[2023-06-08 09:32:24,540] [INFO] DFAST_QC pipeline started.
[2023-06-08 09:32:24,544] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 09:32:24,544] [INFO] DQC Reference Directory: /var/lib/cwl/stg2ec550e7-e5c0-4c41-93b7-7b92b557801b/dqc_reference
[2023-06-08 09:32:27,083] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 09:32:27,084] [INFO] Task started: Prodigal
[2023-06-08 09:32:27,084] [INFO] Running command: gunzip -c /var/lib/cwl/stg8dd7bd43-ad15-443e-8239-b72ef10e3ef2/GCA_947451855.1_Jr-25may17-178_genomic.fna.gz | prodigal -d GCA_947451855.1_Jr-25may17-178_genomic.fna/cds.fna -a GCA_947451855.1_Jr-25may17-178_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 09:32:38,036] [INFO] Task succeeded: Prodigal
[2023-06-08 09:32:38,037] [INFO] Task started: HMMsearch
[2023-06-08 09:32:38,037] [INFO] Running command: hmmsearch --tblout GCA_947451855.1_Jr-25may17-178_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2ec550e7-e5c0-4c41-93b7-7b92b557801b/dqc_reference/reference_markers.hmm GCA_947451855.1_Jr-25may17-178_genomic.fna/protein.faa > /dev/null
[2023-06-08 09:32:38,316] [INFO] Task succeeded: HMMsearch
[2023-06-08 09:32:38,317] [INFO] Found 6/6 markers.
[2023-06-08 09:32:38,349] [INFO] Query marker FASTA was written to GCA_947451855.1_Jr-25may17-178_genomic.fna/markers.fasta
[2023-06-08 09:32:38,350] [INFO] Task started: Blastn
[2023-06-08 09:32:38,350] [INFO] Running command: blastn -query GCA_947451855.1_Jr-25may17-178_genomic.fna/markers.fasta -db /var/lib/cwl/stg2ec550e7-e5c0-4c41-93b7-7b92b557801b/dqc_reference/reference_markers.fasta -out GCA_947451855.1_Jr-25may17-178_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 09:32:39,160] [INFO] Task succeeded: Blastn
[2023-06-08 09:32:39,164] [INFO] Selected 31 target genomes.
[2023-06-08 09:32:39,164] [INFO] Target genome list was writen to GCA_947451855.1_Jr-25may17-178_genomic.fna/target_genomes.txt
[2023-06-08 09:32:39,202] [INFO] Task started: fastANI
[2023-06-08 09:32:39,203] [INFO] Running command: fastANI --query /var/lib/cwl/stg8dd7bd43-ad15-443e-8239-b72ef10e3ef2/GCA_947451855.1_Jr-25may17-178_genomic.fna.gz --refList GCA_947451855.1_Jr-25may17-178_genomic.fna/target_genomes.txt --output GCA_947451855.1_Jr-25may17-178_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 09:33:05,953] [INFO] Task succeeded: fastANI
[2023-06-08 09:33:05,954] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2ec550e7-e5c0-4c41-93b7-7b92b557801b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 09:33:05,954] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2ec550e7-e5c0-4c41-93b7-7b92b557801b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 09:33:05,987] [INFO] Found 31 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 09:33:05,988] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 09:33:05,988] [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
Rhodoblastus acidophilus	strain=DSM 137	GCA_002937135.1	1074	1074	suspected-type	True	77.1758	134	1020	95	below_threshold
Rhodoblastus acidophilus	strain=DSM 137	GCA_900187365.1	1074	1074	suspected-type	True	77.1469	136	1020	95	below_threshold
Rhodoblastus acidophilus	strain=DSM 137	GCA_003258765.1	1074	1074	suspected-type	True	77.0769	136	1020	95	below_threshold
Bosea psychrotolerans	strain=1131	GCA_002917105.1	1871628	1871628	type	True	76.7769	194	1020	95	below_threshold
Bosea lathyri	strain=DSM 26656	GCA_900108245.1	1036778	1036778	type	True	76.7673	169	1020	95	below_threshold
Bosea vaviloviae	strain=Vaf18	GCA_001741865.1	1526658	1526658	type	True	76.7521	205	1020	95	below_threshold
Bosea robiniae	strain=DSM 26672	GCA_900102525.1	1036780	1036780	type	True	76.6546	173	1020	95	below_threshold
Hoeflea olei	strain=JC234	GCA_001703635.1	1480615	1480615	type	True	76.6507	127	1020	95	below_threshold
Alsobacter soli	strain=SH9	GCA_003004785.1	2109933	2109933	type	True	76.5817	134	1020	95	below_threshold
Bradyrhizobium valentinum	strain=LmjM3	GCA_001440405.1	1518501	1518501	type	True	76.5683	154	1020	95	below_threshold
Bosea thiooxidans	strain=DSM 9653	GCA_900168195.1	53254	53254	type	True	76.5601	174	1020	95	below_threshold
