[2023-03-18 23:48:46,561] [INFO] DFAST_QC pipeline started.
[2023-03-18 23:48:46,562] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 23:48:46,562] [INFO] DQC Reference Directory: /var/lib/cwl/stgaceda956-6fd9-4889-b017-76d1a38eea31/dqc_reference
[2023-03-18 23:48:47,643] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 23:48:47,644] [INFO] Task started: Prodigal
[2023-03-18 23:48:47,644] [INFO] Running command: cat /var/lib/cwl/stge09e2e69-1e3b-4565-b7eb-76e67532cf31/OceanDNA-b26627.fa | prodigal -d OceanDNA-b26627/cds.fna -a OceanDNA-b26627/protein.faa -g 11 -q > /dev/null
[2023-03-18 23:49:12,281] [INFO] Task succeeded: Prodigal
[2023-03-18 23:49:12,282] [INFO] Task started: HMMsearch
[2023-03-18 23:49:12,282] [INFO] Running command: hmmsearch --tblout OceanDNA-b26627/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaceda956-6fd9-4889-b017-76d1a38eea31/dqc_reference/reference_markers.hmm OceanDNA-b26627/protein.faa > /dev/null
[2023-03-18 23:49:12,499] [INFO] Task succeeded: HMMsearch
[2023-03-18 23:49:12,499] [INFO] Found 6/6 markers.
[2023-03-18 23:49:12,530] [INFO] Query marker FASTA was written to OceanDNA-b26627/markers.fasta
[2023-03-18 23:49:12,530] [INFO] Task started: Blastn
[2023-03-18 23:49:12,530] [INFO] Running command: blastn -query OceanDNA-b26627/markers.fasta -db /var/lib/cwl/stgaceda956-6fd9-4889-b017-76d1a38eea31/dqc_reference/reference_markers.fasta -out OceanDNA-b26627/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:49:13,377] [INFO] Task succeeded: Blastn
[2023-03-18 23:49:13,378] [INFO] Selected 14 target genomes.
[2023-03-18 23:49:13,378] [INFO] Target genome list was writen to OceanDNA-b26627/target_genomes.txt
[2023-03-18 23:49:13,413] [INFO] Task started: fastANI
[2023-03-18 23:49:13,413] [INFO] Running command: fastANI --query /var/lib/cwl/stge09e2e69-1e3b-4565-b7eb-76e67532cf31/OceanDNA-b26627.fa --refList OceanDNA-b26627/target_genomes.txt --output OceanDNA-b26627/fastani_result.tsv --threads 1
[2023-03-18 23:49:27,849] [INFO] Task succeeded: fastANI
[2023-03-18 23:49:27,849] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaceda956-6fd9-4889-b017-76d1a38eea31/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 23:49:27,849] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaceda956-6fd9-4889-b017-76d1a38eea31/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 23:49:27,858] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 23:49:27,858] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 23:49:27,858] [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
Reyranella aquatilis	strain=KCTC 52223	GCA_020880995.1	2035356	2035356	type	True	81.7851	943	1289	95	below_threshold
Reyranella soli	strain=NBRC 108950	GCA_007992495.1	1230389	1230389	type	True	81.7392	955	1289	95	below_threshold
Reyranella massiliensis	strain=521	GCA_000312425.1	445220	445220	type	True	81.4862	911	1289	95	below_threshold
Vineibacter terrae	strain=CC-CFT640	GCA_008039615.1	2586908	2586908	type	True	78.1382	559	1289	95	below_threshold
Oceanibaculum indicum	strain=P24	GCA_000299935.1	526216	526216	type	True	76.4232	185	1289	95	below_threshold
Rhodopseudomonas pseudopalustris	strain=DSM 123	GCA_900110435.1	1513892	1513892	type	True	76.3263	167	1289	95	below_threshold
Hypericibacter adhaerens	strain=R5959	GCA_008728835.1	2602016	2602016	type	True	76.316	220	1289	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	76.3145	288	1289	95	below_threshold
Azospirillum thiophilum	strain=DSM 21654	GCA_000960825.1	528244	528244	type	True	76.2769	243	1289	95	below_threshold
Methylobrevis pamukkalensis	strain=PK2	GCA_001720135.1	1439726	1439726	type	True	76.238	166	1289	95	below_threshold
Pelagibius marinus	strain=NBU2595	GCA_014925385.1	2762760	2762760	type	True	76.2265	200	1289	95	below_threshold
Ferruginivarius sediminum	strain=WD2A32	GCA_003344765.1	2661937	2661937	type	True	75.9691	129	1289	95	below_threshold
Rhodoligotrophos defluvii	strain=lm1	GCA_005281615.1	2561934	2561934	type	True	75.6958	111	1289	95	below_threshold
Amaricoccus solimangrovi	strain=HB172011	GCA_006385685.1	2589815	2589815	type	True	75.6351	143	1289	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 23:49:27,858] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26627/tc_result.tsv
[2023-03-18 23:49:27,858] [INFO] ===== Taxonomy check completed =====
[2023-03-18 23:49:27,858] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 23:49:27,858] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaceda956-6fd9-4889-b017-76d1a38eea31/dqc_reference/checkm_data
