[2024-01-24 10:56:34,374] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:56:34,376] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:56:34,376] [INFO] DQC Reference Directory: /var/lib/cwl/stga044ab2f-4637-4392-b589-d2e81974d5d7/dqc_reference
[2024-01-24 10:56:36,716] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:56:36,717] [INFO] Task started: Prodigal
[2024-01-24 10:56:36,718] [INFO] Running command: gunzip -c /var/lib/cwl/stge1eb6cda-b349-45d2-ab11-542f482de185/GCF_005844085.1_ASM584408v1_genomic.fna.gz | prodigal -d GCF_005844085.1_ASM584408v1_genomic.fna/cds.fna -a GCF_005844085.1_ASM584408v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:56:52,227] [INFO] Task succeeded: Prodigal
[2024-01-24 10:56:52,227] [INFO] Task started: HMMsearch
[2024-01-24 10:56:52,227] [INFO] Running command: hmmsearch --tblout GCF_005844085.1_ASM584408v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga044ab2f-4637-4392-b589-d2e81974d5d7/dqc_reference/reference_markers.hmm GCF_005844085.1_ASM584408v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:56:52,498] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:56:52,499] [INFO] Found 6/6 markers.
[2024-01-24 10:56:52,543] [INFO] Query marker FASTA was written to GCF_005844085.1_ASM584408v1_genomic.fna/markers.fasta
[2024-01-24 10:56:52,543] [INFO] Task started: Blastn
[2024-01-24 10:56:52,543] [INFO] Running command: blastn -query GCF_005844085.1_ASM584408v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga044ab2f-4637-4392-b589-d2e81974d5d7/dqc_reference/reference_markers.fasta -out GCF_005844085.1_ASM584408v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:56:53,502] [INFO] Task succeeded: Blastn
[2024-01-24 10:56:53,505] [INFO] Selected 20 target genomes.
[2024-01-24 10:56:53,506] [INFO] Target genome list was writen to GCF_005844085.1_ASM584408v1_genomic.fna/target_genomes.txt
[2024-01-24 10:56:53,584] [INFO] Task started: fastANI
[2024-01-24 10:56:53,585] [INFO] Running command: fastANI --query /var/lib/cwl/stge1eb6cda-b349-45d2-ab11-542f482de185/GCF_005844085.1_ASM584408v1_genomic.fna.gz --refList GCF_005844085.1_ASM584408v1_genomic.fna/target_genomes.txt --output GCF_005844085.1_ASM584408v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:57:08,108] [INFO] Task succeeded: fastANI
[2024-01-24 10:57:08,109] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga044ab2f-4637-4392-b589-d2e81974d5d7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:57:08,110] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga044ab2f-4637-4392-b589-d2e81974d5d7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:57:08,132] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 10:57:08,132] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 10:57:08,133] [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
Endobacter medicaginis	strain=LMG 26838	GCA_013376135.1	1181271	1181271	type	True	79.2646	298	1586	95	below_threshold
Endobacter medicaginis	strain=CECT 8088	GCA_014192375.1	1181271	1181271	type	True	78.9132	454	1586	95	below_threshold
Gluconacetobacter diazotrophicus	strain=PAl 5; ATCC 49037	GCA_000021325.1	33996	33996	type	True	78.1587	348	1586	95	below_threshold
Acidisphaera rubrifaciens	strain=HS-AP3	GCA_000964365.1	50715	50715	type	True	78.1514	268	1586	95	below_threshold
Gluconacetobacter diazotrophicus	strain=PAl 5	GCA_000067045.1	33996	33996	type	True	78.0981	348	1586	95	below_threshold
Gluconacetobacter diazotrophicus	strain=LMG 7603	GCA_014174315.1	33996	33996	type	True	77.9926	353	1586	95	below_threshold
Gluconacetobacter dulcium	strain=LMG 1728	GCA_014174165.1	2729096	2729096	type	True	77.988	324	1586	95	below_threshold
Komagataeibacter nataicola	strain=LMG 1536	GCA_003207795.1	265960	265960	type	True	77.7425	196	1586	95	below_threshold
Komagataeibacter swingsii	strain=LMG 22125	GCA_003207895.1	215220	215220	type	True	77.6348	183	1586	95	below_threshold
Komagataeibacter xylinus	strain=NBRC 15237	GCA_001571345.1	28448	28448	suspected-type	True	77.5982	207	1586	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	77.5811	485	1586	95	below_threshold
Komagataeibacter melomenusus	strain=AV436	GCA_013155395.1	2766578	2766578	type	True	77.5802	227	1586	95	below_threshold
Komagataeibacter xylinus	strain=LMG 1515	GCA_003207915.1	28448	28448	suspected-type	True	77.5681	202	1586	95	below_threshold
Novacetimonas maltaceti	strain=LMG 1529	GCA_003206475.1	1203393	1203393	type	True	77.418	207	1586	95	below_threshold
Novacetimonas maltaceti	strain=LMG 1529	GCA_002906255.1	1203393	1203393	type	True	77.3839	210	1586	95	below_threshold
Rhodopila globiformis	strain=DSM 161	GCA_002937115.1	1071	1071	type	True	77.2946	412	1586	95	below_threshold
Roseomonas rubea	strain=MO17	GCA_016106015.1	2748666	2748666	type	True	77.1649	281	1586	95	below_threshold
Methylobacterium crusticola	strain=KCTC 52305	GCA_022179145.1	1697972	1697972	type	True	76.2151	323	1586	95	below_threshold
Sphingomonas corticis	strain=36D10-4-7	GCA_012035195.1	2722791	2722791	type	True	75.9657	198	1586	95	below_threshold
Sphingomonas citri	strain=RRHST34	GCA_019429485.1	2862499	2862499	type	True	75.9281	220	1586	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:57:08,135] [INFO] DFAST Taxonomy check result was written to GCF_005844085.1_ASM584408v1_genomic.fna/tc_result.tsv
