[2024-01-24 11:42:20,309] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:42:20,311] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:42:20,311] [INFO] DQC Reference Directory: /var/lib/cwl/stg76f5689d-1a23-4a11-a6a4-3c28b2e2bef4/dqc_reference
[2024-01-24 11:42:24,523] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:42:24,524] [INFO] Task started: Prodigal
[2024-01-24 11:42:24,525] [INFO] Running command: gunzip -c /var/lib/cwl/stgb0b88cef-1e68-4ef5-8085-c805a34fab87/GCF_026130545.1_ASM2613054v1_genomic.fna.gz | prodigal -d GCF_026130545.1_ASM2613054v1_genomic.fna/cds.fna -a GCF_026130545.1_ASM2613054v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:42:46,721] [INFO] Task succeeded: Prodigal
[2024-01-24 11:42:46,721] [INFO] Task started: HMMsearch
[2024-01-24 11:42:46,721] [INFO] Running command: hmmsearch --tblout GCF_026130545.1_ASM2613054v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg76f5689d-1a23-4a11-a6a4-3c28b2e2bef4/dqc_reference/reference_markers.hmm GCF_026130545.1_ASM2613054v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:42:47,069] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:42:47,070] [INFO] Found 6/6 markers.
[2024-01-24 11:42:47,161] [INFO] Query marker FASTA was written to GCF_026130545.1_ASM2613054v1_genomic.fna/markers.fasta
[2024-01-24 11:42:47,161] [INFO] Task started: Blastn
[2024-01-24 11:42:47,162] [INFO] Running command: blastn -query GCF_026130545.1_ASM2613054v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg76f5689d-1a23-4a11-a6a4-3c28b2e2bef4/dqc_reference/reference_markers.fasta -out GCF_026130545.1_ASM2613054v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:42:47,937] [INFO] Task succeeded: Blastn
[2024-01-24 11:42:47,941] [INFO] Selected 23 target genomes.
[2024-01-24 11:42:47,941] [INFO] Target genome list was writen to GCF_026130545.1_ASM2613054v1_genomic.fna/target_genomes.txt
[2024-01-24 11:42:47,950] [INFO] Task started: fastANI
[2024-01-24 11:42:47,951] [INFO] Running command: fastANI --query /var/lib/cwl/stgb0b88cef-1e68-4ef5-8085-c805a34fab87/GCF_026130545.1_ASM2613054v1_genomic.fna.gz --refList GCF_026130545.1_ASM2613054v1_genomic.fna/target_genomes.txt --output GCF_026130545.1_ASM2613054v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:43:08,558] [INFO] Task succeeded: fastANI
[2024-01-24 11:43:08,558] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg76f5689d-1a23-4a11-a6a4-3c28b2e2bef4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:43:08,559] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg76f5689d-1a23-4a11-a6a4-3c28b2e2bef4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:43:08,577] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:43:08,577] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:43:08,577] [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
Lichenibacterium ramalinae	strain=RmlP001	GCA_004137085.1	2316527	2316527	type	True	77.7374	537	2433	95	below_threshold
Lichenibacterium minor	strain=RmlP026	GCA_004137685.1	2316528	2316528	type	True	77.3799	463	2433	95	below_threshold
Methylocystis hirsuta	strain=CSC1	GCA_003722355.1	369798	369798	type	True	76.8499	146	2433	95	below_threshold
Bosea lathyri	strain=DSM 26656	GCA_900108245.1	1036778	1036778	type	True	76.8442	243	2433	95	below_threshold
Chelatococcus composti	strain=DSM 101465	GCA_018398355.1	1743235	1743235	type	True	76.8056	219	2433	95	below_threshold
Methylocystis rosea	strain=SV97	GCA_000372845.1	173366	173366	type	True	76.8047	157	2433	95	below_threshold
