: Blastn
[2023-03-19 02:42:05,589] [INFO] Selected 17 target genomes.
[2023-03-19 02:42:05,589] [INFO] Target genome list was writen to OceanDNA-b46204/target_genomes_gtdb.txt
[2023-03-19 02:42:05,609] [INFO] Task started: fastANI
[2023-03-19 02:42:05,609] [INFO] Running command: fastANI --query /var/lib/cwl/stg2c225077-558d-477c-894a-1b8b6538cbcc/OceanDNA-b46204.fa --refList OceanDNA-b46204/target_genomes_gtdb.txt --output OceanDNA-b46204/fastani_result_gtdb.tsv --threads 1
[2023-03-19 02:42:13,885] [INFO] Task succeeded: fastANI
[2023-03-19 02:42:13,888] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 02:42:13,888] [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_002346535.1	s__UBA2995 sp002346535	77.5961	51	1189	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__UBA2995;g__UBA2995	95.0	99.50	99.50	0.90	0.90	2	-
GCA_014529675.1	s__UBA2995 sp014529675	76.4558	146	1189	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__UBA2995;g__UBA2995	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-03-19 02:42:13,889] [INFO] GTDB search result was written to OceanDNA-b46204/result_gtdb.tsv
[2023-03-19 02:42:13,889] [INFO] ===== GTDB Search completed =====
[2023-03-19 02:42:13,890] [INFO] DFAST_QC result json was written to OceanDNA-b46204/dqc_result.json
[2023-03-19 02:42:13,890] [INFO] DFAST_QC completed!
[2023-03-19 02:42:13,890] [INFO] Total running time: 0h1m58s