[2023-03-18 06:37:01,798] [INFO] DFAST_QC pipeline started.
[2023-03-18 06:37:01,798] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 06:37:01,798] [INFO] DQC Reference Directory: /var/lib/cwl/stge42cb3d8-66df-4d85-b88a-7c3f6cbd5625/dqc_reference
[2023-03-18 06:37:03,369] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 06:37:03,369] [INFO] Task started: Prodigal
[2023-03-18 06:37:03,369] [INFO] Running command: cat /var/lib/cwl/stg7c8bd771-baf5-427e-bc1d-920463753d7f/OceanDNA-b40755.fa | prodigal -d OceanDNA-b40755/cds.fna -a OceanDNA-b40755/protein.faa -g 11 -q > /dev/null
[2023-03-18 06:37:16,892] [INFO] Task succeeded: Prodigal
[2023-03-18 06:37:16,892] [INFO] Task started: HMMsearch
[2023-03-18 06:37:16,892] [INFO] Running command: hmmsearch --tblout OceanDNA-b40755/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge42cb3d8-66df-4d85-b88a-7c3f6cbd5625/dqc_reference/reference_markers.hmm OceanDNA-b40755/protein.faa > /dev/null
[2023-03-18 06:37:17,076] [INFO] Task succeeded: HMMsearch
[2023-03-18 06:37:17,076] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg7c8bd771-baf5-427e-bc1d-920463753d7f/OceanDNA-b40755.fa]
[2023-03-18 06:37:17,094] [INFO] Query marker FASTA was written to OceanDNA-b40755/markers.fasta
[2023-03-18 06:37:17,094] [INFO] Task started: Blastn
[2023-03-18 06:37:17,094] [INFO] Running command: blastn -query OceanDNA-b40755/markers.fasta -db /var/lib/cwl/stge42cb3d8-66df-4d85-b88a-7c3f6cbd5625/dqc_reference/reference_markers.fasta -out OceanDNA-b40755/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 06:37:17,662] [INFO] Task succeeded: Blastn
[2023-03-18 06:37:17,663] [INFO] Selected 26 target genomes.
[2023-03-18 06:37:17,663] [INFO] Target genome list was writen to OceanDNA-b40755/target_genomes.txt
[2023-03-18 06:37:17,679] [INFO] Task started: fastANI
[2023-03-18 06:37:17,679] [INFO] Running command: fastANI --query /var/lib/cwl/stg7c8bd771-baf5-427e-bc1d-920463753d7f/OceanDNA-b40755.fa --refList OceanDNA-b40755/target_genomes.txt --output OceanDNA-b40755/fastani_result.tsv --threads 1
[2023-03-18 06:37:32,878] [INFO] Task succeeded: fastANI
[2023-03-18 06:37:32,878] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge42cb3d8-66df-4d85-b88a-7c3f6cbd5625/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 06:37:32,879] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge42cb3d8-66df-4d85-b88a-7c3f6cbd5625/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 06:37:32,879] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 06:37:32,879] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 06:37:32,879] [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 06:37:32,879] [INFO] DFAST Taxonomy check result was written to OceanDNA-b40755/tc_result.tsv
[2023-03-18 06:37:32,879] [INFO] ===== Taxonomy check completed =====
[2023-03-18 06:37:32,879] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 06:37:32,879] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge42cb3d8-66df-4d85-b88a-7c3f6cbd5625/dqc_reference/checkm_data
[2023-03-18 06:37:32,882] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 06:37:32,886] [INFO] Task started: CheckM
[2023-03-18 06:37:32,886] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b40755/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b40755/checkm_input OceanDNA-b40755/checkm_result
[2023-03-18 06:38:09,677] [INFO] Task succeeded: CheckM
[2023-03-18 06:38:09,677] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 76.93%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 06:38:09,679] [INFO] ===== Completeness check finished =====
[2023-03-18 06:38:09,679] [INFO] ===== Start GTDB Search =====
[2023-03-18 06:38:09,679] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b40755/markers.fasta)
[2023-03-18 06:38:09,680] [INFO] Task started: Blastn
[2023-03-18 06:38:09,680] [INFO] Running command: blastn -query OceanDNA-b40755/markers.fasta -db /var/lib/cwl/stge42cb3d8-66df-4d85-b88a-7c3f6cbd5625/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b40755/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 06:38:10,621] [INFO] Task succeeded: Blastn
[2023-03-18 06:38:10,622] [INFO] Selected 24 target genomes.
[2023-03-18 06:38:10,622] [INFO] Target genome list was writen to OceanDNA-b40755/target_genomes_gtdb.txt
[2023-03-18 06:38:10,854] [INFO] Task started: fastANI
[2023-03-18 06:38:10,854] [INFO] Running command: fastANI --query /var/lib/cwl/stg7c8bd771-baf5-427e-bc1d-920463753d7f/OceanDNA-b40755.fa --refList OceanDNA-b40755/target_genomes_gtdb.txt --output OceanDNA-b40755/fastani_result_gtdb.tsv --threads 1
[2023-03-18 06:38:24,940] [INFO] Task succeeded: fastANI
[2023-03-18 06:38:24,942] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 06:38:24,943] [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_002377605.1	s__UBA9145 sp002377605	99.0414	604	811	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002723195.1	s__UBA9145 sp002723195	79.2763	156	811	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012103535.1	s__UBA9145 sp012103535	77.6091	226	811	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 06:38:25,066] [INFO] GTDB search result was written to OceanDNA-b40755/result_gtdb.tsv
[2023-03-18 06:38:25,381] [INFO] ===== GTDB Search completed =====
[2023-03-18 06:38:25,381] [INFO] DFAST_QC result json was written to OceanDNA-b40755/dqc_result.json
[2023-03-18 06:38:25,381] [INFO] DFAST_QC completed!
[2023-03-18 06:38:25,382] [INFO] Total running time: 0h1m24s