[2023-03-16 16:43:21,354] [INFO] DFAST_QC pipeline started.
[2023-03-16 16:43:21,354] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 16:43:21,354] [INFO] DQC Reference Directory: /var/lib/cwl/stg385eeca8-c899-4739-af8d-29d9005ed137/dqc_reference
[2023-03-16 16:43:22,503] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 16:43:22,503] [INFO] Task started: Prodigal
[2023-03-16 16:43:22,503] [INFO] Running command: cat /var/lib/cwl/stgbf553980-365d-47b2-b917-42d716bb6732/OceanDNA-b33468.fa | prodigal -d OceanDNA-b33468/cds.fna -a OceanDNA-b33468/protein.faa -g 11 -q > /dev/null
[2023-03-16 16:43:39,343] [INFO] Task succeeded: Prodigal
[2023-03-16 16:43:39,343] [INFO] Task started: HMMsearch
[2023-03-16 16:43:39,343] [INFO] Running command: hmmsearch --tblout OceanDNA-b33468/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg385eeca8-c899-4739-af8d-29d9005ed137/dqc_reference/reference_markers.hmm OceanDNA-b33468/protein.faa > /dev/null
[2023-03-16 16:43:39,705] [INFO] Task succeeded: HMMsearch
[2023-03-16 16:43:39,706] [INFO] Found 6/6 markers.
[2023-03-16 16:43:39,733] [INFO] Query marker FASTA was written to OceanDNA-b33468/markers.fasta
[2023-03-16 16:43:39,733] [INFO] Task started: Blastn
[2023-03-16 16:43:39,733] [INFO] Running command: blastn -query OceanDNA-b33468/markers.fasta -db /var/lib/cwl/stg385eeca8-c899-4739-af8d-29d9005ed137/dqc_reference/reference_markers.fasta -out OceanDNA-b33468/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 16:43:40,589] [INFO] Task succeeded: Blastn
[2023-03-16 16:43:40,590] [INFO] Selected 28 target genomes.
[2023-03-16 16:43:40,591] [INFO] Target genome list was writen to OceanDNA-b33468/target_genomes.txt
[2023-03-16 16:43:40,627] [INFO] Task started: fastANI
[2023-03-16 16:43:40,627] [INFO] Running command: fastANI --query /var/lib/cwl/stgbf553980-365d-47b2-b917-42d716bb6732/OceanDNA-b33468.fa --refList OceanDNA-b33468/target_genomes.txt --output OceanDNA-b33468/fastani_result.tsv --threads 1
[2023-03-16 16:44:08,690] [INFO] Task succeeded: fastANI
[2023-03-16 16:44:08,690] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg385eeca8-c899-4739-af8d-29d9005ed137/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 16:44:08,690] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg385eeca8-c899-4739-af8d-29d9005ed137/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 16:44:08,700] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 16:44:08,700] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 16:44:08,700] [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
Rhodoferax saidenbachensis	strain=DSM 22694	GCA_001955715.1	1484693	1484693	type	True	76.5829	78	706	95	below_threshold
Limnohabitans planktonicus	strain=II-D5	GCA_001270065.2	540060	540060	type	True	76.5801	87	706	95	below_threshold
Limnohabitans curvus	strain=MWH-C5	GCA_003063475.1	323423	323423	type	True	76.5513	99	706	95	below_threshold
Rhodoferax saidenbachensis	strain=ED16	GCA_000498435.1	1484693	1484693	type	True	76.527	79	706	95	below_threshold
Comamonas aquatica	strain=NBRC 14918	GCA_000739875.1	225991	225991	type	True	76.5156	68	706	95	below_threshold
Delftia acidovorans	strain=FDAARGOS_997	GCA_016127415.1	80866	80866	type	True	76.4079	66	706	95	below_threshold
Delftia acidovorans	strain=NBRC 14950	GCA_001598795.1	80866	80866	type	True	76.3365	65	706	95	below_threshold
Rhodoferax ferrireducens	strain=DSM 15236	GCA_000013605.1	192843	192843	type	True	76.292	67	706	95	below_threshold
Rhodoferax fermentans	strain=JCM 7819	GCA_002017865.1	28066	28066	type	True	76.2869	59	706	95	below_threshold
Hydrogenophaga flava	strain=NBRC 102514	GCA_001571145.1	65657	65657	type	True	76.2608	67	706	95	below_threshold
Comamonas fluminis	strain=CJ34	GCA_019186805.1	2796366	2796366	type	True	76.0729	55	706	95	below_threshold
Variovorax paradoxus	strain=NBRC 15149	GCA_001591365.1	34073	34073	suspected-type	True	76.0487	65	706	95	below_threshold
Ramlibacter agri	strain=G-1-2-2	GCA_012927085.1	2728837	2728837	type	True	76.0084	61	706	95	below_threshold
Comamonas testosteroni	strain=NCTC10698	GCA_900461225.1	285	285	suspected-type	True	76.0017	58	706	95	below_threshold
Comamonas testosteroni	strain=ATCC 11996	GCA_000241525.2	285	285	suspected-type	True	76.0016	58	706	95	below_threshold
Comamonas suwonensis	strain=EJ-4	GCA_012844455.2	2606214	2606214	type	True	75.9249	60	706	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 16:44:08,700] [INFO] DFAST Taxonomy check result was written to OceanDNA-b33468/tc_result.tsv
[2023-03-16 16:44:08,700] [INFO] ===== Taxonomy check completed =====
[2023-03-16 16:44:08,701] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 16:44:08,701] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg385eeca8-c899-4739-af8d-29d9005ed137/dqc_reference/checkm_data
[2023-03-16 16:44:08,701] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 16:44:08,708] [INFO] Task started: CheckM
[2023-03-16 16:44:08,708] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b33468/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b33468/checkm_input OceanDNA-b33468/checkm_result
[2023-03-16 16:44:46,305] [INFO] Task succeeded: CheckM
[2023-03-16 16:44:46,306] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 16:44:46,308] [INFO] ===== Completeness check finished =====
[2023-03-16 16:44:46,308] [INFO] ===== Start GTDB Search =====
[2023-03-16 16:44:46,308] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b33468/markers.fasta)
[2023-03-16 16:44:46,309] [INFO] Task started: Blastn
[2023-03-16 16:44:46,309] [INFO] Running command: blastn -query OceanDNA-b33468/markers.fasta -db /var/lib/cwl/stg385eeca8-c899-4739-af8d-29d9005ed137/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b33468/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 16:44:47,384] [INFO] Task succeeded: Blastn
[2023-03-16 16:44:47,385] [INFO] Selected 27 target genomes.
