[2023-03-19 02:16:59,673] [INFO] DFAST_QC pipeline started.
[2023-03-19 02:16:59,675] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 02:16:59,675] [INFO] DQC Reference Directory: /var/lib/cwl/stgc435e7d6-0111-40b1-99dd-a80d8cd7fd85/dqc_reference
[2023-03-19 02:17:00,765] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 02:17:00,765] [INFO] Task started: Prodigal
[2023-03-19 02:17:00,765] [INFO] Running command: cat /var/lib/cwl/stg5b5e511d-3186-4c5e-83c3-9faba3500774/OceanDNA-b42261.fa | prodigal -d OceanDNA-b42261/cds.fna -a OceanDNA-b42261/protein.faa -g 11 -q > /dev/null
[2023-03-19 02:17:06,182] [INFO] Task succeeded: Prodigal
[2023-03-19 02:17:06,183] [INFO] Task started: HMMsearch
[2023-03-19 02:17:06,183] [INFO] Running command: hmmsearch --tblout OceanDNA-b42261/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc435e7d6-0111-40b1-99dd-a80d8cd7fd85/dqc_reference/reference_markers.hmm OceanDNA-b42261/protein.faa > /dev/null
[2023-03-19 02:17:06,325] [INFO] Task succeeded: HMMsearch
[2023-03-19 02:17:06,326] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg5b5e511d-3186-4c5e-83c3-9faba3500774/OceanDNA-b42261.fa]
[2023-03-19 02:17:06,334] [INFO] Query marker FASTA was written to OceanDNA-b42261/markers.fasta
[2023-03-19 02:17:06,335] [INFO] Task started: Blastn
[2023-03-19 02:17:06,335] [INFO] Running command: blastn -query OceanDNA-b42261/markers.fasta -db /var/lib/cwl/stgc435e7d6-0111-40b1-99dd-a80d8cd7fd85/dqc_reference/reference_markers.fasta -out OceanDNA-b42261/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:17:06,850] [INFO] Task succeeded: Blastn
[2023-03-19 02:17:06,860] [INFO] Selected 16 target genomes.
[2023-03-19 02:17:06,860] [INFO] Target genome list was writen to OceanDNA-b42261/target_genomes.txt
[2023-03-19 02:17:06,867] [INFO] Task started: fastANI
[2023-03-19 02:17:06,867] [INFO] Running command: fastANI --query /var/lib/cwl/stg5b5e511d-3186-4c5e-83c3-9faba3500774/OceanDNA-b42261.fa --refList OceanDNA-b42261/target_genomes.txt --output OceanDNA-b42261/fastani_result.tsv --threads 1
[2023-03-19 02:17:14,232] [INFO] Task succeeded: fastANI
[2023-03-19 02:17:14,232] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc435e7d6-0111-40b1-99dd-a80d8cd7fd85/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 02:17:14,233] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc435e7d6-0111-40b1-99dd-a80d8cd7fd85/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 02:17:14,233] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 02:17:14,233] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 02:17:14,233] [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
--------------------------------------------------------------------------------
[2023-03-19 02:17:14,235] [INFO] DFAST Taxonomy check result was written to OceanDNA-b42261/tc_result.tsv
[2023-03-19 02:17:14,237] [INFO] ===== Taxonomy check completed =====
[2023-03-19 02:17:14,237] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 02:17:14,237] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc435e7d6-0111-40b1-99dd-a80d8cd7fd85/dqc_reference/checkm_data
[2023-03-19 02:17:14,240] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 02:17:14,265] [INFO] Task started: CheckM
[2023-03-19 02:17:14,265] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b42261/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b42261/checkm_input OceanDNA-b42261/checkm_result
[2023-03-19 02:17:33,521] [INFO] Task succeeded: CheckM
[2023-03-19 02:17:33,521] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 73.61%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 02:17:33,523] [INFO] ===== Completeness check finished =====
[2023-03-19 02:17:33,523] [INFO] ===== Start GTDB Search =====
[2023-03-19 02:17:33,523] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b42261/markers.fasta)
[2023-03-19 02:17:33,525] [INFO] Task started: Blastn
[2023-03-19 02:17:33,525] [INFO] Running command: blastn -query OceanDNA-b42261/markers.fasta -db /var/lib/cwl/stgc435e7d6-0111-40b1-99dd-a80d8cd7fd85/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b42261/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:17:34,327] [INFO] Task succeeded: Blastn
[2023-03-19 02:17:34,327] [INFO] Selected 12 target genomes.
[2023-03-19 02:17:34,328] [INFO] Target genome list was writen to OceanDNA-b42261/target_genomes_gtdb.txt
[2023-03-19 02:17:34,342] [INFO] Task started: fastANI
[2023-03-19 02:17:34,343] [INFO] Running command: fastANI --query /var/lib/cwl/stg5b5e511d-3186-4c5e-83c3-9faba3500774/OceanDNA-b42261.fa --refList OceanDNA-b42261/target_genomes_gtdb.txt --output OceanDNA-b42261/fastani_result_gtdb.tsv --threads 1
[2023-03-19 02:17:36,813] [INFO] Task succeeded: fastANI
[2023-03-19 02:17:36,821] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 02:17:36,821] [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_902558095.1	s__SAR86A sp902558095	83.7805	275	354	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902559345.1	s__SAR86A sp902559345	81.25	180	354	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902520495.1	s__SAR86A sp902520495	81.0583	218	354	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902517425.1	s__SAR86A sp902517425	79.3065	165	354	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002169105.1	s__SAR86A sp002169105	79.2697	137	354	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902520725.1	s__SAR86A sp902520725	79.078	172	354	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	99.82	99.82	0.73	0.73	2	-
GCA_902583575.1	s__SAR86A sp902583575	78.339	158	354	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003213495.1	s__SAR86A sp003213495	78.0034	174	354	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	98.20	96.41	0.97	0.94	3	-
GCA_902617045.1	s__SAR86A sp902617045	77.8861	145	354	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	96.06	95.32	0.86	0.86	4	-
GCA_902551185.1	s__SAR86A sp902551185	77.7966	134	354	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	99.17	99.17	0.78	0.78	2	-
GCA_002169625.2	s__SAR86A sp002169625	77.7068	121	354	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	98.57	98.54	0.85	0.74	4	-
GCA_902630885.1	s__SAR86A sp902630885	77.6956	147	354	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 02:17:36,821] [INFO] GTDB search result was written to OceanDNA-b42261/result_gtdb.tsv
[2023-03-19 02:17:36,821] [INFO] ===== GTDB Search completed =====
[2023-03-19 02:17:36,822] [INFO] DFAST_QC result json was written to OceanDNA-b42261/dqc_result.json
[2023-03-19 02:17:36,822] [INFO] DFAST_QC completed!
[2023-03-19 02:17:36,822] [INFO] Total running time: 0h0m37s