[2023-03-14 12:03:55,346] [INFO] DFAST_QC pipeline started.
[2023-03-14 12:03:55,350] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 12:03:55,350] [INFO] DQC Reference Directory: /var/lib/cwl/stgfa7109a2-d240-4515-8072-b3a543664dd3/dqc_reference
[2023-03-14 12:03:56,868] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 12:03:56,868] [INFO] Task started: Prodigal
[2023-03-14 12:03:56,868] [INFO] Running command: cat /var/lib/cwl/stg937b5441-fa55-46d6-850b-6cf1d0a5ed4b/OceanDNA-b33411.fa | prodigal -d OceanDNA-b33411/cds.fna -a OceanDNA-b33411/protein.faa -g 11 -q > /dev/null
[2023-03-14 12:04:14,874] [INFO] Task succeeded: Prodigal
[2023-03-14 12:04:14,874] [INFO] Task started: HMMsearch
[2023-03-14 12:04:14,875] [INFO] Running command: hmmsearch --tblout OceanDNA-b33411/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfa7109a2-d240-4515-8072-b3a543664dd3/dqc_reference/reference_markers.hmm OceanDNA-b33411/protein.faa > /dev/null
[2023-03-14 12:04:15,101] [INFO] Task succeeded: HMMsearch
[2023-03-14 12:04:15,101] [INFO] Found 6/6 markers.
[2023-03-14 12:04:15,138] [INFO] Query marker FASTA was written to OceanDNA-b33411/markers.fasta
[2023-03-14 12:04:15,139] [INFO] Task started: Blastn
[2023-03-14 12:04:15,139] [INFO] Running command: blastn -query OceanDNA-b33411/markers.fasta -db /var/lib/cwl/stgfa7109a2-d240-4515-8072-b3a543664dd3/dqc_reference/reference_markers.fasta -out OceanDNA-b33411/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:04:15,755] [INFO] Task succeeded: Blastn
[2023-03-14 12:04:15,759] [INFO] Selected 23 target genomes.
[2023-03-14 12:04:15,759] [INFO] Target genome list was writen to OceanDNA-b33411/target_genomes.txt
[2023-03-14 12:04:15,774] [INFO] Task started: fastANI
[2023-03-14 12:04:15,774] [INFO] Running command: fastANI --query /var/lib/cwl/stg937b5441-fa55-46d6-850b-6cf1d0a5ed4b/OceanDNA-b33411.fa --refList OceanDNA-b33411/target_genomes.txt --output OceanDNA-b33411/fastani_result.tsv --threads 1
[2023-03-14 12:04:29,772] [INFO] Task succeeded: fastANI
[2023-03-14 12:04:29,773] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfa7109a2-d240-4515-8072-b3a543664dd3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 12:04:29,773] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfa7109a2-d240-4515-8072-b3a543664dd3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 12:04:29,781] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2023-03-14 12:04:29,781] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-14 12:04:29,781] [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
Pusillimonas maritima	strain=17-4A	GCA_003576595.1	2026239	2026239	type	True	96.611	836	947	95	conclusive
Pusillimonas minor	strain=YC-7-48	GCA_014237865.1	2697024	2697024	type	True	77.8092	228	947	95	below_threshold
Pusillimonas ginsengisoli	strain=KCTC 22046	GCA_004153455.1	453575	453575	type	True	77.5729	79	947	95	below_threshold
Paracandidimonas soli	strain=DSM 100048	GCA_004342005.1	1917182	1917182	type	True	77.0719	76	947	95	below_threshold
Pusillimonas harenae	strain=DSM 25667	GCA_013416515.1	657015	657015	type	True	76.9727	114	947	95	below_threshold
Pusillimonas harenae	strain=JCM 16917	GCA_004153685.1	657015	657015	type	True	76.8939	114	947	95	below_threshold
Parapusillimonas granuli	strain=DSM 18079	GCA_014202705.1	380911	380911	type	True	76.7057	93	947	95	below_threshold
Parapusillimonas granuli	strain=LMG 24012	GCA_013416525.1	380911	380911	type	True	76.7022	92	947	95	below_threshold
Achromobacter denitrificans	strain=NBRC 15125	GCA_001571365.1	32002	32002	type	True	76.4624	78	947	95	below_threshold
Achromobacter spanius	strain=LMG 5911	GCA_902859605.1	217203	217203	suspected-type	True	76.3261	88	947	95	below_threshold
Achromobacter spanius	strain=DSM 23806	GCA_002812705.1	217203	217203	suspected-type	True	76.3157	90	947	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 12:04:29,783] [INFO] DFAST Taxonomy check result was written to OceanDNA-b33411/tc_result.tsv
[2023-03-14 12:04:29,783] [INFO] ===== Taxonomy check completed =====