[2024-01-24 10:57:08,135] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:57:08,136] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:57:08,136] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga044ab2f-4637-4392-b589-d2e81974d5d7/dqc_reference/checkm_data
[2024-01-24 10:57:08,137] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:57:08,186] [INFO] Task started: CheckM
[2024-01-24 10:57:08,186] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005844085.1_ASM584408v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005844085.1_ASM584408v1_genomic.fna/checkm_input GCF_005844085.1_ASM584408v1_genomic.fna/checkm_result
[2024-01-24 10:57:55,318] [INFO] Task succeeded: CheckM
[2024-01-24 10:57:55,320] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:57:55,339] [INFO] ===== Completeness check finished =====
[2024-01-24 10:57:55,339] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:57:55,340] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005844085.1_ASM584408v1_genomic.fna/markers.fasta)
[2024-01-24 10:57:55,340] [INFO] Task started: Blastn
[2024-01-24 10:57:55,340] [INFO] Running command: blastn -query GCF_005844085.1_ASM584408v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga044ab2f-4637-4392-b589-d2e81974d5d7/dqc_reference/reference_markers_gtdb.fasta -out GCF_005844085.1_ASM584408v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:57,120] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:57,124] [INFO] Selected 17 target genomes.
[2024-01-24 10:57:57,125] [INFO] Target genome list was writen to GCF_005844085.1_ASM584408v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:57:57,143] [INFO] Task started: fastANI
[2024-01-24 10:57:57,143] [INFO] Running command: fastANI --query /var/lib/cwl/stge1eb6cda-b349-45d2-ab11-542f482de185/GCF_005844085.1_ASM584408v1_genomic.fna.gz --refList GCF_005844085.1_ASM584408v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005844085.1_ASM584408v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:58:12,225] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:12,243] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:58:12,244] [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_005844085.1	s__Lichenicoccus roseus	100.0	1586	1586	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Lichenicoccus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_903844135.1	s__Lichenicola sp903844135	80.1059	660	1586	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Lichenicola	95.0	99.79	99.79	0.94	0.94	2	-
GCF_013201075.1	s__Lichenicola cladoniae	79.6708	671	1586	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Lichenicola	95.0	99.99	99.99	1.00	1.00	2	-
GCF_014192375.1	s__Endobacter medicaginis	78.9287	453	1586	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Endobacter	95.0	99.99	99.99	0.99	0.99	2	-
GCF_014174275.1	s__Gluconacetobacter takamatsuzukensis	78.3012	359	1586	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014174395.1	s__Gluconacetobacter aggeris	78.1585	330	1586	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	96.2181	N/A	N/A	N/A	N/A	1	-
GCF_000021325.1	s__Gluconacetobacter diazotrophicus	78.1484	349	1586	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	95.0	99.14	98.86	0.90	0.85	4	-
GCF_014174355.1	s__Gluconacetobacter azotocaptans	78.1122	339	1586	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	95.0	99.32	99.32	0.91	0.91	2	-
GCA_003133265.1	s__PALSA-911 sp003133265	78.0375	275	1586	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__PALSA-911	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903644035.1	s__CAHJXG01 sp903644035	78.034	239	1586	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__CAHJXG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019240635.1	s__JAFAYA01 sp019240635	77.8932	250	1586	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__JAFAYA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017304945.1	s__69-11 sp017304945	77.798	406	1586	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__69-11	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008630155.1	s__Rhodovastum atsumiense	77.6134	474	1586	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Rhodovastum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003258945.1	s__Paracraurococcus frigidaeris	77.3475	448	1586	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Paracraurococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013112485.1	s__Paracraurococcus sp013112485	77.2242	436	1586	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Paracraurococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004761865.1	s__Crenalkalicoccus roseus	77.1441	382	1586	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Crenalkalicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019084075.1	s__G192 sp019084075	76.9991	343	1586	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__G192	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:58:12,245] [INFO] GTDB search result was written to GCF_005844085.1_ASM584408v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:58:12,246] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:58:12,250] [INFO] DFAST_QC result json was written to GCF_005844085.1_ASM584408v1_genomic.fna/dqc_result.json
[2024-01-24 10:58:12,251] [INFO] DFAST_QC completed!
[2024-01-24 10:58:12,251] [INFO] Total running time: 0h1m38s