Mesorhizobium intechi	strain=BD68	GCA_002879535.2	537601	537601	type	True	76.5596	116	1020	95	below_threshold
Microvirga guangxiensis	strain=CGMCC 1.7666	GCA_900102135.1	549386	549386	type	True	76.5424	131	1020	95	below_threshold
Microvirga flocculans	strain=ATCC BAA-817	GCA_000518665.1	217168	217168	type	True	76.5296	127	1020	95	below_threshold
Alsobacter metallidurans	strain=CGMCC 1.12214	GCA_014636935.1	340221	340221	type	True	76.5237	190	1020	95	below_threshold
Bradyrhizobium amphicarpaeae	strain=39S1MB	GCA_002266435.2	1404768	1404768	type	True	76.5226	146	1020	95	below_threshold
Microvirga arabica	strain=SV2184P	GCA_016811235.1	1128671	1128671	type	True	76.5072	132	1020	95	below_threshold
Chelatococcus sambhunathii	strain=DSM 18167	GCA_001517345.1	363953	363953	type	True	76.411	122	1020	95	below_threshold
Chelatococcus sambhunathii	strain=DSM 18167	GCA_001418005.1	363953	363953	type	True	76.398	123	1020	95	below_threshold
Bradyrhizobium sediminis	strain=S2-20-1	GCA_018736085.1	2840469	2840469	type	True	76.3837	137	1020	95	below_threshold
Beijerinckia indica subsp. indica	strain=ATCC 9039	GCA_000019845.1	31994	533	type	True	76.3555	97	1020	95	below_threshold
Oricola indica	strain=JL-62	GCA_019966595.1	2872591	2872591	type	True	76.3071	79	1020	95	below_threshold
Kaistia hirudinis	strain=DSM 25966	GCA_014196455.1	1293440	1293440	type	True	76.293	110	1020	95	below_threshold
Methylobacterium terrae	strain=17Sr1-28	GCA_003173755.1	2202827	2202827	type	True	76.2847	112	1020	95	below_threshold
Microvirga alba	strain=BT350	GCA_015694465.1	2791025	2791025	type	True	76.2591	132	1020	95	below_threshold
Stappia albiluteola	strain=F7233	GCA_014050225.1	2758565	2758565	type	True	76.1837	97	1020	95	below_threshold
Methylobacterium marchantiae	strain=DSM 21328	GCA_022179405.1	600331	600331	type	True	76.176	102	1020	95	below_threshold
Rhizobium vallis	strain=CCBAU 65647	GCA_003985155.1	634290	634290	type	True	76.1392	95	1020	95	below_threshold
Methylobacterium platani	strain=PMB02	GCA_001653715.1	427683	427683	type	True	76.0022	130	1020	95	below_threshold
Methylobacterium platani	strain=JCM 14648	GCA_001043885.1	427683	427683	type	True	75.9959	119	1020	95	below_threshold
Rhodoligotrophos defluvii	strain=lm1	GCA_005281615.1	2561934	2561934	type	True	75.6241	59	1020	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 09:33:05,990] [INFO] DFAST Taxonomy check result was written to GCA_947451855.1_Jr-25may17-178_genomic.fna/tc_result.tsv
[2023-06-08 09:33:05,991] [INFO] ===== Taxonomy check completed =====
[2023-06-08 09:33:05,991] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 09:33:05,991] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2ec550e7-e5c0-4c41-93b7-7b92b557801b/dqc_reference/checkm_data
[2023-06-08 09:33:05,993] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 09:33:06,030] [INFO] Task started: CheckM
[2023-06-08 09:33:06,030] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947451855.1_Jr-25may17-178_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947451855.1_Jr-25may17-178_genomic.fna/checkm_input GCA_947451855.1_Jr-25may17-178_genomic.fna/checkm_result
[2023-06-08 09:33:45,153] [INFO] Task succeeded: CheckM
[2023-06-08 09:33:45,154] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 69.27%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 09:33:45,173] [INFO] ===== Completeness check finished =====
[2023-06-08 09:33:45,174] [INFO] ===== Start GTDB Search =====
[2023-06-08 09:33:45,174] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947451855.1_Jr-25may17-178_genomic.fna/markers.fasta)
[2023-06-08 09:33:45,175] [INFO] Task started: Blastn
[2023-06-08 09:33:45,175] [INFO] Running command: blastn -query GCA_947451855.1_Jr-25may17-178_genomic.fna/markers.fasta -db /var/lib/cwl/stg2ec550e7-e5c0-4c41-93b7-7b92b557801b/dqc_reference/reference_markers_gtdb.fasta -out GCA_947451855.1_Jr-25may17-178_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 09:33:46,598] [INFO] Task succeeded: Blastn
[2023-06-08 09:33:46,603] [INFO] Selected 28 target genomes.