Methylobacterium oryzihabitans	strain=TER-1	GCA_004004555.2	2499852	2499852	type	True	76.7818	311	2433	95	below_threshold
Methylobacterium nodulans	strain=ORS 2060	GCA_000022085.1	114616	114616	type	True	76.7162	286	2433	95	below_threshold
Microvirga zambiensis	strain=WSM3693	GCA_016735695.1	1402137	1402137	type	True	76.7073	241	2433	95	below_threshold
Bosea vaviloviae	strain=Vaf18	GCA_001741865.1	1526658	1526658	type	True	76.6979	274	2433	95	below_threshold
Rhodoblastus acidophilus	strain=DSM 137	GCA_002937135.1	1074	1074	suspected-type	True	76.6596	226	2433	95	below_threshold
Rhodoblastus acidophilus	strain=DSM 137	GCA_003258765.1	1074	1074	suspected-type	True	76.6592	222	2433	95	below_threshold
Methylosinus trichosporium	strain=OB3b	GCA_000178815.2	426	426	type	True	76.6204	234	2433	95	below_threshold
Methylosinus trichosporium	strain=OB3b	GCA_002752655.1	426	426	type	True	76.6149	227	2433	95	below_threshold
Methylocystis silviterrae	strain=FS	GCA_013350005.1	2743612	2743612	type	True	76.6089	155	2433	95	below_threshold
Rhodoblastus acidophilus	strain=DSM 137	GCA_900187365.1	1074	1074	suspected-type	True	76.5937	228	2433	95	below_threshold
Methylocapsa acidiphila	strain=B2	GCA_000427445.1	133552	133552	type	True	76.5485	177	2433	95	below_threshold
Bradyrhizobium betae	strain=CECT 5829	GCA_024806875.1	244734	244734	type	True	76.5449	264	2433	95	below_threshold
Bradyrhizobium viridifuturi	strain=SEMIA 690	GCA_001238275.1	1654716	1654716	type	True	76.4914	254	2433	95	below_threshold
Microvirga calopogonii	strain=CCBAU 65841	GCA_003347665.1	2078013	2078013	type	True	76.4827	233	2433	95	below_threshold
Bradyrhizobium cajani	strain=1010	GCA_009759665.1	1928661	1928661	type	True	76.4685	284	2433	95	below_threshold
Methylorubrum rhodesianum	strain=DSM 5687	GCA_014199985.1	29427	29427	type	True	76.4591	268	2433	95	below_threshold
Sphingomonas rubra	strain=CGMCC 1.9113	GCA_900115745.1	634430	634430	type	True	75.5962	105	2433	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:43:08,579] [INFO] DFAST Taxonomy check result was written to GCF_026130545.1_ASM2613054v1_genomic.fna/tc_result.tsv
[2024-01-24 11:43:08,579] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:43:08,579] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:43:08,579] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg76f5689d-1a23-4a11-a6a4-3c28b2e2bef4/dqc_reference/checkm_data
[2024-01-24 11:43:08,580] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:43:08,659] [INFO] Task started: CheckM
[2024-01-24 11:43:08,659] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_026130545.1_ASM2613054v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_026130545.1_ASM2613054v1_genomic.fna/checkm_input GCF_026130545.1_ASM2613054v1_genomic.fna/checkm_result
[2024-01-24 11:44:13,545] [INFO] Task succeeded: CheckM
[2024-01-24 11:44:13,546] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:44:13,567] [INFO] ===== Completeness check finished =====
[2024-01-24 11:44:13,568] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:44:13,568] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_026130545.1_ASM2613054v1_genomic.fna/markers.fasta)
[2024-01-24 11:44:13,569] [INFO] Task started: Blastn
[2024-01-24 11:44:13,569] [INFO] Running command: blastn -query GCF_026130545.1_ASM2613054v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg76f5689d-1a23-4a11-a6a4-3c28b2e2bef4/dqc_reference/reference_markers_gtdb.fasta -out GCF_026130545.1_ASM2613054v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:14,905] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:14,910] [INFO] Selected 30 target genomes.
