[2023-03-17 10:48:45,573] [INFO] DFAST_QC pipeline started.
[2023-03-17 10:48:45,574] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 10:48:45,574] [INFO] DQC Reference Directory: /var/lib/cwl/stgc0c6252f-f7b6-4459-8cf3-7e2e477a9189/dqc_reference
[2023-03-17 10:48:46,693] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 10:48:46,694] [INFO] Task started: Prodigal
[2023-03-17 10:48:46,694] [INFO] Running command: cat /var/lib/cwl/stg1bd865d3-bfd3-4f5f-9daf-136d39ab4dfa/OceanDNA-b42022.fa | prodigal -d OceanDNA-b42022/cds.fna -a OceanDNA-b42022/protein.faa -g 11 -q > /dev/null
[2023-03-17 10:48:51,756] [INFO] Task succeeded: Prodigal
[2023-03-17 10:48:51,757] [INFO] Task started: HMMsearch
[2023-03-17 10:48:51,757] [INFO] Running command: hmmsearch --tblout OceanDNA-b42022/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc0c6252f-f7b6-4459-8cf3-7e2e477a9189/dqc_reference/reference_markers.hmm OceanDNA-b42022/protein.faa > /dev/null
[2023-03-17 10:48:51,922] [INFO] Task succeeded: HMMsearch
[2023-03-17 10:48:51,922] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg1bd865d3-bfd3-4f5f-9daf-136d39ab4dfa/OceanDNA-b42022.fa]
[2023-03-17 10:48:51,931] [INFO] Query marker FASTA was written to OceanDNA-b42022/markers.fasta
[2023-03-17 10:48:51,942] [INFO] Task started: Blastn
[2023-03-17 10:48:51,942] [INFO] Running command: blastn -query OceanDNA-b42022/markers.fasta -db /var/lib/cwl/stgc0c6252f-f7b6-4459-8cf3-7e2e477a9189/dqc_reference/reference_markers.fasta -out OceanDNA-b42022/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 10:48:52,516] [INFO] Task succeeded: Blastn
[2023-03-17 10:48:52,517] [INFO] Selected 16 target genomes.
[2023-03-17 10:48:52,517] [INFO] Target genome list was writen to OceanDNA-b42022/target_genomes.txt
[2023-03-17 10:48:52,544] [INFO] Task started: fastANI
[2023-03-17 10:48:52,544] [INFO] Running command: fastANI --query /var/lib/cwl/stg1bd865d3-bfd3-4f5f-9daf-136d39ab4dfa/OceanDNA-b42022.fa --refList OceanDNA-b42022/target_genomes.txt --output OceanDNA-b42022/fastani_result.tsv --threads 1
[2023-03-17 10:48:59,734] [INFO] Task succeeded: fastANI
[2023-03-17 10:48:59,734] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc0c6252f-f7b6-4459-8cf3-7e2e477a9189/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 10:48:59,734] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc0c6252f-f7b6-4459-8cf3-7e2e477a9189/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 10:48:59,735] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 10:48:59,735] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 10:48:59,735] [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 10:48:59,735] [INFO] DFAST Taxonomy check result was written to OceanDNA-b42022/tc_result.tsv
[2023-03-17 10:48:59,735] [INFO] ===== Taxonomy check completed =====
[2023-03-17 10:48:59,735] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 10:48:59,735] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc0c6252f-f7b6-4459-8cf3-7e2e477a9189/dqc_reference/checkm_data
[2023-03-17 10:48:59,738] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 10:48:59,741] [INFO] Task started: CheckM
[2023-03-17 10:48:59,741] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b42022/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b42022/checkm_input OceanDNA-b42022/checkm_result
[2023-03-17 10:49:18,646] [INFO] Task succeeded: CheckM
[2023-03-17 10:49:18,647] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 57.99%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 10:49:18,648] [INFO] ===== Completeness check finished =====
[2023-03-17 10:49:18,649] [INFO] ===== Start GTDB Search =====
[2023-03-17 10:49:18,649] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b42022/markers.fasta)
[2023-03-17 10:49:18,649] [INFO] Task started: Blastn
[2023-03-17 10:49:18,649] [INFO] Running command: blastn -query OceanDNA-b42022/markers.fasta -db /var/lib/cwl/stgc0c6252f-f7b6-4459-8cf3-7e2e477a9189/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b42022/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 10:49:19,329] [INFO] Task succeeded: Blastn
[2023-03-17 10:49:19,330] [INFO] Selected 26 target genomes.
[2023-03-17 10:49:19,330] [INFO] Target genome list was writen to OceanDNA-b42022/target_genomes_gtdb.txt
[2023-03-17 10:49:19,662] [INFO] Task started: fastANI
[2023-03-17 10:49:19,663] [INFO] Running command: fastANI --query /var/lib/cwl/stg1bd865d3-bfd3-4f5f-9daf-136d39ab4dfa/OceanDNA-b42022.fa --refList OceanDNA-b42022/target_genomes_gtdb.txt --output OceanDNA-b42022/fastani_result_gtdb.tsv --threads 1
[2023-03-17 10:49:25,749] [INFO] Task succeeded: fastANI
[2023-03-17 10:49:25,756] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 10:49:25,756] [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_905478015.1	s__CAJQGY01 sp905478015	99.0681	257	318	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__CAJQGY01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_905478035.1	s__SCGC-AAA076-P13 sp905478035	77.0624	77	318	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902558395.1	s__SCGC-AAA076-P13 sp902558395	77.0194	69	318	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	97.77	97.77	0.94	0.94	2	-
GCA_000384935.1	s__SCGC-AAA076-P13 sp000384935	76.8207	81	318	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905182885.1	s__SCGC-AAA076-P13 sp905182885	76.7425	63	318	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_010024215.1	s__SCGC-AAA076-P13 sp010024215	76.7292	56	318	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	98.04	96.58	0.74	0.68	5	-
GCA_902560315.1	s__SAR86A sp902560315	76.6833	54	318	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	95.47	95.47	0.82	0.82	2	-
GCA_003331505.1	s__MED-G85 sp003331505	76.6606	57	318	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__MED-G85	95.0	98.80	96.15	0.89	0.83	6	-
GCA_902610905.1	s__SCGC-AAA076-P13 sp902610905	76.5009	61	318	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902591925.1	s__SAR86A sp902591925	76.4903	57	318	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	97.32	97.27	0.90	0.89	3	-
GCA_902516285.1	s__SAR86A sp902516285	76.423	52	318	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	96.51	96.51	0.92	0.92	2	-
GCA_902626385.1	s__SAR86A sp902626385	76.2184	53	318	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 10:49:25,756] [INFO] GTDB search result was written to OceanDNA-b42022/result_gtdb.tsv
[2023-03-17 10:49:25,756] [INFO] ===== GTDB Search completed =====
[2023-03-17 10:49:25,757] [INFO] DFAST_QC result json was written to OceanDNA-b42022/dqc_result.json
[2023-03-17 10:49:25,758] [INFO] DFAST_QC completed!
[2023-03-17 10:49:25,758] [INFO] Total running time: 0h0m40s