[2023-03-17 10:10:44,410] [INFO] DFAST_QC pipeline started.
[2023-03-17 10:10:44,411] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 10:10:44,411] [INFO] DQC Reference Directory: /var/lib/cwl/stg17544169-eca0-45dd-8f2c-f2a87ab5e9d8/dqc_reference
[2023-03-17 10:10:45,579] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 10:10:45,580] [INFO] Task started: Prodigal
[2023-03-17 10:10:45,580] [INFO] Running command: cat /var/lib/cwl/stgef7329e5-ffd2-4669-824f-04863208d140/OceanDNA-b42569.fa | prodigal -d OceanDNA-b42569/cds.fna -a OceanDNA-b42569/protein.faa -g 11 -q > /dev/null
[2023-03-17 10:10:51,084] [INFO] Task succeeded: Prodigal
[2023-03-17 10:10:51,084] [INFO] Task started: HMMsearch
[2023-03-17 10:10:51,084] [INFO] Running command: hmmsearch --tblout OceanDNA-b42569/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg17544169-eca0-45dd-8f2c-f2a87ab5e9d8/dqc_reference/reference_markers.hmm OceanDNA-b42569/protein.faa > /dev/null
[2023-03-17 10:10:51,236] [INFO] Task succeeded: HMMsearch
[2023-03-17 10:10:51,237] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgef7329e5-ffd2-4669-824f-04863208d140/OceanDNA-b42569.fa]
[2023-03-17 10:10:51,254] [INFO] Query marker FASTA was written to OceanDNA-b42569/markers.fasta
[2023-03-17 10:10:51,256] [INFO] Task started: Blastn
[2023-03-17 10:10:51,256] [INFO] Running command: blastn -query OceanDNA-b42569/markers.fasta -db /var/lib/cwl/stg17544169-eca0-45dd-8f2c-f2a87ab5e9d8/dqc_reference/reference_markers.fasta -out OceanDNA-b42569/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 10:10:51,926] [INFO] Task succeeded: Blastn
[2023-03-17 10:10:51,993] [INFO] Selected 17 target genomes.
[2023-03-17 10:10:51,994] [INFO] Target genome list was writen to OceanDNA-b42569/target_genomes.txt
[2023-03-17 10:10:52,019] [INFO] Task started: fastANI
[2023-03-17 10:10:52,019] [INFO] Running command: fastANI --query /var/lib/cwl/stgef7329e5-ffd2-4669-824f-04863208d140/OceanDNA-b42569.fa --refList OceanDNA-b42569/target_genomes.txt --output OceanDNA-b42569/fastani_result.tsv --threads 1
[2023-03-17 10:10:59,598] [INFO] Task succeeded: fastANI
[2023-03-17 10:10:59,599] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg17544169-eca0-45dd-8f2c-f2a87ab5e9d8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 10:10:59,599] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg17544169-eca0-45dd-8f2c-f2a87ab5e9d8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 10:10:59,599] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 10:10:59,599] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 10:10:59,599] [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 10:10:59,611] [INFO] DFAST Taxonomy check result was written to OceanDNA-b42569/tc_result.tsv
[2023-03-17 10:10:59,612] [INFO] ===== Taxonomy check completed =====
[2023-03-17 10:10:59,612] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 10:10:59,612] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg17544169-eca0-45dd-8f2c-f2a87ab5e9d8/dqc_reference/checkm_data
[2023-03-17 10:10:59,615] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 10:10:59,618] [INFO] Task started: CheckM
[2023-03-17 10:10:59,618] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b42569/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b42569/checkm_input OceanDNA-b42569/checkm_result
[2023-03-17 10:11:19,081] [INFO] Task succeeded: CheckM
[2023-03-17 10:11:19,081] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.64%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 10:11:19,098] [INFO] ===== Completeness check finished =====
[2023-03-17 10:11:19,098] [INFO] ===== Start GTDB Search =====
[2023-03-17 10:11:19,099] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b42569/markers.fasta)
[2023-03-17 10:11:19,100] [INFO] Task started: Blastn
[2023-03-17 10:11:19,100] [INFO] Running command: blastn -query OceanDNA-b42569/markers.fasta -db /var/lib/cwl/stg17544169-eca0-45dd-8f2c-f2a87ab5e9d8/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b42569/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 10:11:19,896] [INFO] Task succeeded: Blastn
[2023-03-17 10:11:19,910] [INFO] Selected 18 target genomes.
[2023-03-17 10:11:19,910] [INFO] Target genome list was writen to OceanDNA-b42569/target_genomes_gtdb.txt
[2023-03-17 10:11:19,929] [INFO] Task started: fastANI
[2023-03-17 10:11:19,929] [INFO] Running command: fastANI --query /var/lib/cwl/stgef7329e5-ffd2-4669-824f-04863208d140/OceanDNA-b42569.fa --refList OceanDNA-b42569/target_genomes_gtdb.txt --output OceanDNA-b42569/fastani_result_gtdb.tsv --threads 1
[2023-03-17 10:11:23,762] [INFO] Task succeeded: fastANI
[2023-03-17 10:11:23,770] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 10:11:23,770] [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_004214065.1	s__GCA-2707915 sp004214065	90.4539	260	356	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_902517565.1	s__GCA-2707915 sp902517565	80.3935	169	356	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_003212335.1	s__GCA-2707915 sp003212335	79.2472	164	356	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__GCA-2707915	95.0	96.12	95.05	0.82	0.77	11	-
GCA_902594545.1	s__GCA-2707915 sp902594545	78.6682	102	356	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_902604855.1	s__GCA-2707915 sp902604855	78.6071	129	356	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_902605935.1	s__GCA-2707915 sp902605935	78.5571	84	356	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_902606175.1	s__GCA-2707915 sp902606175	78.3982	126	356	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_016777005.1	s__GCA-2707915 sp016777005	78.2955	101	356	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	78.2232	140	356	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_902574355.1	s__GCA-2707915 sp902574355	78.1128	135	356	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	77.2885	83	356	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_902532015.1	s__GCA-2730855 sp902532015	76.9707	57	356	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__GCA-2730855	95.0	97.85	97.68	0.69	0.68	3	-
--------------------------------------------------------------------------------
[2023-03-17 10:11:23,770] [INFO] GTDB search result was written to OceanDNA-b42569/result_gtdb.tsv
[2023-03-17 10:11:23,770] [INFO] ===== GTDB Search completed =====
[2023-03-17 10:11:23,771] [INFO] DFAST_QC result json was written to OceanDNA-b42569/dqc_result.json
[2023-03-17 10:11:23,771] [INFO] DFAST_QC completed!
[2023-03-17 10:11:23,771] [INFO] Total running time: 0h0m39s