[2024-01-24 11:44:14,910] [INFO] Target genome list was writen to GCF_026130545.1_ASM2613054v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:44:14,933] [INFO] Task started: fastANI
[2024-01-24 11:44:14,933] [INFO] Running command: fastANI --query /var/lib/cwl/stgb0b88cef-1e68-4ef5-8085-c805a34fab87/GCF_026130545.1_ASM2613054v1_genomic.fna.gz --refList GCF_026130545.1_ASM2613054v1_genomic.fna/target_genomes_gtdb.txt --output GCF_026130545.1_ASM2613054v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:44:36,675] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:36,705] [INFO] Found 30 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:44:36,705] [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_004137085.1	s__Lichenihabitans ramalinae	77.7554	534	2433	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Lichenihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004137685.1	s__Lichenihabitans minor	77.3922	459	2433	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Lichenihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009765775.1	s__RH-AL1 sp009765775	77.1071	265	2433	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__RH-AL1	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003151255.1	s__Microvirga sp003151255	76.924	178	2433	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003722355.1	s__Methylocystis hirsuta	76.866	145	2433	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocystis	95.0	95.95	95.95	0.95	0.95	2	-
GCA_016716745.1	s__GCA-013693735 sp016716745	76.7798	283	2433	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__GCA-013693735	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000685825.1	s__Methylosinus sp000685825	76.7479	196	2433	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylosinus	95.0	99.04	98.49	0.94	0.91	4	-
GCF_015709515.1	s__Methylocystis sp015709515	76.7421	168	2433	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocystis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008040035.1	s__Methylobacterium sp008040035	76.7411	209	2433	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903902915.1	s__28-YEA-48 sp903902915	76.737	185	2433	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__28-YEA-48	95.0	99.59	99.16	0.95	0.92	5	-
GCF_001423265.1	s__Methylobacterium sp001423265	76.7322	219	2433	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	98.78	98.73	0.95	0.94	3	-
GCF_000022085.1	s__Methylobacterium nodulans	76.7049	289	2433	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900466745.1	s__Bosea sp900466745	76.7006	268	2433	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	99.99	99.98	0.99	0.99	7	-
GCF_018398315.1	s__Chelatococcus sp018398315	76.6964	165	2433	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Chelatococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900470775.1	s__Bosea sp900470775	76.6419	260	2433	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009811655.1	s__Methylosinus sp009811655	76.6357	205	2433	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylosinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793505.1	s__GCA-013693735 sp016793505	76.6221	269	2433	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__GCA-013693735	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016869555.1	s__Methylocystis sp016869555	76.6204	157	2433	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocystis	95.0	99.54	99.54	0.92	0.92	2	-
GCF_002752655.1	s__Methylosinus trichosporium	76.6141	227	2433	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylosinus	95.0	99.98	99.98	1.00	1.00	3	-
GCF_018383585.1	s__Microvirga sp018383585	76.6034	172	2433	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015709455.1	s__Methylosinus sp015709455	76.6029	208	2433	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylosinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903918155.1	s__28-YEA-48 sp903918155	76.5137	126	2433	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__28-YEA-48	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002929055.1	s__Methylocystis sp002929055	76.5062	157	2433	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocystis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016869435.1	s__Methylocystis sp016869435	76.4904	126	2433	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocystis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001579845.1	s__Z2-YC6860 sp001579845	76.3838	212	2433	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Z2-YC6860	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014359855.1	s__Parvibaculum sp014359855	76.1513	61	2433	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018401495.1	s__Thalassobaculum_A sp018401495	75.8604	172	2433	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Thalassobaculum_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115745.1	s__Sphingomonas rubra	75.7117	106	2433	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_903643065.1	s__Sphingomonas sp903643065	75.4945	68	2433	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016872755.1	s__GW928-bin9 sp016872755	74.78	62	2433	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__GW928-bin9	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:44:36,707] [INFO] GTDB search result was written to GCF_026130545.1_ASM2613054v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:44:36,707] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:44:36,715] [INFO] DFAST_QC result json was written to GCF_026130545.1_ASM2613054v1_genomic.fna/dqc_result.json
[2024-01-24 11:44:36,716] [INFO] DFAST_QC completed!
[2024-01-24 11:44:36,716] [INFO] Total running time: 0h2m16s