[2023-06-08 09:33:46,603] [INFO] Target genome list was writen to GCA_947451855.1_Jr-25may17-178_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 09:33:46,641] [INFO] Task started: fastANI
[2023-06-08 09:33:46,641] [INFO] Running command: fastANI --query /var/lib/cwl/stg8dd7bd43-ad15-443e-8239-b72ef10e3ef2/GCA_947451855.1_Jr-25may17-178_genomic.fna.gz --refList GCA_947451855.1_Jr-25may17-178_genomic.fna/target_genomes_gtdb.txt --output GCA_947451855.1_Jr-25may17-178_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 09:34:06,649] [INFO] Task succeeded: fastANI
[2023-06-08 09:34:06,673] [INFO] Found 28 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 09:34:06,673] [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_903930675.1	s__CAIYZJ01 sp903930675	95.8839	760	1020	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__CAIYZJ01	95.0	97.85	97.85	0.78	0.78	2	conclusive
GCA_903824185.1	s__CAIYZJ01 sp903824185	78.7404	364	1020	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__CAIYZJ01	95.0	99.80	99.69	0.95	0.94	4	-
GCA_019083985.1	s__TNE-4 sp019083985	77.0945	176	1020	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__TNE-4	95.0	100.00	100.00	1.00	1.00	2	-
GCA_903877935.1	s__CAIUPE01 sp903877935	76.9159	89	1020	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__CAIUPE01	95.0	99.17	98.91	0.86	0.81	14	-
GCA_903900975.1	s__CAIUPE01 sp903900975	76.8865	133	1020	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__CAIUPE01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001741865.1	s__Bosea vaviloviae	76.7521	205	1020	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018882635.1	s__TNE-4 sp018882635	76.6829	142	1020	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__TNE-4	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102525.1	s__Bosea robiniae	76.6785	171	1020	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	97.62	97.45	0.92	0.88	4	-
GCA_900470775.1	s__Bosea sp900470775	76.6708	179	1020	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001713455.1	s__Bosea sp001713455	76.6265	169	1020	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	97.00	96.54	0.90	0.82	3	-
GCA_017308575.1	s__Afipia sp001897905	76.6111	140	1020	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Afipia	95.0	99.90	99.90	0.96	0.96	2	-
GCF_000026145.1	s__Bradyrhizobium sp000026145	76.5831	131	1020	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003004785.1	s__Alsobacter soli	76.5817	134	1020	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Alsobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000518665.1	s__Microvirga flocculans	76.546	126	1020	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	100.00	100.00	0.99	0.99	2	-
GCF_003208615.1	s__Bosea sp003208615	76.546	183	1020	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156025.1	s__Bosea sp900156025	76.5396	170	1020	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	99.08	99.08	0.82	0.82	2	-
GCF_014636935.1	s__Alsobacter metallidurans	76.5237	190	1020	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Alsobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002256345.1	s__Tardiphaga sp002256345	76.5224	125	1020	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Tardiphaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003567055.1	s__Salinarimonas sp003567055	76.484	103	1020	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Salinarimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001295925.1	s__Bosea sp001295925	76.4799	166	1020	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002279705.1	s__Bosea sp002279705	76.3975	162	1020	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	99.41	99.41	0.89	0.89	2	-
GCF_003046175.1	s__Bosea sp003046175	76.3879	193	1020	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015694425.1	s__Microvirga sp015694425	76.3792	118	1020	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019242285.1	s__Bradyrhizobium sp019242285	76.3453	116	1020	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015694465.1	s__Microvirga sp015694465	76.2722	131	1020	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003248805.1	s__Bosea sp003248805	76.2421	143	1020	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003151255.1	s__Microvirga sp003151255	76.1221	103	1020	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018398335.1	s__Chelatococcus sp018398335	76.1031	119	1020	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Chelatococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 09:34:06,676] [INFO] GTDB search result was written to GCA_947451855.1_Jr-25may17-178_genomic.fna/result_gtdb.tsv
[2023-06-08 09:34:06,676] [INFO] ===== GTDB Search completed =====
[2023-06-08 09:34:06,712] [INFO] DFAST_QC result json was written to GCA_947451855.1_Jr-25may17-178_genomic.fna/dqc_result.json
[2023-06-08 09:34:06,712] [INFO] DFAST_QC completed!
[2023-06-08 09:34:06,712] [INFO] Total running time: 0h1m42s