[2023-03-18 23:49:27,859] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 23:49:28,090] [INFO] Task started: CheckM
[2023-03-18 23:49:28,090] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26627/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26627/checkm_input OceanDNA-b26627/checkm_result
[2023-03-18 23:50:27,996] [INFO] Task succeeded: CheckM
[2023-03-18 23:50:27,997] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 23:50:28,000] [INFO] ===== Completeness check finished =====
[2023-03-18 23:50:28,000] [INFO] ===== Start GTDB Search =====
[2023-03-18 23:50:28,000] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26627/markers.fasta)
[2023-03-18 23:50:28,000] [INFO] Task started: Blastn
[2023-03-18 23:50:28,000] [INFO] Running command: blastn -query OceanDNA-b26627/markers.fasta -db /var/lib/cwl/stgaceda956-6fd9-4889-b017-76d1a38eea31/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26627/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:50:29,625] [INFO] Task succeeded: Blastn
[2023-03-18 23:50:29,626] [INFO] Selected 22 target genomes.
[2023-03-18 23:50:29,626] [INFO] Target genome list was writen to OceanDNA-b26627/target_genomes_gtdb.txt
[2023-03-18 23:50:29,650] [INFO] Task started: fastANI
[2023-03-18 23:50:29,650] [INFO] Running command: fastANI --query /var/lib/cwl/stge09e2e69-1e3b-4565-b7eb-76e67532cf31/OceanDNA-b26627.fa --refList OceanDNA-b26627/target_genomes_gtdb.txt --output OceanDNA-b26627/fastani_result_gtdb.tsv --threads 1
[2023-03-18 23:50:52,410] [INFO] Task succeeded: fastANI
[2023-03-18 23:50:52,422] [INFO] Found 22 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 23:50:52,422] [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_004296935.1	s__Reyranella sp004296935	84.9714	1011	1289	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001767945.1	s__Reyranella sp001767945	84.3561	907	1289	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_010032545.1	s__Reyranella sp010032545	83.5034	865	1289	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004296815.1	s__Reyranella sp004296815	82.5273	745	1289	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019039055.1	s__Reyranella sp019039055	82.0121	948	1289	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002281855.1	s__Reyranella sp002281855	81.9507	927	1289	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	99.99	99.99	0.99	0.99	3	-
GCA_004297265.1	s__Reyranella sp004297265	81.8933	929	1289	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009377525.1	s__Reyranella sp009377525	81.8859	933	1289	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009772935.1	s__Reyranella sp009772935	81.848	926	1289	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900110395.1	s__Reyranella sp900110395	81.8094	969	1289	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013290035.1	s__Reyranella sp013290035	81.6992	574	1289	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001897995.1	s__Reyranella sp001897995	81.5171	809	1289	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	99.19	98.73	0.86	0.86	3	-
GCA_013205335.1	s__Reyranella sp013205335	81.4901	737	1289	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000312425.1	s__Reyranella massiliensis	81.4861	910	1289	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017307275.1	s__Reyranella sp017307275	81.4204	840	1289	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018240695.1	s__Reyranella sp018240695	81.2524	730	1289	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	96.90	96.90	0.84	0.84	2	-
GCA_016780605.1	s__Reyranella sp016780605	81.1278	518	1289	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005884705.1	s__Reyranella sp005884705	81.0254	607	1289	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903832005.1	s__Reyranella aerosaccus_B	80.9259	820	1289	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	99.93	99.93	0.97	0.96	3	-
GCA_903915535.1	s__Reyranella aerosaccus_C	80.762	804	1289	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	99.05	99.05	0.90	0.90	2	-
GCA_903839865.1	s__Reyranella aerosaccus_A	80.6837	735	1289	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	99.29	98.98	0.87	0.83	3	-
GCA_018240685.1	s__Reyranella sp018240685	80.6177	757	1289	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 23:50:52,422] [INFO] GTDB search result was written to OceanDNA-b26627/result_gtdb.tsv
[2023-03-18 23:50:52,422] [INFO] ===== GTDB Search completed =====
[2023-03-18 23:50:52,424] [INFO] DFAST_QC result json was written to OceanDNA-b26627/dqc_result.json
[2023-03-18 23:50:52,424] [INFO] DFAST_QC completed!
[2023-03-18 23:50:52,424] [INFO] Total running time: 0h2m6s