[2023-03-15 13:03:53,434] [INFO] DFAST_QC pipeline started.
[2023-03-15 13:03:53,434] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 13:03:53,434] [INFO] DQC Reference Directory: /var/lib/cwl/stg82c92777-2b39-4667-99bf-1dce8a905b43/dqc_reference
[2023-03-15 13:03:54,621] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 13:03:54,621] [INFO] Task started: Prodigal
[2023-03-15 13:03:54,621] [INFO] Running command: cat /var/lib/cwl/stg61fcef9c-69cd-4f68-80da-baabab2f5443/OceanDNA-b25714.fa | prodigal -d OceanDNA-b25714/cds.fna -a OceanDNA-b25714/protein.faa -g 11 -q > /dev/null
[2023-03-15 13:03:57,396] [INFO] Task succeeded: Prodigal
[2023-03-15 13:03:57,397] [INFO] Task started: HMMsearch
[2023-03-15 13:03:57,397] [INFO] Running command: hmmsearch --tblout OceanDNA-b25714/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg82c92777-2b39-4667-99bf-1dce8a905b43/dqc_reference/reference_markers.hmm OceanDNA-b25714/protein.faa > /dev/null
[2023-03-15 13:03:57,506] [INFO] Task succeeded: HMMsearch
[2023-03-15 13:03:57,507] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg61fcef9c-69cd-4f68-80da-baabab2f5443/OceanDNA-b25714.fa]
[2023-03-15 13:03:57,512] [INFO] Query marker FASTA was written to OceanDNA-b25714/markers.fasta
[2023-03-15 13:03:57,523] [INFO] Task started: Blastn
[2023-03-15 13:03:57,524] [INFO] Running command: blastn -query OceanDNA-b25714/markers.fasta -db /var/lib/cwl/stg82c92777-2b39-4667-99bf-1dce8a905b43/dqc_reference/reference_markers.fasta -out OceanDNA-b25714/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:03:58,107] [INFO] Task succeeded: Blastn
[2023-03-15 13:03:58,107] [INFO] Selected 6 target genomes.
[2023-03-15 13:03:58,107] [INFO] Target genome list was writen to OceanDNA-b25714/target_genomes.txt
[2023-03-15 13:03:58,112] [INFO] Task started: fastANI
[2023-03-15 13:03:58,112] [INFO] Running command: fastANI --query /var/lib/cwl/stg61fcef9c-69cd-4f68-80da-baabab2f5443/OceanDNA-b25714.fa --refList OceanDNA-b25714/target_genomes.txt --output OceanDNA-b25714/fastani_result.tsv --threads 1
[2023-03-15 13:04:00,576] [INFO] Task succeeded: fastANI
[2023-03-15 13:04:00,576] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg82c92777-2b39-4667-99bf-1dce8a905b43/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 13:04:00,576] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg82c92777-2b39-4667-99bf-1dce8a905b43/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 13:04:00,577] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 13:04:00,577] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 13:04:00,577] [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
--------------------------------------------------------------------------------
[2023-03-15 13:04:00,577] [INFO] DFAST Taxonomy check result was written to OceanDNA-b25714/tc_result.tsv
[2023-03-15 13:04:00,577] [INFO] ===== Taxonomy check completed =====
[2023-03-15 13:04:00,577] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 13:04:00,577] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg82c92777-2b39-4667-99bf-1dce8a905b43/dqc_reference/checkm_data
[2023-03-15 13:04:00,631] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 13:04:00,633] [INFO] Task started: CheckM
[2023-03-15 13:04:00,633] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b25714/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b25714/checkm_input OceanDNA-b25714/checkm_result
[2023-03-15 13:04:16,422] [INFO] Task succeeded: CheckM
[2023-03-15 13:04:16,423] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 56.82%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 13:04:16,424] [INFO] ===== Completeness check finished =====
[2023-03-15 13:04:16,424] [INFO] ===== Start GTDB Search =====
[2023-03-15 13:04:16,424] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b25714/markers.fasta)
[2023-03-15 13:04:16,452] [INFO] Task started: Blastn
[2023-03-15 13:04:16,452] [INFO] Running command: blastn -query OceanDNA-b25714/markers.fasta -db /var/lib/cwl/stg82c92777-2b39-4667-99bf-1dce8a905b43/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b25714/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:04:17,354] [INFO] Task succeeded: Blastn
[2023-03-15 13:04:17,355] [INFO] Selected 10 target genomes.
[2023-03-15 13:04:17,355] [INFO] Target genome list was writen to OceanDNA-b25714/target_genomes_gtdb.txt
[2023-03-15 13:04:17,408] [INFO] Task started: fastANI
[2023-03-15 13:04:17,408] [INFO] Running command: fastANI --query /var/lib/cwl/stg61fcef9c-69cd-4f68-80da-baabab2f5443/OceanDNA-b25714.fa --refList OceanDNA-b25714/target_genomes_gtdb.txt --output OceanDNA-b25714/fastani_result_gtdb.tsv --threads 1
[2023-03-15 13:04:19,107] [INFO] Task succeeded: fastANI
[2023-03-15 13:04:19,112] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 13:04:19,112] [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_902562875.1	s__Pelagibacter sp902562875	78.6046	93	182	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902570505.1	s__Pelagibacter sp902570505	77.8925	77	182	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902560245.1	s__Pelagibacter sp902560245	76.7485	63	182	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902612345.1	s__Pelagibacter sp902612345	76.7074	58	182	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902558705.1	s__Pelagibacter sp902558705	76.6955	54	182	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	96.32	96.32	0.77	0.77	2	-
GCA_902600485.1	s__Pelagibacter sp902600485	76.656	53	182	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	95.74	95.74	0.88	0.88	2	-
GCA_902615045.1	s__Pelagibacter sp902615045	76.5592	62	182	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 13:04:19,112] [INFO] GTDB search result was written to OceanDNA-b25714/result_gtdb.tsv
[2023-03-15 13:04:19,112] [INFO] ===== GTDB Search completed =====
[2023-03-15 13:04:19,113] [INFO] DFAST_QC result json was written to OceanDNA-b25714/dqc_result.json
[2023-03-15 13:04:19,113] [INFO] DFAST_QC completed!
[2023-03-15 13:04:19,113] [INFO] Total running time: 0h0m26s