[2024-01-24 11:35:11,882] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:35:11,889] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:35:11,890] [INFO] DQC Reference Directory: /var/lib/cwl/stga5b9a7a1-cbed-4754-b4b7-1f72d06f8111/dqc_reference
[2024-01-24 11:35:14,425] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:35:14,425] [INFO] Task started: Prodigal
[2024-01-24 11:35:14,426] [INFO] Running command: gunzip -c /var/lib/cwl/stg334d7fc4-266c-4adc-be67-d4977087fdfb/GCF_014852685.1_ASM1485268v1_genomic.fna.gz | prodigal -d GCF_014852685.1_ASM1485268v1_genomic.fna/cds.fna -a GCF_014852685.1_ASM1485268v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:35:22,999] [INFO] Task succeeded: Prodigal
[2024-01-24 11:35:22,999] [INFO] Task started: HMMsearch
[2024-01-24 11:35:22,999] [INFO] Running command: hmmsearch --tblout GCF_014852685.1_ASM1485268v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga5b9a7a1-cbed-4754-b4b7-1f72d06f8111/dqc_reference/reference_markers.hmm GCF_014852685.1_ASM1485268v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:35:23,275] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:35:23,276] [INFO] Found 6/6 markers.
[2024-01-24 11:35:23,313] [INFO] Query marker FASTA was written to GCF_014852685.1_ASM1485268v1_genomic.fna/markers.fasta
[2024-01-24 11:35:23,313] [INFO] Task started: Blastn
[2024-01-24 11:35:23,313] [INFO] Running command: blastn -query GCF_014852685.1_ASM1485268v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga5b9a7a1-cbed-4754-b4b7-1f72d06f8111/dqc_reference/reference_markers.fasta -out GCF_014852685.1_ASM1485268v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:24,538] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:24,541] [INFO] Selected 27 target genomes.
[2024-01-24 11:35:24,542] [INFO] Target genome list was writen to GCF_014852685.1_ASM1485268v1_genomic.fna/target_genomes.txt
[2024-01-24 11:35:24,551] [INFO] Task started: fastANI
[2024-01-24 11:35:24,551] [INFO] Running command: fastANI --query /var/lib/cwl/stg334d7fc4-266c-4adc-be67-d4977087fdfb/GCF_014852685.1_ASM1485268v1_genomic.fna.gz --refList GCF_014852685.1_ASM1485268v1_genomic.fna/target_genomes.txt --output GCF_014852685.1_ASM1485268v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:45,310] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:45,311] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga5b9a7a1-cbed-4754-b4b7-1f72d06f8111/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:45,312] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga5b9a7a1-cbed-4754-b4b7-1f72d06f8111/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:45,336] [INFO] Found 27 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:35:45,336] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:35:45,336] [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
Flavimobilis marinus	strain=CGMCC 1.3457	GCA_014653315.1	285351	285351	type	True	79.7693	500	1010	95	below_threshold
Flavimobilis marinus	strain=DSM 19083	GCA_900113055.1	285351	285351	type	True	79.7434	501	1010	95	below_threshold
Sediminihabitans luteus	strain=DSM 25478	GCA_002797595.1	1138585	1138585	type	True	79.4959	486	1010	95	below_threshold
Cellulosimicrobium funkei	strain=JCM 14302	GCA_004519295.1	264251	264251	suspected-type	True	79.4688	542	1010	95	below_threshold
Sediminihabitans luteus	strain=NBRC 108568	GCA_016863455.1	1138585	1138585	type	True	79.4282	496	1010	95	below_threshold
Cellulosimicrobium funkei	strain=NBRC 104118	GCA_001570825.1	264251	264251	suspected-type	True	79.3364	544	1010	95	below_threshold
Oerskovia merdavium	strain=Sa2CUA9	GCA_014836755.1	2762227	2762227	type	True	79.2433	491	1010	95	below_threshold
Oerskovia douganii	strain=Sa1BUA8	GCA_015142735.1	2762210	2762210	type	True	79.1273	505	1010	95	below_threshold
Oerskovia jenensis	strain=DSM 46000	GCA_016907235.1	162169	162169	type	True	79.0775	485	1010	95	below_threshold
Cellulomonas cellasea	strain=NBRC 3753	GCA_006538745.1	43670	43670	type	True	79.0433	551	1010	95	below_threshold
Cellulomonas cellasea	strain=DSM 20118	GCA_000767135.1	43670	43670	type	True	78.9944	449	1010	95	below_threshold
Cellulomonas fimi	strain=NCTC7547	GCA_900637695.1	1708	1708	type	True	78.9801	507	1010	95	below_threshold
Cellulomonas fimi	strain=ATCC 484	GCA_000212695.1	1708	1708	type	True	78.9355	516	1010	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	78.9222	517	1010	95	below_threshold
Cellulomonas carbonis	strain=T26	GCA_000767175.1	1386092	1386092	type	True	78.8807	466	1010	95	below_threshold
Sanguibacter suarezii	strain=NBRC 16159	GCA_001552735.1	60921	60921	type	True	78.875	398	1010	95	below_threshold
Cellulomonas carbonis	strain=CGMCC 1.10786	GCA_014636275.1	1386092	1386092	type	True	78.7971	498	1010	95	below_threshold
Cellulomonas telluris	strain=CPCC 204705	GCA_004886325.1	2306636	2306636	type	True	78.6935	496	1010	95	below_threshold
Actinotalea solisilvae	strain=KACC 19191	GCA_016464425.1	2072922	2072922	type	True	78.6303	514	1010	95	below_threshold
Cellulomonas fulva	strain=DKR-3	GCA_018531375.1	2835530	2835530	type	True	78.6061	460	1010	95	below_threshold
Cellulomonas soli	strain=DSM 24484	GCA_013409305.1	931535	931535	type	True	78.6057	446	1010	95	below_threshold
Cellulomonas hominis	strain=NBRC 16055	GCA_007989225.1	156981	156981	suspected-type	True	78.5668	431	1010	95	below_threshold
Cellulomonas avistercoris	strain=Sa3CUA2	GCA_014836445.1	2762242	2762242	type	True	78.5651	470	1010	95	below_threshold
Cellulomonas hominis	strain=DSM 9581	GCA_014201095.1	156981	156981	suspected-type	True	78.5374	452	1010	95	below_threshold
