[2023-03-15 18:39:13,542] [INFO] DFAST_QC pipeline started.
[2023-03-15 18:39:13,542] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 18:39:13,542] [INFO] DQC Reference Directory: /var/lib/cwl/stg34d75561-84a4-424a-b7e1-e3401497eb2d/dqc_reference
[2023-03-15 18:39:15,256] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 18:39:15,256] [INFO] Task started: Prodigal
[2023-03-15 18:39:15,256] [INFO] Running command: cat /var/lib/cwl/stg12417a33-1940-4fa6-add2-6b1da4e06d8d/OceanDNA-b25908.fa | prodigal -d OceanDNA-b25908/cds.fna -a OceanDNA-b25908/protein.faa -g 11 -q > /dev/null
[2023-03-15 18:39:17,017] [INFO] Task succeeded: Prodigal
[2023-03-15 18:39:17,017] [INFO] Task started: HMMsearch
[2023-03-15 18:39:17,017] [INFO] Running command: hmmsearch --tblout OceanDNA-b25908/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg34d75561-84a4-424a-b7e1-e3401497eb2d/dqc_reference/reference_markers.hmm OceanDNA-b25908/protein.faa > /dev/null
[2023-03-15 18:39:17,272] [INFO] Task succeeded: HMMsearch
[2023-03-15 18:39:17,273] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg12417a33-1940-4fa6-add2-6b1da4e06d8d/OceanDNA-b25908.fa]
[2023-03-15 18:39:17,277] [INFO] Query marker FASTA was written to OceanDNA-b25908/markers.fasta
[2023-03-15 18:39:17,278] [INFO] Task started: Blastn
[2023-03-15 18:39:17,278] [INFO] Running command: blastn -query OceanDNA-b25908/markers.fasta -db /var/lib/cwl/stg34d75561-84a4-424a-b7e1-e3401497eb2d/dqc_reference/reference_markers.fasta -out OceanDNA-b25908/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 18:39:20,258] [INFO] Task succeeded: Blastn
[2023-03-15 18:39:20,259] [INFO] Selected 11 target genomes.
[2023-03-15 18:39:20,259] [INFO] Target genome list was writen to OceanDNA-b25908/target_genomes.txt
[2023-03-15 18:39:20,269] [INFO] Task started: fastANI
[2023-03-15 18:39:20,269] [INFO] Running command: fastANI --query /var/lib/cwl/stg12417a33-1940-4fa6-add2-6b1da4e06d8d/OceanDNA-b25908.fa --refList OceanDNA-b25908/target_genomes.txt --output OceanDNA-b25908/fastani_result.tsv --threads 1
[2023-03-15 18:39:24,243] [INFO] Task succeeded: fastANI
[2023-03-15 18:39:24,243] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg34d75561-84a4-424a-b7e1-e3401497eb2d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 18:39:24,243] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg34d75561-84a4-424a-b7e1-e3401497eb2d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 18:39:24,243] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 18:39:24,243] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 18:39:24,243] [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 18:39:24,244] [INFO] DFAST Taxonomy check result was written to OceanDNA-b25908/tc_result.tsv
[2023-03-15 18:39:24,244] [INFO] ===== Taxonomy check completed =====
[2023-03-15 18:39:24,244] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 18:39:24,244] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg34d75561-84a4-424a-b7e1-e3401497eb2d/dqc_reference/checkm_data
[2023-03-15 18:39:24,247] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 18:39:24,249] [INFO] Task started: CheckM
[2023-03-15 18:39:24,250] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b25908/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b25908/checkm_input OceanDNA-b25908/checkm_result
[2023-03-15 18:39:43,019] [INFO] Task succeeded: CheckM
[2023-03-15 18:39:43,020] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 54.88%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 18:39:43,021] [INFO] ===== Completeness check finished =====
[2023-03-15 18:39:43,021] [INFO] ===== Start GTDB Search =====
[2023-03-15 18:39:43,022] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b25908/markers.fasta)
[2023-03-15 18:39:43,023] [INFO] Task started: Blastn
[2023-03-15 18:39:43,023] [INFO] Running command: blastn -query OceanDNA-b25908/markers.fasta -db /var/lib/cwl/stg34d75561-84a4-424a-b7e1-e3401497eb2d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b25908/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 18:39:45,357] [INFO] Task succeeded: Blastn
[2023-03-15 18:39:45,358] [INFO] Selected 23 target genomes.
[2023-03-15 18:39:45,358] [INFO] Target genome list was writen to OceanDNA-b25908/target_genomes_gtdb.txt
[2023-03-15 18:39:46,252] [INFO] Task started: fastANI
[2023-03-15 18:39:46,252] [INFO] Running command: fastANI --query /var/lib/cwl/stg12417a33-1940-4fa6-add2-6b1da4e06d8d/OceanDNA-b25908.fa --refList OceanDNA-b25908/target_genomes_gtdb.txt --output OceanDNA-b25908/fastani_result_gtdb.tsv --threads 1
[2023-03-15 18:39:49,638] [INFO] Task succeeded: fastANI
[2023-03-15 18:39:49,644] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 18:39:49,644] [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_902595625.1	s__Pelagibacter_A sp902595625	79.8554	58	78	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902609855.1	s__Pelagibacter_A sp902609855	79.6446	62	78	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902591415.1	s__Pelagibacter_A sp902591415	79.4432	50	78	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902615435.1	s__Pelagibacter_A sp902615435	79.1808	56	78	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902623395.1	s__Pelagibacter_A sp902623395	79.0846	60	78	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902615715.1	s__Pelagibacter_A sp902615715	79.0433	64	78	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902613915.1	s__Pelagibacter_A sp902613915	78.8272	55	78	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 18:39:49,644] [INFO] GTDB search result was written to OceanDNA-b25908/result_gtdb.tsv
[2023-03-15 18:39:49,644] [INFO] ===== GTDB Search completed =====
[2023-03-15 18:39:49,645] [INFO] DFAST_QC result json was written to OceanDNA-b25908/dqc_result.json
[2023-03-15 18:39:49,645] [INFO] DFAST_QC completed!
[2023-03-15 18:39:49,645] [INFO] Total running time: 0h0m36s