[2023-03-15 15:18:22,085] [INFO] DFAST_QC pipeline started.
[2023-03-15 15:18:22,085] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 15:18:22,085] [INFO] DQC Reference Directory: /var/lib/cwl/stga8d2a1ab-bad9-4ac1-9707-ffd5137dd129/dqc_reference
[2023-03-15 15:18:23,208] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 15:18:23,208] [INFO] Task started: Prodigal
[2023-03-15 15:18:23,209] [INFO] Running command: cat /var/lib/cwl/stg5d94e334-6134-4520-b440-ee141cf2acd8/OceanDNA-b42274.fa | prodigal -d OceanDNA-b42274/cds.fna -a OceanDNA-b42274/protein.faa -g 11 -q > /dev/null
[2023-03-15 15:18:27,527] [INFO] Task succeeded: Prodigal
[2023-03-15 15:18:27,528] [INFO] Task started: HMMsearch
[2023-03-15 15:18:27,528] [INFO] Running command: hmmsearch --tblout OceanDNA-b42274/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga8d2a1ab-bad9-4ac1-9707-ffd5137dd129/dqc_reference/reference_markers.hmm OceanDNA-b42274/protein.faa > /dev/null
[2023-03-15 15:18:27,690] [INFO] Task succeeded: HMMsearch
[2023-03-15 15:18:27,690] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg5d94e334-6134-4520-b440-ee141cf2acd8/OceanDNA-b42274.fa]
[2023-03-15 15:18:27,713] [INFO] Query marker FASTA was written to OceanDNA-b42274/markers.fasta
[2023-03-15 15:18:27,714] [INFO] Task started: Blastn
[2023-03-15 15:18:27,715] [INFO] Running command: blastn -query OceanDNA-b42274/markers.fasta -db /var/lib/cwl/stga8d2a1ab-bad9-4ac1-9707-ffd5137dd129/dqc_reference/reference_markers.fasta -out OceanDNA-b42274/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 15:18:28,211] [INFO] Task succeeded: Blastn
[2023-03-15 15:18:28,218] [INFO] Selected 13 target genomes.
[2023-03-15 15:18:28,218] [INFO] Target genome list was writen to OceanDNA-b42274/target_genomes.txt
[2023-03-15 15:18:28,229] [INFO] Task started: fastANI
[2023-03-15 15:18:28,229] [INFO] Running command: fastANI --query /var/lib/cwl/stg5d94e334-6134-4520-b440-ee141cf2acd8/OceanDNA-b42274.fa --refList OceanDNA-b42274/target_genomes.txt --output OceanDNA-b42274/fastani_result.tsv --threads 1
[2023-03-15 15:18:34,321] [INFO] Task succeeded: fastANI
[2023-03-15 15:18:34,322] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga8d2a1ab-bad9-4ac1-9707-ffd5137dd129/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 15:18:34,322] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga8d2a1ab-bad9-4ac1-9707-ffd5137dd129/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 15:18:34,322] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 15:18:34,322] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 15:18:34,322] [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 15:18:34,325] [INFO] DFAST Taxonomy check result was written to OceanDNA-b42274/tc_result.tsv
[2023-03-15 15:18:34,329] [INFO] ===== Taxonomy check completed =====
[2023-03-15 15:18:34,329] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 15:18:34,329] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga8d2a1ab-bad9-4ac1-9707-ffd5137dd129/dqc_reference/checkm_data
[2023-03-15 15:18:34,332] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 15:18:34,356] [INFO] Task started: CheckM
[2023-03-15 15:18:34,357] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b42274/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b42274/checkm_input OceanDNA-b42274/checkm_result
[2023-03-15 15:18:51,588] [INFO] Task succeeded: CheckM
[2023-03-15 15:18:51,588] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 45.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 15:18:51,611] [INFO] ===== Completeness check finished =====
[2023-03-15 15:18:51,611] [INFO] ===== Start GTDB Search =====
[2023-03-15 15:18:51,611] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b42274/markers.fasta)
[2023-03-15 15:18:51,612] [INFO] Task started: Blastn
[2023-03-15 15:18:51,613] [INFO] Running command: blastn -query OceanDNA-b42274/markers.fasta -db /var/lib/cwl/stga8d2a1ab-bad9-4ac1-9707-ffd5137dd129/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b42274/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 15:18:52,301] [INFO] Task succeeded: Blastn
[2023-03-15 15:18:52,314] [INFO] Selected 9 target genomes.
[2023-03-15 15:18:52,315] [INFO] Target genome list was writen to OceanDNA-b42274/target_genomes_gtdb.txt
[2023-03-15 15:18:52,325] [INFO] Task started: fastANI
[2023-03-15 15:18:52,325] [INFO] Running command: fastANI --query /var/lib/cwl/stg5d94e334-6134-4520-b440-ee141cf2acd8/OceanDNA-b42274.fa --refList OceanDNA-b42274/target_genomes_gtdb.txt --output OceanDNA-b42274/fastani_result_gtdb.tsv --threads 1
[2023-03-15 15:18:54,343] [INFO] Task succeeded: fastANI
[2023-03-15 15:18:54,352] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 15:18:54,352] [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_004212975.1	s__SAR86A sp004212975	99.0912	209	284	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	97.30	95.02	0.85	0.76	8	conclusive
GCA_902612915.1	s__SAR86A sp902612915	94.7754	235	284	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	97.80	95.61	0.84	0.75	10	-
GCA_902617045.1	s__SAR86A sp902617045	94.7511	251	284	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	96.06	95.32	0.86	0.86	4	-
GCA_902547295.1	s__SAR86A sp902547295	93.9858	214	284	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902541175.1	s__SAR86A sp902541175	93.9696	253	284	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	97.65	95.31	0.89	0.85	3	-
GCA_902591925.1	s__SAR86A sp902591925	90.9552	236	284	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	97.32	97.27	0.90	0.89	3	-
GCA_902631785.1	s__SAR86A sp902631785	83.6579	207	284	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	96.84	96.84	0.79	0.79	2	-
GCA_902630885.1	s__SAR86A sp902630885	83.3604	217	284	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000252525.1	s__SAR86A sp000252525	81.994	151	284	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	96.49	95.25	0.88	0.84	16	-
--------------------------------------------------------------------------------
[2023-03-15 15:18:54,356] [INFO] GTDB search result was written to OceanDNA-b42274/result_gtdb.tsv
[2023-03-15 15:18:54,361] [INFO] ===== GTDB Search completed =====
[2023-03-15 15:18:54,363] [INFO] DFAST_QC result json was written to OceanDNA-b42274/dqc_result.json
[2023-03-15 15:18:54,364] [INFO] DFAST_QC completed!
[2023-03-15 15:18:54,364] [INFO] Total running time: 0h0m32s