[2023-03-17 09:33:10,324] [INFO] DFAST_QC pipeline started.
[2023-03-17 09:33:10,324] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 09:33:10,324] [INFO] DQC Reference Directory: /var/lib/cwl/stgbb1ca4ec-1dbb-42c9-8286-41d778820836/dqc_reference
[2023-03-17 09:33:11,410] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 09:33:11,410] [INFO] Task started: Prodigal
[2023-03-17 09:33:11,411] [INFO] Running command: cat /var/lib/cwl/stgb0da1aa1-dc72-4cc5-9c3d-ff5871b72211/OceanDNA-b25819.fa | prodigal -d OceanDNA-b25819/cds.fna -a OceanDNA-b25819/protein.faa -g 11 -q > /dev/null
[2023-03-17 09:33:15,946] [INFO] Task succeeded: Prodigal
[2023-03-17 09:33:15,946] [INFO] Task started: HMMsearch
[2023-03-17 09:33:15,946] [INFO] Running command: hmmsearch --tblout OceanDNA-b25819/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbb1ca4ec-1dbb-42c9-8286-41d778820836/dqc_reference/reference_markers.hmm OceanDNA-b25819/protein.faa > /dev/null
[2023-03-17 09:33:16,097] [INFO] Task succeeded: HMMsearch
[2023-03-17 09:33:16,097] [WARNING] Found 2/6 markers. [/var/lib/cwl/stgb0da1aa1-dc72-4cc5-9c3d-ff5871b72211/OceanDNA-b25819.fa]
[2023-03-17 09:33:16,117] [INFO] Query marker FASTA was written to OceanDNA-b25819/markers.fasta
[2023-03-17 09:33:16,119] [INFO] Task started: Blastn
[2023-03-17 09:33:16,119] [INFO] Running command: blastn -query OceanDNA-b25819/markers.fasta -db /var/lib/cwl/stgbb1ca4ec-1dbb-42c9-8286-41d778820836/dqc_reference/reference_markers.fasta -out OceanDNA-b25819/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 09:33:16,910] [INFO] Task succeeded: Blastn
[2023-03-17 09:33:16,919] [INFO] Selected 9 target genomes.
[2023-03-17 09:33:16,919] [INFO] Target genome list was writen to OceanDNA-b25819/target_genomes.txt
[2023-03-17 09:33:17,056] [INFO] Task started: fastANI
[2023-03-17 09:33:17,056] [INFO] Running command: fastANI --query /var/lib/cwl/stgb0da1aa1-dc72-4cc5-9c3d-ff5871b72211/OceanDNA-b25819.fa --refList OceanDNA-b25819/target_genomes.txt --output OceanDNA-b25819/fastani_result.tsv --threads 1
[2023-03-17 09:33:19,502] [INFO] Task succeeded: fastANI
[2023-03-17 09:33:19,502] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbb1ca4ec-1dbb-42c9-8286-41d778820836/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 09:33:19,503] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbb1ca4ec-1dbb-42c9-8286-41d778820836/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 09:33:19,645] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 09:33:19,645] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 09:33:19,645] [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
Candidatus Pelagibacter ubique	strain=HTCC1062	GCA_000012345.1	198252	198252	suspected-type	True	77.4013	94	219	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 09:33:19,651] [INFO] DFAST Taxonomy check result was written to OceanDNA-b25819/tc_result.tsv
[2023-03-17 09:33:19,652] [INFO] ===== Taxonomy check completed =====
[2023-03-17 09:33:19,652] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 09:33:19,652] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbb1ca4ec-1dbb-42c9-8286-41d778820836/dqc_reference/checkm_data
[2023-03-17 09:33:19,653] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 09:33:19,753] [INFO] Task started: CheckM
[2023-03-17 09:33:19,753] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b25819/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b25819/checkm_input OceanDNA-b25819/checkm_result
[2023-03-17 09:33:42,316] [INFO] Task succeeded: CheckM
[2023-03-17 09:33:42,317] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 68.98%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 09:33:42,319] [INFO] ===== Completeness check finished =====
[2023-03-17 09:33:42,319] [INFO] ===== Start GTDB Search =====
[2023-03-17 09:33:42,319] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b25819/markers.fasta)
[2023-03-17 09:33:42,320] [INFO] Task started: Blastn
[2023-03-17 09:33:42,320] [INFO] Running command: blastn -query OceanDNA-b25819/markers.fasta -db /var/lib/cwl/stgbb1ca4ec-1dbb-42c9-8286-41d778820836/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b25819/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 09:33:43,891] [INFO] Task succeeded: Blastn
[2023-03-17 09:33:43,892] [INFO] Selected 7 target genomes.
[2023-03-17 09:33:43,892] [INFO] Target genome list was writen to OceanDNA-b25819/target_genomes_gtdb.txt
[2023-03-17 09:33:44,363] [INFO] Task started: fastANI
[2023-03-17 09:33:44,364] [INFO] Running command: fastANI --query /var/lib/cwl/stgb0da1aa1-dc72-4cc5-9c3d-ff5871b72211/OceanDNA-b25819.fa --refList OceanDNA-b25819/target_genomes_gtdb.txt --output OceanDNA-b25819/fastani_result_gtdb.tsv --threads 1
[2023-03-17 09:33:45,782] [INFO] Task succeeded: fastANI
[2023-03-17 09:33:45,787] [INFO] Found 7 fastANI hits (3 hits with ANI > circumscription radius)
[2023-03-17 09:33:45,787] [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
GCF_002101295.1	s__Pelagibacter sp002101295	98.0474	218	219	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	95.97	95.60	0.92	0.90	4	inconclusive
GCA_902576045.1	s__Pelagibacter sp902576045	96.7478	167	219	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	95.81	95.50	0.75	0.71	6	inconclusive
GCA_902614125.1	s__Pelagibacter sp902614125	95.4961	181	219	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	inconclusive
GCA_902634935.1	s__Pelagibacter sp902634935	94.9128	168	219	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902546765.1	s__Pelagibacter sp902546765	94.5609	158	219	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	97.47	97.47	0.71	0.71	2	-
GCA_902592445.1	s__Pelagibacter sp902592445	94.1997	173	219	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	95.56	95.56	0.78	0.78	2	-
GCA_902616205.1	s__Pelagibacter sp902616205	93.8246	130	219	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 09:33:45,787] [INFO] GTDB search result was written to OceanDNA-b25819/result_gtdb.tsv
[2023-03-17 09:33:45,788] [INFO] ===== GTDB Search completed =====
[2023-03-17 09:33:45,788] [INFO] DFAST_QC result json was written to OceanDNA-b25819/dqc_result.json
[2023-03-17 09:33:45,788] [INFO] DFAST_QC completed!
[2023-03-17 09:33:45,788] [INFO] Total running time: 0h0m35s