[2023-03-16 17:56:33,766] [INFO] DFAST_QC pipeline started.
[2023-03-16 17:56:33,767] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 17:56:33,767] [INFO] DQC Reference Directory: /var/lib/cwl/stgd55abfc5-1db9-488b-b78d-e7c21a167ec9/dqc_reference
[2023-03-16 17:56:35,077] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 17:56:35,078] [INFO] Task started: Prodigal
[2023-03-16 17:56:35,079] [INFO] Running command: cat /var/lib/cwl/stg936ad163-e950-4206-8867-fa72a3c3dcf0/OceanDNA-b42608.fa | prodigal -d OceanDNA-b42608/cds.fna -a OceanDNA-b42608/protein.faa -g 11 -q > /dev/null
[2023-03-16 17:56:43,425] [INFO] Task succeeded: Prodigal
[2023-03-16 17:56:43,425] [INFO] Task started: HMMsearch
[2023-03-16 17:56:43,425] [INFO] Running command: hmmsearch --tblout OceanDNA-b42608/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd55abfc5-1db9-488b-b78d-e7c21a167ec9/dqc_reference/reference_markers.hmm OceanDNA-b42608/protein.faa > /dev/null
[2023-03-16 17:56:43,699] [INFO] Task succeeded: HMMsearch
[2023-03-16 17:56:43,700] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg936ad163-e950-4206-8867-fa72a3c3dcf0/OceanDNA-b42608.fa]
[2023-03-16 17:56:43,711] [INFO] Query marker FASTA was written to OceanDNA-b42608/markers.fasta
[2023-03-16 17:56:43,712] [INFO] Task started: Blastn
[2023-03-16 17:56:43,712] [INFO] Running command: blastn -query OceanDNA-b42608/markers.fasta -db /var/lib/cwl/stgd55abfc5-1db9-488b-b78d-e7c21a167ec9/dqc_reference/reference_markers.fasta -out OceanDNA-b42608/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 17:56:44,272] [INFO] Task succeeded: Blastn
[2023-03-16 17:56:44,273] [INFO] Selected 21 target genomes.
[2023-03-16 17:56:44,273] [INFO] Target genome list was writen to OceanDNA-b42608/target_genomes.txt
[2023-03-16 17:56:44,284] [INFO] Task started: fastANI
[2023-03-16 17:56:44,285] [INFO] Running command: fastANI --query /var/lib/cwl/stg936ad163-e950-4206-8867-fa72a3c3dcf0/OceanDNA-b42608.fa --refList OceanDNA-b42608/target_genomes.txt --output OceanDNA-b42608/fastani_result.tsv --threads 1
[2023-03-16 17:57:01,684] [INFO] Task succeeded: fastANI
[2023-03-16 17:57:01,684] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd55abfc5-1db9-488b-b78d-e7c21a167ec9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 17:57:01,684] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd55abfc5-1db9-488b-b78d-e7c21a167ec9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 17:57:01,685] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 17:57:01,685] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 17:57:01,685] [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
--------------------------------------------------------------------------------
[2023-03-16 17:57:01,685] [INFO] DFAST Taxonomy check result was written to OceanDNA-b42608/tc_result.tsv
[2023-03-16 17:57:01,686] [INFO] ===== Taxonomy check completed =====
[2023-03-16 17:57:01,686] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 17:57:01,686] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd55abfc5-1db9-488b-b78d-e7c21a167ec9/dqc_reference/checkm_data
[2023-03-16 17:57:01,697] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 17:57:01,701] [INFO] Task started: CheckM
[2023-03-16 17:57:01,701] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b42608/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b42608/checkm_input OceanDNA-b42608/checkm_result
[2023-03-16 17:57:23,202] [INFO] Task succeeded: CheckM
[2023-03-16 17:57:23,203] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 17:57:23,204] [INFO] ===== Completeness check finished =====
[2023-03-16 17:57:23,204] [INFO] ===== Start GTDB Search =====
[2023-03-16 17:57:23,205] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b42608/markers.fasta)
[2023-03-16 17:57:23,205] [INFO] Task started: Blastn
[2023-03-16 17:57:23,205] [INFO] Running command: blastn -query OceanDNA-b42608/markers.fasta -db /var/lib/cwl/stgd55abfc5-1db9-488b-b78d-e7c21a167ec9/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b42608/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 17:57:24,241] [INFO] Task succeeded: Blastn
[2023-03-16 17:57:24,242] [INFO] Selected 25 target genomes.
[2023-03-16 17:57:24,242] [INFO] Target genome list was writen to OceanDNA-b42608/target_genomes_gtdb.txt
[2023-03-16 17:57:24,265] [INFO] Task started: fastANI
[2023-03-16 17:57:24,265] [INFO] Running command: fastANI --query /var/lib/cwl/stg936ad163-e950-4206-8867-fa72a3c3dcf0/OceanDNA-b42608.fa --refList OceanDNA-b42608/target_genomes_gtdb.txt --output OceanDNA-b42608/fastani_result_gtdb.tsv --threads 1
[2023-03-16 17:57:31,431] [INFO] Task succeeded: fastANI
[2023-03-16 17:57:31,439] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 17:57:31,439] [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_003212335.1	s__GCA-2707915 sp003212335	95.3378	323	368	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__GCA-2707915	95.0	96.12	95.05	0.82	0.77	11	conclusive
GCA_902594545.1	s__GCA-2707915 sp902594545	79.2014	119	368	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_902618945.1	s__GCA-2707915 sp902618945	78.1683	114	368	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_902574355.1	s__GCA-2707915 sp902574355	77.9306	134	368	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_902604855.1	s__GCA-2707915 sp902604855	77.7464	124	368	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_902542325.1	s__GCA-2707915 sp902542325	77.7119	118	368	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_902606175.1	s__GCA-2707915 sp902606175	77.6306	109	368	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_902517565.1	s__GCA-2707915 sp902517565	77.5657	118	368	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_902620785.1	s__GCA-2707915 sp902620785	77.4931	118	368	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_016777005.1	s__GCA-2707915 sp016777005	77.1813	95	368	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_902630715.1	s__GCA-2707915 sp902630715	77.0342	88	368	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_902532675.1	s__GCA-2730855 sp902532675	76.8654	63	368	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	76.6636	50	368	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__GCA-2730855	95.0	97.85	97.68	0.69	0.68	3	-
--------------------------------------------------------------------------------
[2023-03-16 17:57:31,439] [INFO] GTDB search result was written to OceanDNA-b42608/result_gtdb.tsv
[2023-03-16 17:57:31,439] [INFO] ===== GTDB Search completed =====
[2023-03-16 17:57:31,440] [INFO] DFAST_QC result json was written to OceanDNA-b42608/dqc_result.json
[2023-03-16 17:57:31,440] [INFO] DFAST_QC completed!
[2023-03-16 17:57:31,440] [INFO] Total running time: 0h0m58s