[2023-03-16 16:44:47,385] [INFO] Target genome list was writen to OceanDNA-b33468/target_genomes_gtdb.txt
[2023-03-16 16:44:47,492] [INFO] Task started: fastANI
[2023-03-16 16:44:47,492] [INFO] Running command: fastANI --query /var/lib/cwl/stgbf553980-365d-47b2-b917-42d716bb6732/OceanDNA-b33468.fa --refList OceanDNA-b33468/target_genomes_gtdb.txt --output OceanDNA-b33468/fastani_result_gtdb.tsv --threads 1
[2023-03-16 16:45:03,018] [INFO] Task succeeded: fastANI
[2023-03-16 16:45:03,032] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 16:45:03,032] [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_018607835.1	s__RS62 sp002340675	99.0988	640	706	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__RS62	95.0	99.19	98.96	0.91	0.88	5	conclusive
GCA_000496475.1	s__RS62 sp000496475	77.6931	121	706	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__RS62	95.0	98.53	98.53	0.95	0.95	2	-
GCF_010104355.1	s__Hydrogenophaga sp010104355	76.9728	83	706	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003063355.1	s__Limnohabitans_A sp003063355	76.7922	88	706	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002778325.1	s__Limnohabitans sp002778325	76.7151	91	706	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903935585.1	s__Limnohabitans_A sp903935585	76.646	76	706	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	99.77	99.67	0.93	0.90	6	-
GCF_003063475.1	s__Limnohabitans curvus	76.5726	98	706	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	98.49	98.49	0.87	0.87	2	-
GCA_002842215.1	s__Hydrogenophaga sp002842215	76.4763	81	706	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002001205.1	s__Hydrogenophaga sp002001205	76.4288	79	706	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903832625.1	s__Limnohabitans sp903832625	76.4196	82	706	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	97.24	97.19	0.90	0.89	4	-
GCF_018474005.1	s__Rhodoferax sp018474005	76.3985	56	706	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903828535.1	s__Curvibacter sp903828535	76.3965	61	706	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Curvibacter	95.0	99.64	99.54	0.96	0.96	4	-
GCF_003347515.1	s__Rhodoferax sp003347515	76.3851	62	706	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000293865.2	s__Limnohabitans_A sp000293865	76.3804	70	706	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003063545.1	s__Limnohabitans sp003063545	76.3143	84	706	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012927445.1	s__Rhodoferax sp012927445	76.305	64	706	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	98.76	98.76	0.94	0.94	2	-
GCF_001571145.1	s__Hydrogenophaga flava	76.2608	67	706	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012932145.1	s__Giesbergeria sp012932145	76.1908	63	706	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	98.72	98.72	0.89	0.89	2	-
GCA_001770955.1	s__Giesbergeria sp001770955	76.1776	52	706	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	97.11	95.02	0.83	0.80	5	-
GCF_000175235.1	s__Acidovorax delafieldii_B	76.1686	74	706	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003053545.1	s__Acidovorax sp003053545	76.0574	72	706	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	98.66	97.32	0.95	0.90	3	-
GCA_003241965.1	s__Hydrogenophaga sp003241965	76.0529	93	706	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016721925.1	s__JAABQG01 sp016721925	76.0155	71	706	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__JAABQG01	95.0	98.62	98.32	0.93	0.90	9	-
GCA_001771065.1	s__Rhodoferax sp001771065	75.9611	59	706	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903902035.1	s__Curvibacter sp903902035	75.9368	66	706	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Curvibacter	95.0	98.85	97.80	0.89	0.83	3	-
--------------------------------------------------------------------------------
[2023-03-16 16:45:03,033] [INFO] GTDB search result was written to OceanDNA-b33468/result_gtdb.tsv
[2023-03-16 16:45:03,033] [INFO] ===== GTDB Search completed =====
[2023-03-16 16:45:03,035] [INFO] DFAST_QC result json was written to OceanDNA-b33468/dqc_result.json
[2023-03-16 16:45:03,035] [INFO] DFAST_QC completed!
[2023-03-16 16:45:03,035] [INFO] Total running time: 0h1m42s