[2023-03-18 21:15:29,376] [INFO] DFAST_QC pipeline started.
[2023-03-18 21:15:29,377] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 21:15:29,377] [INFO] DQC Reference Directory: /var/lib/cwl/stg8b0d4497-9fad-4c71-99b0-8fa7ce228ab1/dqc_reference
[2023-03-18 21:15:31,044] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 21:15:31,045] [INFO] Task started: Prodigal
[2023-03-18 21:15:31,045] [INFO] Running command: cat /var/lib/cwl/stg66dd2c24-22ea-4a2f-bfbc-661e1775544c/OceanDNA-b39176.fa | prodigal -d OceanDNA-b39176/cds.fna -a OceanDNA-b39176/protein.faa -g 11 -q > /dev/null
[2023-03-18 21:15:40,034] [INFO] Task succeeded: Prodigal
[2023-03-18 21:15:40,035] [INFO] Task started: HMMsearch
[2023-03-18 21:15:40,035] [INFO] Running command: hmmsearch --tblout OceanDNA-b39176/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8b0d4497-9fad-4c71-99b0-8fa7ce228ab1/dqc_reference/reference_markers.hmm OceanDNA-b39176/protein.faa > /dev/null
[2023-03-18 21:15:40,232] [INFO] Task succeeded: HMMsearch
[2023-03-18 21:15:40,233] [INFO] Found 6/6 markers.
[2023-03-18 21:15:40,253] [INFO] Query marker FASTA was written to OceanDNA-b39176/markers.fasta
[2023-03-18 21:15:40,254] [INFO] Task started: Blastn
[2023-03-18 21:15:40,254] [INFO] Running command: blastn -query OceanDNA-b39176/markers.fasta -db /var/lib/cwl/stg8b0d4497-9fad-4c71-99b0-8fa7ce228ab1/dqc_reference/reference_markers.fasta -out OceanDNA-b39176/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:15:40,800] [INFO] Task succeeded: Blastn
[2023-03-18 21:15:40,803] [INFO] Selected 28 target genomes.
[2023-03-18 21:15:40,803] [INFO] Target genome list was writen to OceanDNA-b39176/target_genomes.txt
[2023-03-18 21:15:40,819] [INFO] Task started: fastANI
[2023-03-18 21:15:40,819] [INFO] Running command: fastANI --query /var/lib/cwl/stg66dd2c24-22ea-4a2f-bfbc-661e1775544c/OceanDNA-b39176.fa --refList OceanDNA-b39176/target_genomes.txt --output OceanDNA-b39176/fastani_result.tsv --threads 1
[2023-03-18 21:15:57,388] [INFO] Task succeeded: fastANI
[2023-03-18 21:15:57,389] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8b0d4497-9fad-4c71-99b0-8fa7ce228ab1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 21:15:57,389] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8b0d4497-9fad-4c71-99b0-8fa7ce228ab1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 21:15:57,389] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 21:15:57,389] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 21:15:57,389] [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 21:15:57,390] [INFO] DFAST Taxonomy check result was written to OceanDNA-b39176/tc_result.tsv
[2023-03-18 21:15:57,390] [INFO] ===== Taxonomy check completed =====
[2023-03-18 21:15:57,390] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 21:15:57,391] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8b0d4497-9fad-4c71-99b0-8fa7ce228ab1/dqc_reference/checkm_data
[2023-03-18 21:15:57,393] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 21:15:57,399] [INFO] Task started: CheckM
[2023-03-18 21:15:57,399] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b39176/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b39176/checkm_input OceanDNA-b39176/checkm_result
[2023-03-18 21:16:25,207] [INFO] Task succeeded: CheckM
[2023-03-18 21:16:25,207] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.75%
Contamintation: 1.97%
Strain heterogeneity: 33.33%
--------------------------------------------------------------------------------
[2023-03-18 21:16:25,213] [INFO] ===== Completeness check finished =====
[2023-03-18 21:16:25,213] [INFO] ===== Start GTDB Search =====
[2023-03-18 21:16:25,213] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b39176/markers.fasta)
[2023-03-18 21:16:25,215] [INFO] Task started: Blastn
[2023-03-18 21:16:25,215] [INFO] Running command: blastn -query OceanDNA-b39176/markers.fasta -db /var/lib/cwl/stg8b0d4497-9fad-4c71-99b0-8fa7ce228ab1/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b39176/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:16:26,046] [INFO] Task succeeded: Blastn
[2023-03-18 21:16:26,050] [INFO] Selected 21 target genomes.
[2023-03-18 21:16:26,050] [INFO] Target genome list was writen to OceanDNA-b39176/target_genomes_gtdb.txt
[2023-03-18 21:16:26,076] [INFO] Task started: fastANI
[2023-03-18 21:16:26,076] [INFO] Running command: fastANI --query /var/lib/cwl/stg66dd2c24-22ea-4a2f-bfbc-661e1775544c/OceanDNA-b39176.fa --refList OceanDNA-b39176/target_genomes_gtdb.txt --output OceanDNA-b39176/fastani_result_gtdb.tsv --threads 1
[2023-03-18 21:16:36,530] [INFO] Task succeeded: fastANI
[2023-03-18 21:16:36,536] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 21:16:36,536] [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_003646355.1	s__50-400-T64 sp003646355	79.4761	143	449	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__50-400-T64	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002746135.1	s__50-400-T64 sp002746135	79.0455	228	449	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__50-400-T64	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002162755.1	s__50-400-T64 sp002162755	78.9101	232	449	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__50-400-T64	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002162815.1	s__50-400-T64 sp002162815	78.7747	209	449	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__50-400-T64	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002162825.1	s__50-400-T64 sp002162825	78.7247	170	449	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__50-400-T64	95.0	96.90	96.90	0.90	0.90	2	-
GCA_018069465.1	s__50-400-T64 sp018069465	78.5258	272	449	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__50-400-T64	95.0	100.00	100.00	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2023-03-18 21:16:36,537] [INFO] GTDB search result was written to OceanDNA-b39176/result_gtdb.tsv
[2023-03-18 21:16:36,537] [INFO] ===== GTDB Search completed =====
[2023-03-18 21:16:36,539] [INFO] DFAST_QC result json was written to OceanDNA-b39176/dqc_result.json
[2023-03-18 21:16:36,539] [INFO] DFAST_QC completed!
[2023-03-18 21:16:36,539] [INFO] Total running time: 0h1m7s