[2023-03-14 13:50:59,175] [INFO] DFAST_QC pipeline started.
[2023-03-14 13:50:59,175] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 13:50:59,175] [INFO] DQC Reference Directory: /var/lib/cwl/stg3d337f11-d0fb-44e0-afce-12254deafe17/dqc_reference
[2023-03-14 13:51:00,342] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 13:51:00,343] [INFO] Task started: Prodigal
[2023-03-14 13:51:00,343] [INFO] Running command: cat /var/lib/cwl/stgaa24a493-37a3-4d8e-819b-619b8ed51326/OceanDNA-b25052.fa | prodigal -d OceanDNA-b25052/cds.fna -a OceanDNA-b25052/protein.faa -g 11 -q > /dev/null
[2023-03-14 13:51:09,857] [INFO] Task succeeded: Prodigal
[2023-03-14 13:51:09,857] [INFO] Task started: HMMsearch
[2023-03-14 13:51:09,857] [INFO] Running command: hmmsearch --tblout OceanDNA-b25052/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3d337f11-d0fb-44e0-afce-12254deafe17/dqc_reference/reference_markers.hmm OceanDNA-b25052/protein.faa > /dev/null
[2023-03-14 13:51:10,139] [INFO] Task succeeded: HMMsearch
[2023-03-14 13:51:10,139] [INFO] Found 6/6 markers.
[2023-03-14 13:51:10,152] [INFO] Query marker FASTA was written to OceanDNA-b25052/markers.fasta
[2023-03-14 13:51:10,154] [INFO] Task started: Blastn
[2023-03-14 13:51:10,154] [INFO] Running command: blastn -query OceanDNA-b25052/markers.fasta -db /var/lib/cwl/stg3d337f11-d0fb-44e0-afce-12254deafe17/dqc_reference/reference_markers.fasta -out OceanDNA-b25052/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 13:51:10,984] [INFO] Task succeeded: Blastn
[2023-03-14 13:51:10,985] [INFO] Selected 28 target genomes.
[2023-03-14 13:51:10,986] [INFO] Target genome list was writen to OceanDNA-b25052/target_genomes.txt
[2023-03-14 13:51:11,005] [INFO] Task started: fastANI
[2023-03-14 13:51:11,006] [INFO] Running command: fastANI --query /var/lib/cwl/stgaa24a493-37a3-4d8e-819b-619b8ed51326/OceanDNA-b25052.fa --refList OceanDNA-b25052/target_genomes.txt --output OceanDNA-b25052/fastani_result.tsv --threads 1
[2023-03-14 13:51:33,561] [INFO] Task succeeded: fastANI
[2023-03-14 13:51:33,561] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3d337f11-d0fb-44e0-afce-12254deafe17/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 13:51:33,561] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3d337f11-d0fb-44e0-afce-12254deafe17/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 13:51:33,565] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 13:51:33,565] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-14 13:51:33,565] [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
Parvibaculum indicum	strain=DSM 25305	GCA_011762095.1	562969	562969	type	True	75.6362	53	486	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 13:51:33,565] [INFO] DFAST Taxonomy check result was written to OceanDNA-b25052/tc_result.tsv
[2023-03-14 13:51:33,565] [INFO] ===== Taxonomy check completed =====
[2023-03-14 13:51:33,565] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 13:51:33,565] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3d337f11-d0fb-44e0-afce-12254deafe17/dqc_reference/checkm_data
[2023-03-14 13:51:33,566] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 13:51:33,569] [INFO] Task started: CheckM
[2023-03-14 13:51:33,569] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b25052/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b25052/checkm_input OceanDNA-b25052/checkm_result
[2023-03-14 13:52:11,200] [INFO] Task succeeded: CheckM
[2023-03-14 13:52:11,200] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.79%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 13:52:11,203] [INFO] ===== Completeness check finished =====
[2023-03-14 13:52:11,203] [INFO] ===== Start GTDB Search =====
[2023-03-14 13:52:11,203] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b25052/markers.fasta)
[2023-03-14 13:52:11,205] [INFO] Task started: Blastn
[2023-03-14 13:52:11,205] [INFO] Running command: blastn -query OceanDNA-b25052/markers.fasta -db /var/lib/cwl/stg3d337f11-d0fb-44e0-afce-12254deafe17/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b25052/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 13:52:12,709] [INFO] Task succeeded: Blastn
[2023-03-14 13:52:12,710] [INFO] Selected 17 target genomes.
[2023-03-14 13:52:12,710] [INFO] Target genome list was writen to OceanDNA-b25052/target_genomes_gtdb.txt
[2023-03-14 13:52:12,732] [INFO] Task started: fastANI
[2023-03-14 13:52:12,733] [INFO] Running command: fastANI --query /var/lib/cwl/stgaa24a493-37a3-4d8e-819b-619b8ed51326/OceanDNA-b25052.fa --refList OceanDNA-b25052/target_genomes_gtdb.txt --output OceanDNA-b25052/fastani_result_gtdb.tsv --threads 1
[2023-03-14 13:52:20,519] [INFO] Task succeeded: fastANI
[2023-03-14 13:52:20,525] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 13:52:20,526] [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_002689195.1	s__UBA7378 sp002689195	98.4197	372	486	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__RS24;g__UBA7378	95.0	98.73	98.05	0.85	0.80	4	conclusive
GCA_902624095.1	s__UBA7378 sp902624095	84.6912	329	486	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__RS24;g__UBA7378	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002469805.1	s__UBA7378 sp002469805	78.9081	269	486	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__RS24;g__UBA7378	95.0	99.20	98.74	0.81	0.77	5	-
GCA_009920875.1	s__UBA8337 sp009920875	77.4722	127	486	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__RS24;g__UBA8337	95.0	97.55	97.55	0.89	0.89	2	-
GCA_900197605.1	s__UBA8337 sp900197605	77.4102	164	486	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	77.3364	127	486	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__RS24;g__UBA8337	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002721725.1	s__UBA8337 sp002721725	77.0013	139	486	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__RS24;g__UBA8337	95.0	99.29	99.29	0.93	0.93	2	-
GCA_018673175.1	s__UBA8337 sp018673175	76.5614	134	486	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__RS24;g__UBA8337	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 13:52:20,526] [INFO] GTDB search result was written to OceanDNA-b25052/result_gtdb.tsv
[2023-03-14 13:52:20,526] [INFO] ===== GTDB Search completed =====
[2023-03-14 13:52:20,527] [INFO] DFAST_QC result json was written to OceanDNA-b25052/dqc_result.json
[2023-03-14 13:52:20,527] [INFO] DFAST_QC completed!
[2023-03-14 13:52:20,527] [INFO] Total running time: 0h1m21s