[2023-03-17 09:41:39,966] [INFO] DFAST_QC pipeline started.
[2023-03-17 09:41:39,969] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 09:41:39,969] [INFO] DQC Reference Directory: /var/lib/cwl/stg751402e0-2b62-4fd4-9107-192db521a5eb/dqc_reference
[2023-03-17 09:41:41,757] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 09:41:41,758] [INFO] Task started: Prodigal
[2023-03-17 09:41:41,758] [INFO] Running command: cat /var/lib/cwl/stg53777ec0-f7b9-4160-a4d6-9f1e0d2d91f0/OceanDNA-b17052.fa | prodigal -d OceanDNA-b17052/cds.fna -a OceanDNA-b17052/protein.faa -g 11 -q > /dev/null
[2023-03-17 09:41:46,284] [INFO] Task succeeded: Prodigal
[2023-03-17 09:41:46,285] [INFO] Task started: HMMsearch
[2023-03-17 09:41:46,285] [INFO] Running command: hmmsearch --tblout OceanDNA-b17052/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg751402e0-2b62-4fd4-9107-192db521a5eb/dqc_reference/reference_markers.hmm OceanDNA-b17052/protein.faa > /dev/null
[2023-03-17 09:41:46,656] [INFO] Task succeeded: HMMsearch
[2023-03-17 09:41:46,657] [INFO] Found 6/6 markers.
[2023-03-17 09:41:46,670] [INFO] Query marker FASTA was written to OceanDNA-b17052/markers.fasta
[2023-03-17 09:41:46,671] [INFO] Task started: Blastn
[2023-03-17 09:41:46,671] [INFO] Running command: blastn -query OceanDNA-b17052/markers.fasta -db /var/lib/cwl/stg751402e0-2b62-4fd4-9107-192db521a5eb/dqc_reference/reference_markers.fasta -out OceanDNA-b17052/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 09:41:49,802] [INFO] Task succeeded: Blastn
[2023-03-17 09:41:49,805] [INFO] Selected 16 target genomes.
[2023-03-17 09:41:49,805] [INFO] Target genome list was writen to OceanDNA-b17052/target_genomes.txt
[2023-03-17 09:41:50,222] [INFO] Task started: fastANI
[2023-03-17 09:41:50,222] [INFO] Running command: fastANI --query /var/lib/cwl/stg53777ec0-f7b9-4160-a4d6-9f1e0d2d91f0/OceanDNA-b17052.fa --refList OceanDNA-b17052/target_genomes.txt --output OceanDNA-b17052/fastani_result.tsv --threads 1
[2023-03-17 09:41:58,069] [INFO] Task succeeded: fastANI
[2023-03-17 09:41:58,070] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg751402e0-2b62-4fd4-9107-192db521a5eb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 09:41:58,070] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg751402e0-2b62-4fd4-9107-192db521a5eb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 09:41:58,070] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 09:41:58,070] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 09:41:58,070] [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 09:41:58,072] [INFO] DFAST Taxonomy check result was written to OceanDNA-b17052/tc_result.tsv
[2023-03-17 09:41:58,072] [INFO] ===== Taxonomy check completed =====
[2023-03-17 09:41:58,072] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 09:41:58,072] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg751402e0-2b62-4fd4-9107-192db521a5eb/dqc_reference/checkm_data
[2023-03-17 09:41:58,075] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 09:41:58,111] [INFO] Task started: CheckM
[2023-03-17 09:41:58,111] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b17052/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b17052/checkm_input OceanDNA-b17052/checkm_result
[2023-03-17 09:42:18,403] [INFO] Task succeeded: CheckM
[2023-03-17 09:42:18,403] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 09:42:18,454] [INFO] ===== Completeness check finished =====
[2023-03-17 09:42:18,455] [INFO] ===== Start GTDB Search =====
[2023-03-17 09:42:18,455] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b17052/markers.fasta)
[2023-03-17 09:42:18,456] [INFO] Task started: Blastn
[2023-03-17 09:42:18,456] [INFO] Running command: blastn -query OceanDNA-b17052/markers.fasta -db /var/lib/cwl/stg751402e0-2b62-4fd4-9107-192db521a5eb/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b17052/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 09:42:19,988] [INFO] Task succeeded: Blastn
[2023-03-17 09:42:19,995] [INFO] Selected 14 target genomes.
[2023-03-17 09:42:19,995] [INFO] Target genome list was writen to OceanDNA-b17052/target_genomes_gtdb.txt
[2023-03-17 09:42:20,170] [INFO] Task started: fastANI
[2023-03-17 09:42:20,170] [INFO] Running command: fastANI --query /var/lib/cwl/stg53777ec0-f7b9-4160-a4d6-9f1e0d2d91f0/OceanDNA-b17052.fa --refList OceanDNA-b17052/target_genomes_gtdb.txt --output OceanDNA-b17052/fastani_result_gtdb.tsv --threads 1
[2023-03-17 09:42:23,269] [INFO] Task succeeded: fastANI
[2023-03-17 09:42:23,272] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 09:42:23,272] [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_016183005.1	s__JACPFN01 sp016183005	78.5782	108	294	d__Bacteria;p__Dependentiae;c__Babeliae;o__Babeliales;f__Chromulinavoraceae;g__JACPFN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018061805.1	s__JACPFN01 sp018061805	77.9785	64	294	d__Bacteria;p__Dependentiae;c__Babeliae;o__Babeliales;f__Chromulinavoraceae;g__JACPFN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017992075.1	s__JACPFN01 sp017992075	77.5742	52	294	d__Bacteria;p__Dependentiae;c__Babeliae;o__Babeliales;f__Chromulinavoraceae;g__JACPFN01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 09:42:23,275] [INFO] GTDB search result was written to OceanDNA-b17052/result_gtdb.tsv
[2023-03-17 09:42:23,277] [INFO] ===== GTDB Search completed =====
[2023-03-17 09:42:23,280] [INFO] DFAST_QC result json was written to OceanDNA-b17052/dqc_result.json
[2023-03-17 09:42:23,280] [INFO] DFAST_QC completed!
[2023-03-17 09:42:23,280] [INFO] Total running time: 0h0m43s