[2023-03-15 10:49:28,650] [INFO] DFAST_QC pipeline started.
[2023-03-15 10:49:28,650] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 10:49:28,650] [INFO] DQC Reference Directory: /var/lib/cwl/stg200f5ae6-7bec-4572-b567-8b3cf1f027a9/dqc_reference
[2023-03-15 10:49:29,761] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 10:49:29,761] [INFO] Task started: Prodigal
[2023-03-15 10:49:29,761] [INFO] Running command: cat /var/lib/cwl/stg46e267d6-7251-40bd-be34-b0fe274c2dd8/OceanDNA-b42626.fa | prodigal -d OceanDNA-b42626/cds.fna -a OceanDNA-b42626/protein.faa -g 11 -q > /dev/null
[2023-03-15 10:49:35,519] [INFO] Task succeeded: Prodigal
[2023-03-15 10:49:35,519] [INFO] Task started: HMMsearch
[2023-03-15 10:49:35,519] [INFO] Running command: hmmsearch --tblout OceanDNA-b42626/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg200f5ae6-7bec-4572-b567-8b3cf1f027a9/dqc_reference/reference_markers.hmm OceanDNA-b42626/protein.faa > /dev/null
[2023-03-15 10:49:35,734] [INFO] Task succeeded: HMMsearch
[2023-03-15 10:49:35,734] [INFO] Found 6/6 markers.
[2023-03-15 10:49:35,743] [INFO] Query marker FASTA was written to OceanDNA-b42626/markers.fasta
[2023-03-15 10:49:35,743] [INFO] Task started: Blastn
[2023-03-15 10:49:35,743] [INFO] Running command: blastn -query OceanDNA-b42626/markers.fasta -db /var/lib/cwl/stg200f5ae6-7bec-4572-b567-8b3cf1f027a9/dqc_reference/reference_markers.fasta -out OceanDNA-b42626/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:49:36,288] [INFO] Task succeeded: Blastn
[2023-03-15 10:49:36,288] [INFO] Selected 21 target genomes.
[2023-03-15 10:49:36,289] [INFO] Target genome list was writen to OceanDNA-b42626/target_genomes.txt
[2023-03-15 10:49:36,300] [INFO] Task started: fastANI
[2023-03-15 10:49:36,301] [INFO] Running command: fastANI --query /var/lib/cwl/stg46e267d6-7251-40bd-be34-b0fe274c2dd8/OceanDNA-b42626.fa --refList OceanDNA-b42626/target_genomes.txt --output OceanDNA-b42626/fastani_result.tsv --threads 1
[2023-03-15 10:49:48,406] [INFO] Task succeeded: fastANI
[2023-03-15 10:49:48,406] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg200f5ae6-7bec-4572-b567-8b3cf1f027a9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 10:49:48,406] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg200f5ae6-7bec-4572-b567-8b3cf1f027a9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 10:49:48,407] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 10:49:48,407] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 10:49:48,407] [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 10:49:48,407] [INFO] DFAST Taxonomy check result was written to OceanDNA-b42626/tc_result.tsv
[2023-03-15 10:49:48,408] [INFO] ===== Taxonomy check completed =====
[2023-03-15 10:49:48,408] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 10:49:48,408] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg200f5ae6-7bec-4572-b567-8b3cf1f027a9/dqc_reference/checkm_data
[2023-03-15 10:49:48,410] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 10:49:48,414] [INFO] Task started: CheckM
[2023-03-15 10:49:48,414] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b42626/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b42626/checkm_input OceanDNA-b42626/checkm_result
[2023-03-15 10:50:09,042] [INFO] Task succeeded: CheckM
[2023-03-15 10:50:09,042] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 10:50:09,044] [INFO] ===== Completeness check finished =====
[2023-03-15 10:50:09,044] [INFO] ===== Start GTDB Search =====
[2023-03-15 10:50:09,045] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b42626/markers.fasta)
[2023-03-15 10:50:09,046] [INFO] Task started: Blastn
[2023-03-15 10:50:09,046] [INFO] Running command: blastn -query OceanDNA-b42626/markers.fasta -db /var/lib/cwl/stg200f5ae6-7bec-4572-b567-8b3cf1f027a9/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b42626/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:50:10,011] [INFO] Task succeeded: Blastn
[2023-03-15 10:50:10,013] [INFO] Selected 28 target genomes.
[2023-03-15 10:50:10,013] [INFO] Target genome list was writen to OceanDNA-b42626/target_genomes_gtdb.txt
[2023-03-15 10:50:10,058] [INFO] Task started: fastANI
[2023-03-15 10:50:10,058] [INFO] Running command: fastANI --query /var/lib/cwl/stg46e267d6-7251-40bd-be34-b0fe274c2dd8/OceanDNA-b42626.fa --refList OceanDNA-b42626/target_genomes_gtdb.txt --output OceanDNA-b42626/fastani_result_gtdb.tsv --threads 1
[2023-03-15 10:50:16,452] [INFO] Task succeeded: fastANI
[2023-03-15 10:50:16,460] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 10:50:16,460] [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_002730855.1	s__GCA-2730855 sp002730855	99.4068	236	375	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__GCA-2730855	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902514295.1	s__GCA-2730855 sp902514295	81.067	165	375	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__GCA-2730855	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902532675.1	s__GCA-2730855 sp902532675	79.9008	157	375	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__GCA-2730855	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902554355.1	s__GCA-2730855 sp902554355	78.7672	130	375	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__GCA-2730855	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902532015.1	s__GCA-2730855 sp902532015	78.7164	127	375	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__GCA-2730855	95.0	97.85	97.68	0.69	0.68	3	-
GCA_902604855.1	s__GCA-2707915 sp902604855	77.1738	58	375	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__GCA-2707915	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902594545.1	s__GCA-2707915 sp902594545	76.9567	55	375	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__GCA-2707915	95.0	99.77	99.77	0.82	0.82	2	-
GCA_902542325.1	s__GCA-2707915 sp902542325	76.9137	63	375	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__GCA-2707915	95.0	99.62	99.62	0.80	0.80	2	-
GCA_902620785.1	s__GCA-2707915 sp902620785	76.8624	66	375	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__GCA-2707915	95.0	95.48	95.02	0.87	0.85	6	-
GCA_004214065.1	s__GCA-2707915 sp004214065	76.7411	71	375	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__GCA-2707915	95.0	97.49	97.45	0.77	0.70	3	-
GCA_902618945.1	s__GCA-2707915 sp902618945	76.5122	52	375	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__GCA-2707915	95.0	95.64	95.64	0.79	0.79	2	-
GCA_902606175.1	s__GCA-2707915 sp902606175	76.4584	54	375	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__GCA-2707915	95.0	95.24	95.17	0.72	0.71	3	-
GCA_002707915.1	s__GCA-2707915 sp002707915	76.2004	51	375	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__GCA-2707915	95.0	97.24	96.30	0.83	0.75	4	-
--------------------------------------------------------------------------------
[2023-03-15 10:50:16,461] [INFO] GTDB search result was written to OceanDNA-b42626/result_gtdb.tsv
[2023-03-15 10:50:16,461] [INFO] ===== GTDB Search completed =====
[2023-03-15 10:50:16,463] [INFO] DFAST_QC result json was written to OceanDNA-b42626/dqc_result.json
[2023-03-15 10:50:16,463] [INFO] DFAST_QC completed!
[2023-03-15 10:50:16,463] [INFO] Total running time: 0h0m48s