[2023-03-17 05:32:05,515] [INFO] DFAST_QC pipeline started.
[2023-03-17 05:32:05,515] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 05:32:05,515] [INFO] DQC Reference Directory: /var/lib/cwl/stg7559dab4-9760-4a00-ae82-0295024406b2/dqc_reference
[2023-03-17 05:32:06,614] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 05:32:06,614] [INFO] Task started: Prodigal
[2023-03-17 05:32:06,614] [INFO] Running command: cat /var/lib/cwl/stgb81b69c0-ff54-46b7-8f3e-ca88c18663c0/OceanDNA-b38880.fa | prodigal -d OceanDNA-b38880/cds.fna -a OceanDNA-b38880/protein.faa -g 11 -q > /dev/null
[2023-03-17 05:32:28,111] [INFO] Task succeeded: Prodigal
[2023-03-17 05:32:28,111] [INFO] Task started: HMMsearch
[2023-03-17 05:32:28,111] [INFO] Running command: hmmsearch --tblout OceanDNA-b38880/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7559dab4-9760-4a00-ae82-0295024406b2/dqc_reference/reference_markers.hmm OceanDNA-b38880/protein.faa > /dev/null
[2023-03-17 05:32:28,326] [INFO] Task succeeded: HMMsearch
[2023-03-17 05:32:28,327] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgb81b69c0-ff54-46b7-8f3e-ca88c18663c0/OceanDNA-b38880.fa]
[2023-03-17 05:32:28,352] [INFO] Query marker FASTA was written to OceanDNA-b38880/markers.fasta
[2023-03-17 05:32:28,354] [INFO] Task started: Blastn
[2023-03-17 05:32:28,354] [INFO] Running command: blastn -query OceanDNA-b38880/markers.fasta -db /var/lib/cwl/stg7559dab4-9760-4a00-ae82-0295024406b2/dqc_reference/reference_markers.fasta -out OceanDNA-b38880/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:32:28,885] [INFO] Task succeeded: Blastn
[2023-03-17 05:32:28,886] [INFO] Selected 26 target genomes.
[2023-03-17 05:32:28,886] [INFO] Target genome list was writen to OceanDNA-b38880/target_genomes.txt
[2023-03-17 05:32:28,938] [INFO] Task started: fastANI
[2023-03-17 05:32:28,938] [INFO] Running command: fastANI --query /var/lib/cwl/stgb81b69c0-ff54-46b7-8f3e-ca88c18663c0/OceanDNA-b38880.fa --refList OceanDNA-b38880/target_genomes.txt --output OceanDNA-b38880/fastani_result.tsv --threads 1
[2023-03-17 05:32:44,657] [INFO] Task succeeded: fastANI
[2023-03-17 05:32:44,657] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7559dab4-9760-4a00-ae82-0295024406b2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 05:32:44,657] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7559dab4-9760-4a00-ae82-0295024406b2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 05:32:44,658] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 05:32:44,658] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 05:32:44,658] [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
--------------------------------------------------------------------------------
[2023-03-17 05:32:44,658] [INFO] DFAST Taxonomy check result was written to OceanDNA-b38880/tc_result.tsv
[2023-03-17 05:32:44,658] [INFO] ===== Taxonomy check completed =====
[2023-03-17 05:32:44,658] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 05:32:44,659] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7559dab4-9760-4a00-ae82-0295024406b2/dqc_reference/checkm_data
[2023-03-17 05:32:44,662] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 05:32:44,888] [INFO] Task started: CheckM
[2023-03-17 05:32:44,888] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b38880/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b38880/checkm_input OceanDNA-b38880/checkm_result
[2023-03-17 05:33:38,883] [INFO] Task succeeded: CheckM
[2023-03-17 05:33:38,883] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 45.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 05:33:38,886] [INFO] ===== Completeness check finished =====
[2023-03-17 05:33:38,886] [INFO] ===== Start GTDB Search =====
[2023-03-17 05:33:38,886] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b38880/markers.fasta)
[2023-03-17 05:33:38,888] [INFO] Task started: Blastn
[2023-03-17 05:33:38,888] [INFO] Running command: blastn -query OceanDNA-b38880/markers.fasta -db /var/lib/cwl/stg7559dab4-9760-4a00-ae82-0295024406b2/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b38880/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:33:39,607] [INFO] Task succeeded: Blastn
[2023-03-17 05:33:39,609] [INFO] Selected 18 target genomes.
[2023-03-17 05:33:39,609] [INFO] Target genome list was writen to OceanDNA-b38880/target_genomes_gtdb.txt
[2023-03-17 05:33:39,627] [INFO] Task started: fastANI
[2023-03-17 05:33:39,627] [INFO] Running command: fastANI --query /var/lib/cwl/stgb81b69c0-ff54-46b7-8f3e-ca88c18663c0/OceanDNA-b38880.fa --refList OceanDNA-b38880/target_genomes_gtdb.txt --output OceanDNA-b38880/fastani_result_gtdb.tsv --threads 1
[2023-03-17 05:33:53,019] [INFO] Task succeeded: fastANI
[2023-03-17 05:33:53,024] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 05:33:53,024] [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_013215445.1	s__Rs1 sp013215445	99.4081	1107	1299	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Rs1	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_013215375.1	s__Rs1 sp013215375	79.1997	468	1299	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Rs1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013215505.1	s__Rs1 sp013215505	79.0243	256	1299	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Rs1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002163025.1	s__Rs1 sp002163025	77.8684	164	1299	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Rs1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000416275.1	s__Rs1 sp000416275	77.6973	192	1299	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Rs1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000416315.1	s__Rs1 sp000416315	77.3857	160	1299	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Rs1	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 05:33:53,025] [INFO] GTDB search result was written to OceanDNA-b38880/result_gtdb.tsv
[2023-03-17 05:33:53,025] [INFO] ===== GTDB Search completed =====
[2023-03-17 05:33:53,026] [INFO] DFAST_QC result json was written to OceanDNA-b38880/dqc_result.json
[2023-03-17 05:33:53,026] [INFO] DFAST_QC completed!
[2023-03-17 05:33:53,026] [INFO] Total running time: 0h1m48s