[2023-03-17 10:35:02,805] [INFO] DFAST_QC pipeline started.
[2023-03-17 10:35:02,806] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 10:35:02,806] [INFO] DQC Reference Directory: /var/lib/cwl/stg02277bfb-ef08-43c1-8c6f-3068cfe2e29f/dqc_reference
[2023-03-17 10:35:04,549] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 10:35:04,550] [INFO] Task started: Prodigal
[2023-03-17 10:35:04,550] [INFO] Running command: cat /var/lib/cwl/stg112ffd5d-9777-4b96-a8af-fa59c48ac8ae/OceanDNA-b43376.fa | prodigal -d OceanDNA-b43376/cds.fna -a OceanDNA-b43376/protein.faa -g 11 -q > /dev/null
[2023-03-17 10:35:07,529] [INFO] Task succeeded: Prodigal
[2023-03-17 10:35:07,529] [INFO] Task started: HMMsearch
[2023-03-17 10:35:07,529] [INFO] Running command: hmmsearch --tblout OceanDNA-b43376/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg02277bfb-ef08-43c1-8c6f-3068cfe2e29f/dqc_reference/reference_markers.hmm OceanDNA-b43376/protein.faa > /dev/null
[2023-03-17 10:35:07,782] [INFO] Task succeeded: HMMsearch
[2023-03-17 10:35:07,783] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg112ffd5d-9777-4b96-a8af-fa59c48ac8ae/OceanDNA-b43376.fa]
[2023-03-17 10:35:07,790] [INFO] Query marker FASTA was written to OceanDNA-b43376/markers.fasta
[2023-03-17 10:35:07,792] [INFO] Task started: Blastn
[2023-03-17 10:35:07,792] [INFO] Running command: blastn -query OceanDNA-b43376/markers.fasta -db /var/lib/cwl/stg02277bfb-ef08-43c1-8c6f-3068cfe2e29f/dqc_reference/reference_markers.fasta -out OceanDNA-b43376/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 10:35:11,403] [INFO] Task succeeded: Blastn
[2023-03-17 10:35:11,404] [INFO] Selected 21 target genomes.
[2023-03-17 10:35:11,404] [INFO] Target genome list was writen to OceanDNA-b43376/target_genomes.txt
[2023-03-17 10:35:11,414] [INFO] Task started: fastANI
[2023-03-17 10:35:11,414] [INFO] Running command: fastANI --query /var/lib/cwl/stg112ffd5d-9777-4b96-a8af-fa59c48ac8ae/OceanDNA-b43376.fa --refList OceanDNA-b43376/target_genomes.txt --output OceanDNA-b43376/fastani_result.tsv --threads 1
[2023-03-17 10:35:22,836] [INFO] Task succeeded: fastANI
[2023-03-17 10:35:22,836] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg02277bfb-ef08-43c1-8c6f-3068cfe2e29f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 10:35:22,836] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg02277bfb-ef08-43c1-8c6f-3068cfe2e29f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 10:35:22,839] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 10:35:22,839] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 10:35:22,839] [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
Candidatus Thioglobus autotrophicus	strain=EF1	GCA_001293165.1	1705394	1705394	type	True	77.4749	71	182	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 10:35:22,840] [INFO] DFAST Taxonomy check result was written to OceanDNA-b43376/tc_result.tsv
[2023-03-17 10:35:22,840] [INFO] ===== Taxonomy check completed =====
[2023-03-17 10:35:22,840] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 10:35:22,840] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg02277bfb-ef08-43c1-8c6f-3068cfe2e29f/dqc_reference/checkm_data
[2023-03-17 10:35:22,841] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 10:35:22,844] [INFO] Task started: CheckM
[2023-03-17 10:35:22,844] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b43376/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b43376/checkm_input OceanDNA-b43376/checkm_result
[2023-03-17 10:35:40,529] [INFO] Task succeeded: CheckM
[2023-03-17 10:35:40,530] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 64.93%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 10:35:40,532] [INFO] ===== Completeness check finished =====
[2023-03-17 10:35:40,532] [INFO] ===== Start GTDB Search =====
[2023-03-17 10:35:40,532] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b43376/markers.fasta)
[2023-03-17 10:35:40,534] [INFO] Task started: Blastn
[2023-03-17 10:35:40,534] [INFO] Running command: blastn -query OceanDNA-b43376/markers.fasta -db /var/lib/cwl/stg02277bfb-ef08-43c1-8c6f-3068cfe2e29f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b43376/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 10:35:41,554] [INFO] Task succeeded: Blastn
[2023-03-17 10:35:41,556] [INFO] Selected 16 target genomes.
[2023-03-17 10:35:41,556] [INFO] Target genome list was writen to OceanDNA-b43376/target_genomes_gtdb.txt
[2023-03-17 10:35:42,178] [INFO] Task started: fastANI
[2023-03-17 10:35:42,178] [INFO] Running command: fastANI --query /var/lib/cwl/stg112ffd5d-9777-4b96-a8af-fa59c48ac8ae/OceanDNA-b43376.fa --refList OceanDNA-b43376/target_genomes_gtdb.txt --output OceanDNA-b43376/fastani_result_gtdb.tsv --threads 1
[2023-03-17 10:35:45,656] [INFO] Task succeeded: fastANI
[2023-03-17 10:35:45,661] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 10:35:45,662] [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_002909145.1	s__Thioglobus_B perditus	94.8777	174	182	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Thioglobus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014384345.1	s__Thioglobus pontius	78.0213	63	182	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Thioglobus	95.0	99.87	99.85	0.90	0.85	3	-
GCA_016845205.1	s__UBA2013 sp016845205	77.4994	57	182	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__UBA2013	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018644675.1	s__Thioglobus sp018644675	77.4702	71	182	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Thioglobus	95.0	99.74	99.56	0.96	0.91	16	-
GCA_012963715.1	s__Thioglobus sp012963715	77.3324	61	182	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Thioglobus	95.0	97.05	95.18	0.84	0.80	5	-
GCA_002335045.1	s__UBA2013 sp002335045	77.1831	58	182	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__UBA2013	95.0	98.42	96.96	0.95	0.94	3	-
GCF_900128515.1	s__Thioglobus sp900128515	77.1385	61	182	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Thioglobus	95.0	99.64	99.26	0.90	0.80	8	-
--------------------------------------------------------------------------------
[2023-03-17 10:35:45,662] [INFO] GTDB search result was written to OceanDNA-b43376/result_gtdb.tsv
[2023-03-17 10:35:45,662] [INFO] ===== GTDB Search completed =====
[2023-03-17 10:35:45,663] [INFO] DFAST_QC result json was written to OceanDNA-b43376/dqc_result.json
[2023-03-17 10:35:45,664] [INFO] DFAST_QC completed!
[2023-03-17 10:35:45,664] [INFO] Total running time: 0h0m43s