[2023-03-18 09:11:00,865] [INFO] DFAST_QC pipeline started.
[2023-03-18 09:11:00,865] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 09:11:00,865] [INFO] DQC Reference Directory: /var/lib/cwl/stgd33a272e-fa44-40ce-b6e7-3fb0264e37dc/dqc_reference
[2023-03-18 09:11:02,002] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 09:11:02,002] [INFO] Task started: Prodigal
[2023-03-18 09:11:02,002] [INFO] Running command: cat /var/lib/cwl/stg6d16ea73-1847-4c06-a506-548a372d8efb/OceanDNA-b43377.fa | prodigal -d OceanDNA-b43377/cds.fna -a OceanDNA-b43377/protein.faa -g 11 -q > /dev/null
[2023-03-18 09:11:06,100] [INFO] Task succeeded: Prodigal
[2023-03-18 09:11:06,101] [INFO] Task started: HMMsearch
[2023-03-18 09:11:06,101] [INFO] Running command: hmmsearch --tblout OceanDNA-b43377/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd33a272e-fa44-40ce-b6e7-3fb0264e37dc/dqc_reference/reference_markers.hmm OceanDNA-b43377/protein.faa > /dev/null
[2023-03-18 09:11:06,289] [INFO] Task succeeded: HMMsearch
[2023-03-18 09:11:06,290] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg6d16ea73-1847-4c06-a506-548a372d8efb/OceanDNA-b43377.fa]
[2023-03-18 09:11:06,299] [INFO] Query marker FASTA was written to OceanDNA-b43377/markers.fasta
[2023-03-18 09:11:06,299] [INFO] Task started: Blastn
[2023-03-18 09:11:06,300] [INFO] Running command: blastn -query OceanDNA-b43377/markers.fasta -db /var/lib/cwl/stgd33a272e-fa44-40ce-b6e7-3fb0264e37dc/dqc_reference/reference_markers.fasta -out OceanDNA-b43377/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:11:06,986] [INFO] Task succeeded: Blastn
[2023-03-18 09:11:06,987] [INFO] Selected 20 target genomes.
[2023-03-18 09:11:06,987] [INFO] Target genome list was writen to OceanDNA-b43377/target_genomes.txt
[2023-03-18 09:11:06,996] [INFO] Task started: fastANI
[2023-03-18 09:11:06,996] [INFO] Running command: fastANI --query /var/lib/cwl/stg6d16ea73-1847-4c06-a506-548a372d8efb/OceanDNA-b43377.fa --refList OceanDNA-b43377/target_genomes.txt --output OceanDNA-b43377/fastani_result.tsv --threads 1
[2023-03-18 09:11:17,220] [INFO] Task succeeded: fastANI
[2023-03-18 09:11:17,221] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd33a272e-fa44-40ce-b6e7-3fb0264e37dc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 09:11:17,221] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd33a272e-fa44-40ce-b6e7-3fb0264e37dc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 09:11:17,269] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 09:11:17,269] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 09:11:17,269] [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	77.3822	94	215	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 09:11:17,270] [INFO] DFAST Taxonomy check result was written to OceanDNA-b43377/tc_result.tsv
[2023-03-18 09:11:17,270] [INFO] ===== Taxonomy check completed =====
[2023-03-18 09:11:17,270] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 09:11:17,270] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd33a272e-fa44-40ce-b6e7-3fb0264e37dc/dqc_reference/checkm_data
[2023-03-18 09:11:17,271] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 09:11:17,273] [INFO] Task started: CheckM
[2023-03-18 09:11:17,274] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b43377/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b43377/checkm_input OceanDNA-b43377/checkm_result
[2023-03-18 09:11:35,737] [INFO] Task succeeded: CheckM
[2023-03-18 09:11:35,737] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 77.86%
Contamintation: 2.08%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 09:11:35,739] [INFO] ===== Completeness check finished =====
[2023-03-18 09:11:35,739] [INFO] ===== Start GTDB Search =====
[2023-03-18 09:11:35,739] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b43377/markers.fasta)
[2023-03-18 09:11:35,740] [INFO] Task started: Blastn
[2023-03-18 09:11:35,740] [INFO] Running command: blastn -query OceanDNA-b43377/markers.fasta -db /var/lib/cwl/stgd33a272e-fa44-40ce-b6e7-3fb0264e37dc/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b43377/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:11:37,016] [INFO] Task succeeded: Blastn
[2023-03-18 09:11:37,017] [INFO] Selected 12 target genomes.
[2023-03-18 09:11:37,017] [INFO] Target genome list was writen to OceanDNA-b43377/target_genomes_gtdb.txt
[2023-03-18 09:11:37,071] [INFO] Task started: fastANI
[2023-03-18 09:11:37,072] [INFO] Running command: fastANI --query /var/lib/cwl/stg6d16ea73-1847-4c06-a506-548a372d8efb/OceanDNA-b43377.fa --refList OceanDNA-b43377/target_genomes_gtdb.txt --output OceanDNA-b43377/fastani_result_gtdb.tsv --threads 1
[2023-03-18 09:11:40,059] [INFO] Task succeeded: fastANI
[2023-03-18 09:11:40,065] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 09:11:40,065] [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_002335045.1	s__UBA2013 sp002335045	88.6599	191	215	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__UBA2013	95.0	98.42	96.96	0.95	0.94	3	-
GCA_003978185.1	s__UBA2013 sp003978185	88.1345	111	215	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__UBA2013	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003978285.1	s__UBA2013 sp003978285	87.1525	125	215	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__UBA2013	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003489145.1	s__UBA2013 sp003489145	85.9208	154	215	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__UBA2013	95.0	99.21	98.78	0.83	0.78	42	-
GCA_018648985.1	s__UBA2013 sp018648985	81.637	134	215	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__UBA2013	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910595805.1	s__UBA2013 sp910595805	81.4986	147	215	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__UBA2013	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016845205.1	s__UBA2013 sp016845205	81.4602	161	215	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__UBA2013	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015658965.1	s__UBA2013 sp015658965	81.0589	133	215	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__UBA2013	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012963565.1	s__DTVJ01 sp012963565	78.9347	104	215	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__DTVJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002909145.1	s__Thioglobus_B perditus	77.5775	91	215	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Thioglobus_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 09:11:40,065] [INFO] GTDB search result was written to OceanDNA-b43377/result_gtdb.tsv
[2023-03-18 09:11:40,065] [INFO] ===== GTDB Search completed =====
[2023-03-18 09:11:40,066] [INFO] DFAST_QC result json was written to OceanDNA-b43377/dqc_result.json
[2023-03-18 09:11:40,066] [INFO] DFAST_QC completed!
[2023-03-18 09:11:40,066] [INFO] Total running time: 0h0m39s