[2023-03-16 16:43:21,347] [INFO] DFAST_QC pipeline started.
[2023-03-16 16:43:21,347] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 16:43:21,348] [INFO] DQC Reference Directory: /var/lib/cwl/stge88133d0-f5dd-438a-bf05-4639a06a5194/dqc_reference
[2023-03-16 16:43:22,503] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 16:43:22,503] [INFO] Task started: Prodigal
[2023-03-16 16:43:22,503] [INFO] Running command: cat /var/lib/cwl/stg9dd71081-4fbe-4dc5-a97e-81f1dc760f73/OceanDNA-b26779.fa | prodigal -d OceanDNA-b26779/cds.fna -a OceanDNA-b26779/protein.faa -g 11 -q > /dev/null
[2023-03-16 16:43:52,487] [INFO] Task succeeded: Prodigal
[2023-03-16 16:43:52,488] [INFO] Task started: HMMsearch
[2023-03-16 16:43:52,488] [INFO] Running command: hmmsearch --tblout OceanDNA-b26779/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge88133d0-f5dd-438a-bf05-4639a06a5194/dqc_reference/reference_markers.hmm OceanDNA-b26779/protein.faa > /dev/null
[2023-03-16 16:43:52,827] [INFO] Task succeeded: HMMsearch
[2023-03-16 16:43:52,828] [INFO] Found 6/6 markers.
[2023-03-16 16:43:52,857] [INFO] Query marker FASTA was written to OceanDNA-b26779/markers.fasta
[2023-03-16 16:43:52,862] [INFO] Task started: Blastn
[2023-03-16 16:43:52,862] [INFO] Running command: blastn -query OceanDNA-b26779/markers.fasta -db /var/lib/cwl/stge88133d0-f5dd-438a-bf05-4639a06a5194/dqc_reference/reference_markers.fasta -out OceanDNA-b26779/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 16:43:53,648] [INFO] Task succeeded: Blastn
[2023-03-16 16:43:53,649] [INFO] Selected 27 target genomes.
[2023-03-16 16:43:53,649] [INFO] Target genome list was writen to OceanDNA-b26779/target_genomes.txt
[2023-03-16 16:43:53,713] [INFO] Task started: fastANI
[2023-03-16 16:43:53,714] [INFO] Running command: fastANI --query /var/lib/cwl/stg9dd71081-4fbe-4dc5-a97e-81f1dc760f73/OceanDNA-b26779.fa --refList OceanDNA-b26779/target_genomes.txt --output OceanDNA-b26779/fastani_result.tsv --threads 1
[2023-03-16 16:44:10,552] [INFO] Task succeeded: fastANI
[2023-03-16 16:44:10,552] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge88133d0-f5dd-438a-bf05-4639a06a5194/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 16:44:10,553] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge88133d0-f5dd-438a-bf05-4639a06a5194/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 16:44:10,555] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 16:44:10,556] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 16:44:10,556] [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
Ahrensia kielensis	strain=DSM 5890	GCA_000374465.1	76980	76980	type	True	76.0108	61	1083	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 16:44:10,556] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26779/tc_result.tsv
[2023-03-16 16:44:10,556] [INFO] ===== Taxonomy check completed =====
[2023-03-16 16:44:10,556] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 16:44:10,556] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge88133d0-f5dd-438a-bf05-4639a06a5194/dqc_reference/checkm_data
[2023-03-16 16:44:10,557] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 16:44:10,561] [INFO] Task started: CheckM
[2023-03-16 16:44:10,561] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26779/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26779/checkm_input OceanDNA-b26779/checkm_result
[2023-03-16 16:45:01,571] [INFO] Task succeeded: CheckM
[2023-03-16 16:45:01,571] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 16:45:01,574] [INFO] ===== Completeness check finished =====
[2023-03-16 16:45:01,574] [INFO] ===== Start GTDB Search =====
[2023-03-16 16:45:01,574] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26779/markers.fasta)
[2023-03-16 16:45:01,575] [INFO] Task started: Blastn
[2023-03-16 16:45:01,575] [INFO] Running command: blastn -query OceanDNA-b26779/markers.fasta -db /var/lib/cwl/stge88133d0-f5dd-438a-bf05-4639a06a5194/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26779/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 16:45:03,004] [INFO] Task succeeded: Blastn
[2023-03-16 16:45:03,005] [INFO] Selected 24 target genomes.
[2023-03-16 16:45:03,005] [INFO] Target genome list was writen to OceanDNA-b26779/target_genomes_gtdb.txt
[2023-03-16 16:45:03,077] [INFO] Task started: fastANI
[2023-03-16 16:45:03,078] [INFO] Running command: fastANI --query /var/lib/cwl/stg9dd71081-4fbe-4dc5-a97e-81f1dc760f73/OceanDNA-b26779.fa --refList OceanDNA-b26779/target_genomes_gtdb.txt --output OceanDNA-b26779/fastani_result_gtdb.tsv --threads 1
[2023-03-16 16:45:20,968] [INFO] Task succeeded: fastANI
[2023-03-16 16:45:20,972] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 16:45:20,972] [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_017644105.1	s__Lentilitoribacter sp017644105	77.3953	283	1083	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Lentilitoribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900537175.1	s__Lentilitoribacter sp900537175	77.2917	201	1083	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Lentilitoribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905479965.1	s__Lentilitoribacter sp905479965	77.1358	141	1083	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Lentilitoribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000374465.1	s__Ahrensia kielensis	76.0108	61	1083	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Ahrensia	95.0	95.90	95.90	0.86	0.86	2	-
--------------------------------------------------------------------------------
[2023-03-16 16:45:20,972] [INFO] GTDB search result was written to OceanDNA-b26779/result_gtdb.tsv
[2023-03-16 16:45:20,972] [INFO] ===== GTDB Search completed =====
[2023-03-16 16:45:20,973] [INFO] DFAST_QC result json was written to OceanDNA-b26779/dqc_result.json
[2023-03-16 16:45:20,973] [INFO] DFAST_QC completed!
[2023-03-16 16:45:20,973] [INFO] Total running time: 0h1m60s