[2023-03-16 00:24:05,788] [INFO] DFAST_QC pipeline started.
[2023-03-16 00:24:05,789] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 00:24:05,789] [INFO] DQC Reference Directory: /var/lib/cwl/stg142ee53a-e661-41af-9df9-952359912759/dqc_reference
[2023-03-16 00:24:06,929] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 00:24:06,930] [INFO] Task started: Prodigal
[2023-03-16 00:24:06,930] [INFO] Running command: cat /var/lib/cwl/stgcb506edd-4a30-4169-b48c-51baf697e7d4/OceanDNA-b34245.fa | prodigal -d OceanDNA-b34245/cds.fna -a OceanDNA-b34245/protein.faa -g 11 -q > /dev/null
[2023-03-16 00:24:19,625] [INFO] Task succeeded: Prodigal
[2023-03-16 00:24:19,626] [INFO] Task started: HMMsearch
[2023-03-16 00:24:19,626] [INFO] Running command: hmmsearch --tblout OceanDNA-b34245/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg142ee53a-e661-41af-9df9-952359912759/dqc_reference/reference_markers.hmm OceanDNA-b34245/protein.faa > /dev/null
[2023-03-16 00:24:19,801] [INFO] Task succeeded: HMMsearch
[2023-03-16 00:24:19,802] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgcb506edd-4a30-4169-b48c-51baf697e7d4/OceanDNA-b34245.fa]
[2023-03-16 00:24:19,816] [INFO] Query marker FASTA was written to OceanDNA-b34245/markers.fasta
[2023-03-16 00:24:19,817] [INFO] Task started: Blastn
[2023-03-16 00:24:19,817] [INFO] Running command: blastn -query OceanDNA-b34245/markers.fasta -db /var/lib/cwl/stg142ee53a-e661-41af-9df9-952359912759/dqc_reference/reference_markers.fasta -out OceanDNA-b34245/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 00:24:20,403] [INFO] Task succeeded: Blastn
[2023-03-16 00:24:20,404] [INFO] Selected 24 target genomes.
[2023-03-16 00:24:20,404] [INFO] Target genome list was writen to OceanDNA-b34245/target_genomes.txt
[2023-03-16 00:24:20,435] [INFO] Task started: fastANI
[2023-03-16 00:24:20,435] [INFO] Running command: fastANI --query /var/lib/cwl/stgcb506edd-4a30-4169-b48c-51baf697e7d4/OceanDNA-b34245.fa --refList OceanDNA-b34245/target_genomes.txt --output OceanDNA-b34245/fastani_result.tsv --threads 1
[2023-03-16 00:24:32,727] [INFO] Task succeeded: fastANI
[2023-03-16 00:24:32,727] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg142ee53a-e661-41af-9df9-952359912759/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 00:24:32,727] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg142ee53a-e661-41af-9df9-952359912759/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 00:24:32,727] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 00:24:32,728] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 00:24:32,728] [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
--------------------------------------------------------------------------------
[2023-03-16 00:24:32,728] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34245/tc_result.tsv
[2023-03-16 00:24:32,728] [INFO] ===== Taxonomy check completed =====
[2023-03-16 00:24:32,728] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 00:24:32,728] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg142ee53a-e661-41af-9df9-952359912759/dqc_reference/checkm_data
[2023-03-16 00:24:32,731] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 00:24:32,793] [INFO] Task started: CheckM
[2023-03-16 00:24:32,793] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34245/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34245/checkm_input OceanDNA-b34245/checkm_result
[2023-03-16 00:25:08,194] [INFO] Task succeeded: CheckM
[2023-03-16 00:25:08,194] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 00:25:08,240] [INFO] ===== Completeness check finished =====
[2023-03-16 00:25:08,240] [INFO] ===== Start GTDB Search =====
[2023-03-16 00:25:08,241] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34245/markers.fasta)
[2023-03-16 00:25:08,242] [INFO] Task started: Blastn
[2023-03-16 00:25:08,242] [INFO] Running command: blastn -query OceanDNA-b34245/markers.fasta -db /var/lib/cwl/stg142ee53a-e661-41af-9df9-952359912759/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34245/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 00:25:09,215] [INFO] Task succeeded: Blastn
[2023-03-16 00:25:09,225] [INFO] Selected 16 target genomes.
[2023-03-16 00:25:09,225] [INFO] Target genome list was writen to OceanDNA-b34245/target_genomes_gtdb.txt
[2023-03-16 00:25:09,242] [INFO] Task started: fastANI
[2023-03-16 00:25:09,242] [INFO] Running command: fastANI --query /var/lib/cwl/stgcb506edd-4a30-4169-b48c-51baf697e7d4/OceanDNA-b34245.fa --refList OceanDNA-b34245/target_genomes_gtdb.txt --output OceanDNA-b34245/fastani_result_gtdb.tsv --threads 1
[2023-03-16 00:25:15,769] [INFO] Task succeeded: fastANI
[2023-03-16 00:25:15,774] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 00:25:15,774] [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_013287435.1	s__2-02-FULL-42-43 sp013287435	76.9373	72	710	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Coxiellales;f__Coxiellaceae;g__2-02-FULL-42-43	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013287505.1	s__2-02-FULL-42-43 sp013287505	76.9348	86	710	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Coxiellales;f__Coxiellaceae;g__2-02-FULL-42-43	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001802455.1	s__2-02-FULL-42-43 sp001802455	76.7268	108	710	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Coxiellales;f__Coxiellaceae;g__2-02-FULL-42-43	95.0	99.99	99.99	0.96	0.96	2	-
GCA_002793195.1	s__2-02-FULL-42-43 sp002793195	76.7221	121	710	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Coxiellales;f__Coxiellaceae;g__2-02-FULL-42-43	95.0	99.97	99.93	0.97	0.97	3	-
GCA_001801815.1	s__2-02-FULL-42-43 sp001801815	76.5415	94	710	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Coxiellales;f__Coxiellaceae;g__2-02-FULL-42-43	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001801515.1	s__2-02-FULL-42-43 sp001801515	75.9594	86	710	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Coxiellales;f__Coxiellaceae;g__2-02-FULL-42-43	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 00:25:15,775] [INFO] GTDB search result was written to OceanDNA-b34245/result_gtdb.tsv
[2023-03-16 00:25:15,777] [INFO] ===== GTDB Search completed =====
[2023-03-16 00:25:15,778] [INFO] DFAST_QC result json was written to OceanDNA-b34245/dqc_result.json
[2023-03-16 00:25:15,778] [INFO] DFAST_QC completed!
[2023-03-16 00:25:15,778] [INFO] Total running time: 0h1m10s