[2023-03-14 12:04:29,783] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 12:04:29,783] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfa7109a2-d240-4515-8072-b3a543664dd3/dqc_reference/checkm_data
[2023-03-14 12:04:29,784] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 12:04:29,832] [INFO] Task started: CheckM
[2023-03-14 12:04:29,832] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b33411/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b33411/checkm_input OceanDNA-b33411/checkm_result
[2023-03-14 12:05:16,657] [INFO] Task succeeded: CheckM
[2023-03-14 12:05:16,658] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 12:05:16,761] [INFO] ===== Completeness check finished =====
[2023-03-14 12:05:16,761] [INFO] ===== Start GTDB Search =====
[2023-03-14 12:05:16,761] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b33411/markers.fasta)
[2023-03-14 12:05:16,762] [INFO] Task started: Blastn
[2023-03-14 12:05:16,762] [INFO] Running command: blastn -query OceanDNA-b33411/markers.fasta -db /var/lib/cwl/stgfa7109a2-d240-4515-8072-b3a543664dd3/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b33411/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:05:17,758] [INFO] Task succeeded: Blastn
[2023-03-14 12:05:17,761] [INFO] Selected 15 target genomes.
[2023-03-14 12:05:17,761] [INFO] Target genome list was writen to OceanDNA-b33411/target_genomes_gtdb.txt
[2023-03-14 12:05:17,776] [INFO] Task started: fastANI
[2023-03-14 12:05:17,776] [INFO] Running command: fastANI --query /var/lib/cwl/stg937b5441-fa55-46d6-850b-6cf1d0a5ed4b/OceanDNA-b33411.fa --refList OceanDNA-b33411/target_genomes_gtdb.txt --output OceanDNA-b33411/fastani_result_gtdb.tsv --threads 1
[2023-03-14 12:05:25,950] [INFO] Task succeeded: fastANI
[2023-03-14 12:05:25,957] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 12:05:25,957] [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
GCF_003576595.1	s__Pusillimonas_A maritima	96.611	836	947	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pusillimonas_A	95.0	96.55	95.88	0.88	0.85	8	conclusive
GCF_011388195.1	s__Pusillimonas_A sp011388195	94.864	808	947	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pusillimonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002694155.1	s__Pusillimonas_A sp002694155	84.4193	332	947	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pusillimonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002384935.1	s__Pusillimonas_A sp002384935	83.8609	694	947	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pusillimonas_A	95.0	98.90	98.23	0.90	0.79	9	-
GCF_002236805.1	s__Pusillimonas_A sp002236805	77.8682	205	947	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pusillimonas_A	95.0	98.07	98.07	0.83	0.83	2	-
GCF_014237865.1	s__Pusillimonas_A sp014237865	77.824	227	947	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pusillimonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013416445.1	s__Candidimonas_A sp013416445	77.4512	101	947	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Candidimonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012744285.1	s__Pusillimonas_A sp012744285	77.2371	138	947	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pusillimonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002849615.1	s__Candidimonas_A sp002849615	77.1977	95	947	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Candidimonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004022565.1	s__Pusillimonas_D thiosulfatoxidans	76.8858	99	947	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pusillimonas_D	95.0	97.98	97.65	0.84	0.81	3	-
GCA_004322135.1	s__Eoetvoesia sp004322135	76.7751	92	947	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Eoetvoesia	95.0	99.95	99.95	0.92	0.92	2	-
GCF_000382185.1	s__Bordetella_B sp000382185	76.6959	58	947	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 12:05:25,959] [INFO] GTDB search result was written to OceanDNA-b33411/result_gtdb.tsv
[2023-03-14 12:05:25,962] [INFO] ===== GTDB Search completed =====
[2023-03-14 12:05:25,966] [INFO] DFAST_QC result json was written to OceanDNA-b33411/dqc_result.json
[2023-03-14 12:05:25,966] [INFO] DFAST_QC completed!
[2023-03-14 12:05:25,966] [INFO] Total running time: 0h1m31s