[2023-03-15 11:09:10,949] [INFO] DFAST_QC pipeline started.
[2023-03-15 11:09:10,949] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 11:09:10,949] [INFO] DQC Reference Directory: /var/lib/cwl/stgd09dc267-ff02-4518-bf83-f6eedc78e1bb/dqc_reference
[2023-03-15 11:09:12,282] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 11:09:12,282] [INFO] Task started: Prodigal
[2023-03-15 11:09:12,282] [INFO] Running command: cat /var/lib/cwl/stg2f903e74-446a-443f-aca5-8bbb23b98068/OceanDNA-b43060.fa | prodigal -d OceanDNA-b43060/cds.fna -a OceanDNA-b43060/protein.faa -g 11 -q > /dev/null
[2023-03-15 11:09:18,704] [INFO] Task succeeded: Prodigal
[2023-03-15 11:09:18,705] [INFO] Task started: HMMsearch
[2023-03-15 11:09:18,705] [INFO] Running command: hmmsearch --tblout OceanDNA-b43060/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd09dc267-ff02-4518-bf83-f6eedc78e1bb/dqc_reference/reference_markers.hmm OceanDNA-b43060/protein.faa > /dev/null
[2023-03-15 11:09:18,889] [INFO] Task succeeded: HMMsearch
[2023-03-15 11:09:18,890] [INFO] Found 6/6 markers.
[2023-03-15 11:09:18,899] [INFO] Query marker FASTA was written to OceanDNA-b43060/markers.fasta
[2023-03-15 11:09:18,900] [INFO] Task started: Blastn
[2023-03-15 11:09:18,900] [INFO] Running command: blastn -query OceanDNA-b43060/markers.fasta -db /var/lib/cwl/stgd09dc267-ff02-4518-bf83-f6eedc78e1bb/dqc_reference/reference_markers.fasta -out OceanDNA-b43060/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:09:19,452] [INFO] Task succeeded: Blastn
[2023-03-15 11:09:19,453] [INFO] Selected 24 target genomes.
[2023-03-15 11:09:19,453] [INFO] Target genome list was writen to OceanDNA-b43060/target_genomes.txt
[2023-03-15 11:09:19,466] [INFO] Task started: fastANI
[2023-03-15 11:09:19,466] [INFO] Running command: fastANI --query /var/lib/cwl/stg2f903e74-446a-443f-aca5-8bbb23b98068/OceanDNA-b43060.fa --refList OceanDNA-b43060/target_genomes.txt --output OceanDNA-b43060/fastani_result.tsv --threads 1
[2023-03-15 11:09:31,451] [INFO] Task succeeded: fastANI
[2023-03-15 11:09:31,451] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd09dc267-ff02-4518-bf83-f6eedc78e1bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 11:09:31,451] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd09dc267-ff02-4518-bf83-f6eedc78e1bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 11:09:31,454] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 11:09:31,454] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 11:09:31,454] [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 Pseudothioglobus singularis	strain=PS1	GCA_001281385.1	1427364	1427364	type	True	77.4769	82	390	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 11:09:31,455] [INFO] DFAST Taxonomy check result was written to OceanDNA-b43060/tc_result.tsv
[2023-03-15 11:09:31,455] [INFO] ===== Taxonomy check completed =====
[2023-03-15 11:09:31,455] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 11:09:31,455] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd09dc267-ff02-4518-bf83-f6eedc78e1bb/dqc_reference/checkm_data
[2023-03-15 11:09:31,456] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 11:09:31,458] [INFO] Task started: CheckM
[2023-03-15 11:09:31,458] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b43060/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b43060/checkm_input OceanDNA-b43060/checkm_result
[2023-03-15 11:09:52,975] [INFO] Task succeeded: CheckM
[2023-03-15 11:09:52,975] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 11:09:52,977] [INFO] ===== Completeness check finished =====
[2023-03-15 11:09:52,977] [INFO] ===== Start GTDB Search =====
[2023-03-15 11:09:52,977] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b43060/markers.fasta)
[2023-03-15 11:09:52,978] [INFO] Task started: Blastn
[2023-03-15 11:09:52,978] [INFO] Running command: blastn -query OceanDNA-b43060/markers.fasta -db /var/lib/cwl/stgd09dc267-ff02-4518-bf83-f6eedc78e1bb/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b43060/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:09:53,878] [INFO] Task succeeded: Blastn
[2023-03-15 11:09:53,879] [INFO] Selected 17 target genomes.
[2023-03-15 11:09:53,879] [INFO] Target genome list was writen to OceanDNA-b43060/target_genomes_gtdb.txt
[2023-03-15 11:09:53,891] [INFO] Task started: fastANI
[2023-03-15 11:09:53,891] [INFO] Running command: fastANI --query /var/lib/cwl/stg2f903e74-446a-443f-aca5-8bbb23b98068/OceanDNA-b43060.fa --refList OceanDNA-b43060/target_genomes_gtdb.txt --output OceanDNA-b43060/fastani_result_gtdb.tsv --threads 1
[2023-03-15 11:09:58,804] [INFO] Task succeeded: fastANI
[2023-03-15 11:09:58,811] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 11:09:58,812] [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_000213395.2	s__Pseudothioglobus sp000213395	91.2612	218	390	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Pseudothioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000372785.1	s__Pseudothioglobus sp000372785	90.3964	261	390	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Pseudothioglobus	95.0	95.69	95.69	0.64	0.64	2	-
GCA_902606745.1	s__Pseudothioglobus sp902606745	89.8482	273	390	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Pseudothioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002698045.1	s__Pseudothioglobus sp002698045	78.7071	96	390	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Pseudothioglobus	95.0	95.47	95.47	0.68	0.68	2	-
GCA_905618925.1	s__Pseudothioglobus sp905618925	78.0751	79	390	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Pseudothioglobus	95.0	95.58	95.58	0.66	0.66	2	-
GCA_905620445.1	s__Pseudothioglobus sp905620445	77.9399	62	390	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Pseudothioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905614365.1	s__Pseudothioglobus sp905614365	77.9108	65	390	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Pseudothioglobus	95.0	96.68	96.27	0.61	0.56	4	-
GCF_001281385.1	s__Pseudothioglobus singularis	77.4769	82	390	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Pseudothioglobus	95.0	96.68	95.87	0.84	0.66	7	-
GCF_003326015.1	s__Pseudothioglobus singularis_A	77.2326	112	390	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Pseudothioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014384565.1	s__Pseudothioglobus aerophilus	77.2313	94	390	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Pseudothioglobus	95.0	99.14	98.97	0.83	0.77	11	-
GCA_902509905.1	s__Pseudothioglobus sp902509905	76.9143	67	390	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Pseudothioglobus	95.0	95.83	95.81	0.73	0.73	3	-
--------------------------------------------------------------------------------
[2023-03-15 11:09:58,812] [INFO] GTDB search result was written to OceanDNA-b43060/result_gtdb.tsv
[2023-03-15 11:09:58,812] [INFO] ===== GTDB Search completed =====
[2023-03-15 11:09:58,813] [INFO] DFAST_QC result json was written to OceanDNA-b43060/dqc_result.json
[2023-03-15 11:09:58,813] [INFO] DFAST_QC completed!
[2023-03-15 11:09:58,813] [INFO] Total running time: 0h0m48s