[2023-03-18 05:17:48,208] [INFO] DFAST_QC pipeline started.
[2023-03-18 05:17:48,208] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 05:17:48,208] [INFO] DQC Reference Directory: /var/lib/cwl/stg25671ec5-defe-42e9-8b9f-070110105727/dqc_reference
[2023-03-18 05:17:49,309] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 05:17:49,309] [INFO] Task started: Prodigal
[2023-03-18 05:17:49,309] [INFO] Running command: cat /var/lib/cwl/stg048b2073-90e1-45d6-9d97-e1ef853d7f82/OceanDNA-b25094.fa | prodigal -d OceanDNA-b25094/cds.fna -a OceanDNA-b25094/protein.faa -g 11 -q > /dev/null
[2023-03-18 05:17:56,037] [INFO] Task succeeded: Prodigal
[2023-03-18 05:17:56,037] [INFO] Task started: HMMsearch
[2023-03-18 05:17:56,037] [INFO] Running command: hmmsearch --tblout OceanDNA-b25094/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg25671ec5-defe-42e9-8b9f-070110105727/dqc_reference/reference_markers.hmm OceanDNA-b25094/protein.faa > /dev/null
[2023-03-18 05:17:56,198] [INFO] Task succeeded: HMMsearch
[2023-03-18 05:17:56,199] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg048b2073-90e1-45d6-9d97-e1ef853d7f82/OceanDNA-b25094.fa]
[2023-03-18 05:17:56,210] [INFO] Query marker FASTA was written to OceanDNA-b25094/markers.fasta
[2023-03-18 05:17:56,211] [INFO] Task started: Blastn
[2023-03-18 05:17:56,211] [INFO] Running command: blastn -query OceanDNA-b25094/markers.fasta -db /var/lib/cwl/stg25671ec5-defe-42e9-8b9f-070110105727/dqc_reference/reference_markers.fasta -out OceanDNA-b25094/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 05:17:56,732] [INFO] Task succeeded: Blastn
[2023-03-18 05:17:56,733] [INFO] Selected 25 target genomes.
[2023-03-18 05:17:56,733] [INFO] Target genome list was writen to OceanDNA-b25094/target_genomes.txt
[2023-03-18 05:17:56,747] [INFO] Task started: fastANI
[2023-03-18 05:17:56,748] [INFO] Running command: fastANI --query /var/lib/cwl/stg048b2073-90e1-45d6-9d97-e1ef853d7f82/OceanDNA-b25094.fa --refList OceanDNA-b25094/target_genomes.txt --output OceanDNA-b25094/fastani_result.tsv --threads 1
[2023-03-18 05:18:10,218] [INFO] Task succeeded: fastANI
[2023-03-18 05:18:10,219] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg25671ec5-defe-42e9-8b9f-070110105727/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 05:18:10,219] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg25671ec5-defe-42e9-8b9f-070110105727/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 05:18:10,219] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 05:18:10,219] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 05:18:10,219] [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
--------------------------------------------------------------------------------
[2023-03-18 05:18:10,220] [INFO] DFAST Taxonomy check result was written to OceanDNA-b25094/tc_result.tsv
[2023-03-18 05:18:10,221] [INFO] ===== Taxonomy check completed =====
[2023-03-18 05:18:10,221] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 05:18:10,221] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg25671ec5-defe-42e9-8b9f-070110105727/dqc_reference/checkm_data
[2023-03-18 05:18:10,223] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 05:18:10,247] [INFO] Task started: CheckM
[2023-03-18 05:18:10,247] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b25094/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b25094/checkm_input OceanDNA-b25094/checkm_result
[2023-03-18 05:18:32,640] [INFO] Task succeeded: CheckM
[2023-03-18 05:18:32,640] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 1.45%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2023-03-18 05:18:32,642] [INFO] ===== Completeness check finished =====
[2023-03-18 05:18:32,642] [INFO] ===== Start GTDB Search =====
[2023-03-18 05:18:32,643] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b25094/markers.fasta)
[2023-03-18 05:18:32,644] [INFO] Task started: Blastn
[2023-03-18 05:18:32,644] [INFO] Running command: blastn -query OceanDNA-b25094/markers.fasta -db /var/lib/cwl/stg25671ec5-defe-42e9-8b9f-070110105727/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b25094/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 05:18:33,386] [INFO] Task succeeded: Blastn
[2023-03-18 05:18:33,386] [INFO] Selected 7 target genomes.
[2023-03-18 05:18:33,387] [INFO] Target genome list was writen to OceanDNA-b25094/target_genomes_gtdb.txt
[2023-03-18 05:18:33,393] [INFO] Task started: fastANI
[2023-03-18 05:18:33,393] [INFO] Running command: fastANI --query /var/lib/cwl/stg048b2073-90e1-45d6-9d97-e1ef853d7f82/OceanDNA-b25094.fa --refList OceanDNA-b25094/target_genomes_gtdb.txt --output OceanDNA-b25094/fastani_result_gtdb.tsv --threads 1
[2023-03-18 05:18:35,462] [INFO] Task succeeded: fastANI
[2023-03-18 05:18:35,467] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 05:18:35,467] [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_009920875.1	s__UBA8337 sp009920875	97.7258	245	306	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__RS24;g__UBA8337	95.0	97.55	97.55	0.89	0.89	2	conclusive
GCA_002721725.1	s__UBA8337 sp002721725	89.2398	277	306	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__RS24;g__UBA8337	95.0	99.29	99.29	0.93	0.93	2	-
GCA_900197605.1	s__UBA8337 sp900197605	82.8743	252	306	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__RS24;g__UBA8337	95.0	96.88	95.59	0.86	0.84	6	-
GCA_016779015.1	s__UBA8337 sp016779015	81.6866	186	306	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__RS24;g__UBA8337	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018660505.1	s__UBA8337 sp018660505	77.9695	167	306	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__RS24;g__UBA8337	95.0	99.75	99.71	0.96	0.95	3	-
GCA_018673175.1	s__UBA8337 sp018673175	77.8731	152	306	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__RS24;g__UBA8337	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002689195.1	s__UBA7378 sp002689195	77.7695	89	306	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__RS24;g__UBA7378	95.0	98.73	98.05	0.85	0.80	4	-
--------------------------------------------------------------------------------
[2023-03-18 05:18:35,468] [INFO] GTDB search result was written to OceanDNA-b25094/result_gtdb.tsv
[2023-03-18 05:18:35,468] [INFO] ===== GTDB Search completed =====
[2023-03-18 05:18:35,468] [INFO] DFAST_QC result json was written to OceanDNA-b25094/dqc_result.json
[2023-03-18 05:18:35,468] [INFO] DFAST_QC completed!
[2023-03-18 05:18:35,468] [INFO] Total running time: 0h0m47s