[2023-03-17 11:25:37,168] [INFO] DFAST_QC pipeline started.
[2023-03-17 11:25:37,168] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 11:25:37,168] [INFO] DQC Reference Directory: /var/lib/cwl/stg26edbe61-a2af-406f-bb9f-9ce7c7f5b606/dqc_reference
[2023-03-17 11:25:38,296] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 11:25:38,296] [INFO] Task started: Prodigal
[2023-03-17 11:25:38,296] [INFO] Running command: cat /var/lib/cwl/stg05fa9731-c517-4aeb-9e61-80406199a7d2/OceanDNA-b26338.fa | prodigal -d OceanDNA-b26338/cds.fna -a OceanDNA-b26338/protein.faa -g 11 -q > /dev/null
[2023-03-17 11:25:43,892] [INFO] Task succeeded: Prodigal
[2023-03-17 11:25:43,892] [INFO] Task started: HMMsearch
[2023-03-17 11:25:43,892] [INFO] Running command: hmmsearch --tblout OceanDNA-b26338/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg26edbe61-a2af-406f-bb9f-9ce7c7f5b606/dqc_reference/reference_markers.hmm OceanDNA-b26338/protein.faa > /dev/null
[2023-03-17 11:25:44,040] [INFO] Task succeeded: HMMsearch
[2023-03-17 11:25:44,040] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg05fa9731-c517-4aeb-9e61-80406199a7d2/OceanDNA-b26338.fa]
[2023-03-17 11:25:44,056] [INFO] Query marker FASTA was written to OceanDNA-b26338/markers.fasta
[2023-03-17 11:25:44,056] [INFO] Task started: Blastn
[2023-03-17 11:25:44,056] [INFO] Running command: blastn -query OceanDNA-b26338/markers.fasta -db /var/lib/cwl/stg26edbe61-a2af-406f-bb9f-9ce7c7f5b606/dqc_reference/reference_markers.fasta -out OceanDNA-b26338/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:25:44,561] [INFO] Task succeeded: Blastn
[2023-03-17 11:25:44,564] [INFO] Selected 24 target genomes.
[2023-03-17 11:25:44,564] [INFO] Target genome list was writen to OceanDNA-b26338/target_genomes.txt
[2023-03-17 11:25:44,581] [INFO] Task started: fastANI
[2023-03-17 11:25:44,581] [INFO] Running command: fastANI --query /var/lib/cwl/stg05fa9731-c517-4aeb-9e61-80406199a7d2/OceanDNA-b26338.fa --refList OceanDNA-b26338/target_genomes.txt --output OceanDNA-b26338/fastani_result.tsv --threads 1
[2023-03-17 11:25:52,367] [INFO] Task succeeded: fastANI
[2023-03-17 11:25:52,368] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg26edbe61-a2af-406f-bb9f-9ce7c7f5b606/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 11:25:52,368] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg26edbe61-a2af-406f-bb9f-9ce7c7f5b606/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 11:25:52,368] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 11:25:52,368] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 11:25:52,368] [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 11:25:52,370] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26338/tc_result.tsv
[2023-03-17 11:25:52,372] [INFO] ===== Taxonomy check completed =====
[2023-03-17 11:25:52,372] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 11:25:52,372] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg26edbe61-a2af-406f-bb9f-9ce7c7f5b606/dqc_reference/checkm_data
[2023-03-17 11:25:52,375] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 11:25:52,405] [INFO] Task started: CheckM
[2023-03-17 11:25:52,405] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26338/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26338/checkm_input OceanDNA-b26338/checkm_result
[2023-03-17 11:26:12,388] [INFO] Task succeeded: CheckM
[2023-03-17 11:26:12,388] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 69.44%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 11:26:12,795] [INFO] ===== Completeness check finished =====
[2023-03-17 11:26:12,795] [INFO] ===== Start GTDB Search =====
[2023-03-17 11:26:12,796] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26338/markers.fasta)
[2023-03-17 11:26:12,796] [INFO] Task started: Blastn
[2023-03-17 11:26:12,796] [INFO] Running command: blastn -query OceanDNA-b26338/markers.fasta -db /var/lib/cwl/stg26edbe61-a2af-406f-bb9f-9ce7c7f5b606/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26338/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:26:13,541] [INFO] Task succeeded: Blastn
[2023-03-17 11:26:13,584] [INFO] Selected 22 target genomes.
[2023-03-17 11:26:13,585] [INFO] Target genome list was writen to OceanDNA-b26338/target_genomes_gtdb.txt
[2023-03-17 11:26:13,608] [INFO] Task started: fastANI
[2023-03-17 11:26:13,608] [INFO] Running command: fastANI --query /var/lib/cwl/stg05fa9731-c517-4aeb-9e61-80406199a7d2/OceanDNA-b26338.fa --refList OceanDNA-b26338/target_genomes_gtdb.txt --output OceanDNA-b26338/fastani_result_gtdb.tsv --threads 1
[2023-03-17 11:26:20,610] [INFO] Task succeeded: fastANI
[2023-03-17 11:26:20,615] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 11:26:20,615] [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_016779005.1	s__UBA5951 sp016779005	79.2001	204	346	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA5951	95.0	96.62	95.51	0.89	0.87	4	-
GCA_009936885.1	s__UBA5951 sp009936885	78.5866	151	346	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA5951	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902516825.1	s__UBA5951 sp902516825	78.3221	131	346	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA5951	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018666135.1	s__UBA5951 sp018666135	76.9334	66	346	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA5951	95.0	99.32	99.32	0.87	0.87	2	-
GCA_012269555.1	s__UBA5951 sp012269555	76.6943	70	346	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA5951	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902625725.1	s__UBA5951 sp902625725	76.6663	59	346	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA5951	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902622515.1	s__UBA5951 sp902622515	76.4155	56	346	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA5951	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902520885.1	s__UBA5951 sp902520885	76.2632	72	346	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA5951	95.0	99.20	99.20	0.88	0.88	2	-
--------------------------------------------------------------------------------
[2023-03-17 11:26:20,622] [INFO] GTDB search result was written to OceanDNA-b26338/result_gtdb.tsv
[2023-03-17 11:26:20,630] [INFO] ===== GTDB Search completed =====
[2023-03-17 11:26:20,635] [INFO] DFAST_QC result json was written to OceanDNA-b26338/dqc_result.json
[2023-03-17 11:26:20,635] [INFO] DFAST_QC completed!
[2023-03-17 11:26:20,635] [INFO] Total running time: 0h0m43s