Promicromonospora citrea	strain=ATCC 15908	GCA_013004695.1	43677	43677	type	True	78.2209	435	1010	95	below_threshold
Promicromonospora citrea	strain=JCM 3051	GCA_014647735.1	43677	43677	type	True	78.1114	469	1010	95	below_threshold
Cellulomonas denverensis	strain=ATCC BAA-788	GCA_012396125.1	264297	264297	type	True	77.8725	272	1010	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:45,338] [INFO] DFAST Taxonomy check result was written to GCF_014852685.1_ASM1485268v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:45,339] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:45,339] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:45,339] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga5b9a7a1-cbed-4754-b4b7-1f72d06f8111/dqc_reference/checkm_data
[2024-01-24 11:35:45,341] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:45,374] [INFO] Task started: CheckM
[2024-01-24 11:35:45,374] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014852685.1_ASM1485268v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014852685.1_ASM1485268v1_genomic.fna/checkm_input GCF_014852685.1_ASM1485268v1_genomic.fna/checkm_result
[2024-01-24 11:36:26,987] [INFO] Task succeeded: CheckM
[2024-01-24 11:36:26,989] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:36:27,010] [INFO] ===== Completeness check finished =====
[2024-01-24 11:36:27,010] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:36:27,011] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014852685.1_ASM1485268v1_genomic.fna/markers.fasta)
[2024-01-24 11:36:27,011] [INFO] Task started: Blastn
[2024-01-24 11:36:27,011] [INFO] Running command: blastn -query GCF_014852685.1_ASM1485268v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga5b9a7a1-cbed-4754-b4b7-1f72d06f8111/dqc_reference/reference_markers_gtdb.fasta -out GCF_014852685.1_ASM1485268v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:36:28,956] [INFO] Task succeeded: Blastn
[2024-01-24 11:36:28,962] [INFO] Selected 16 target genomes.
[2024-01-24 11:36:28,962] [INFO] Target genome list was writen to GCF_014852685.1_ASM1485268v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:36:28,991] [INFO] Task started: fastANI
[2024-01-24 11:36:28,992] [INFO] Running command: fastANI --query /var/lib/cwl/stg334d7fc4-266c-4adc-be67-d4977087fdfb/GCF_014852685.1_ASM1485268v1_genomic.fna.gz --refList GCF_014852685.1_ASM1485268v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014852685.1_ASM1485268v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:36:41,326] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:41,348] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:36:41,348] [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_014852685.1	s__Flavimobilis rhizosphaerae	100.0	1009	1010	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Flavimobilis	95.0	95.20	95.20	0.83	0.83	2	conclusive
GCF_011300875.1	s__Flavimobilis sp011300875	88.8202	854	1010	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Flavimobilis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002564025.1	s__Flavimobilis soli	81.9997	615	1010	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Flavimobilis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012396185.1	s__Flavimobilis hominis	81.6754	618	1010	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Flavimobilis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113055.1	s__Flavimobilis marinus	79.7511	500	1010	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Flavimobilis	95.0	100.00	100.00	1.00	1.00	2	-
GCF_012396155.1	s__Cellulomonas septica	79.6295	335	1010	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004519295.1	s__Cellulosimicrobium funkei	79.5462	533	1010	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	96.0261	98.03	96.84	0.93	0.88	18	-
GCA_003052455.1	s__Cellulosimicrobium cinnabarinum	79.5032	535	1010	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	96.0261	97.94	97.40	0.92	0.90	4	-
GCF_010287905.1	s__Cellulosimicrobium fucosivorans	79.4105	562	1010	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	98.84	98.55	0.94	0.90	6	-
GCF_006538745.1	s__Cellulomonas cellasea	79.0521	550	1010	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	97.79	95.59	0.95	0.91	3	-
GCF_001552735.1	s__Sanguibacter suarezii	78.8827	398	1010	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Sanguibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014042015.1	s__Actinotalea sp014042015	78.8429	441	1010	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Actinotalea	95.0	99.62	99.62	0.98	0.98	2	-
GCF_016862755.1	s__Cellulomonas pakistanensis	78.6223	428	1010	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014201095.1	s__Cellulomonas hominis	78.5566	450	1010	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	99.15	98.63	0.95	0.92	4	-
GCA_014763765.1	s__Cellulomonas sp014763765	78.4196	419	1010	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012396125.1	s__Cellulomonas denverensis	77.8591	273	1010	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	100.00	100.00	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:36:41,350] [INFO] GTDB search result was written to GCF_014852685.1_ASM1485268v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:36:41,351] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:36:41,358] [INFO] DFAST_QC result json was written to GCF_014852685.1_ASM1485268v1_genomic.fna/dqc_result.json
[2024-01-24 11:36:41,359] [INFO] DFAST_QC completed!
[2024-01-24 11:36:41,359] [INFO] Total running time: 0h1m29s