[2023-03-18 22:53:23,464] [INFO] DFAST_QC pipeline started.
[2023-03-18 22:53:23,464] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 22:53:23,465] [INFO] DQC Reference Directory: /var/lib/cwl/stg897dd9c3-27a9-49be-9ca6-8787650dfe9a/dqc_reference
[2023-03-18 22:53:25,705] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 22:53:25,706] [INFO] Task started: Prodigal
[2023-03-18 22:53:25,706] [INFO] Running command: cat /var/lib/cwl/stg384574a8-6897-41fb-bfe8-8b74b6cee45e/OceanDNA-b40613.fa | prodigal -d OceanDNA-b40613/cds.fna -a OceanDNA-b40613/protein.faa -g 11 -q > /dev/null
[2023-03-18 22:53:32,390] [INFO] Task succeeded: Prodigal
[2023-03-18 22:53:32,391] [INFO] Task started: HMMsearch
[2023-03-18 22:53:32,391] [INFO] Running command: hmmsearch --tblout OceanDNA-b40613/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg897dd9c3-27a9-49be-9ca6-8787650dfe9a/dqc_reference/reference_markers.hmm OceanDNA-b40613/protein.faa > /dev/null
[2023-03-18 22:53:32,616] [INFO] Task succeeded: HMMsearch
[2023-03-18 22:53:32,617] [INFO] Found 6/6 markers.
[2023-03-18 22:53:32,633] [INFO] Query marker FASTA was written to OceanDNA-b40613/markers.fasta
[2023-03-18 22:53:32,634] [INFO] Task started: Blastn
[2023-03-18 22:53:32,634] [INFO] Running command: blastn -query OceanDNA-b40613/markers.fasta -db /var/lib/cwl/stg897dd9c3-27a9-49be-9ca6-8787650dfe9a/dqc_reference/reference_markers.fasta -out OceanDNA-b40613/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:53:35,059] [INFO] Task succeeded: Blastn
[2023-03-18 22:53:35,060] [INFO] Selected 35 target genomes.
[2023-03-18 22:53:35,060] [INFO] Target genome list was writen to OceanDNA-b40613/target_genomes.txt
[2023-03-18 22:53:35,166] [INFO] Task started: fastANI
[2023-03-18 22:53:35,166] [INFO] Running command: fastANI --query /var/lib/cwl/stg384574a8-6897-41fb-bfe8-8b74b6cee45e/OceanDNA-b40613.fa --refList OceanDNA-b40613/target_genomes.txt --output OceanDNA-b40613/fastani_result.tsv --threads 1
[2023-03-18 22:53:58,404] [INFO] Task succeeded: fastANI
[2023-03-18 22:53:58,404] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg897dd9c3-27a9-49be-9ca6-8787650dfe9a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 22:53:58,404] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg897dd9c3-27a9-49be-9ca6-8787650dfe9a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 22:53:58,404] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 22:53:58,404] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 22:53:58,405] [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 22:53:58,405] [INFO] DFAST Taxonomy check result was written to OceanDNA-b40613/tc_result.tsv
[2023-03-18 22:53:58,405] [INFO] ===== Taxonomy check completed =====
[2023-03-18 22:53:58,405] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 22:53:58,405] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg897dd9c3-27a9-49be-9ca6-8787650dfe9a/dqc_reference/checkm_data
[2023-03-18 22:53:58,409] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 22:53:58,412] [INFO] Task started: CheckM
[2023-03-18 22:53:58,412] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b40613/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b40613/checkm_input OceanDNA-b40613/checkm_result
[2023-03-18 22:54:20,897] [INFO] Task succeeded: CheckM
[2023-03-18 22:54:20,898] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.33%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 22:54:20,899] [INFO] ===== Completeness check finished =====
[2023-03-18 22:54:20,900] [INFO] ===== Start GTDB Search =====
[2023-03-18 22:54:20,900] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b40613/markers.fasta)
[2023-03-18 22:54:20,901] [INFO] Task started: Blastn
[2023-03-18 22:54:20,901] [INFO] Running command: blastn -query OceanDNA-b40613/markers.fasta -db /var/lib/cwl/stg897dd9c3-27a9-49be-9ca6-8787650dfe9a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b40613/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:54:21,740] [INFO] Task succeeded: Blastn
[2023-03-18 22:54:21,741] [INFO] Selected 24 target genomes.
[2023-03-18 22:54:21,741] [INFO] Target genome list was writen to OceanDNA-b40613/target_genomes_gtdb.txt
[2023-03-18 22:54:21,773] [INFO] Task started: fastANI
[2023-03-18 22:54:21,773] [INFO] Running command: fastANI --query /var/lib/cwl/stg384574a8-6897-41fb-bfe8-8b74b6cee45e/OceanDNA-b40613.fa --refList OceanDNA-b40613/target_genomes_gtdb.txt --output OceanDNA-b40613/fastani_result_gtdb.tsv --threads 1
[2023-03-18 22:54:33,272] [INFO] Task succeeded: fastANI
[2023-03-18 22:54:33,276] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 22:54:33,276] [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_905478195.1	s__UBA9145 sp003483155	93.5276	222	245	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	99.23	98.96	0.87	0.81	6	-
GCA_002401885.1	s__UBA9145 sp002401885	78.2916	113	245	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016762995.1	s__UBA9145 sp016762995	77.6463	90	245	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	96.79	96.79	0.78	0.78	2	-
GCA_016762975.1	s__UBA9145 sp016762975	77.3439	86	245	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 22:54:33,276] [INFO] GTDB search result was written to OceanDNA-b40613/result_gtdb.tsv
[2023-03-18 22:54:33,276] [INFO] ===== GTDB Search completed =====
[2023-03-18 22:54:33,277] [INFO] DFAST_QC result json was written to OceanDNA-b40613/dqc_result.json
[2023-03-18 22:54:33,277] [INFO] DFAST_QC completed!
[2023-03-18 22:54:33,277] [INFO] Total running time: 0h1m10s