[2024-01-25 17:42:05,623] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:42:05,624] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:42:05,625] [INFO] DQC Reference Directory: /var/lib/cwl/stg098e5499-26d4-4397-b548-bbd14fe296a2/dqc_reference
[2024-01-25 17:42:06,800] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:42:06,801] [INFO] Task started: Prodigal
[2024-01-25 17:42:06,801] [INFO] Running command: gunzip -c /var/lib/cwl/stg97af4542-ae3b-4570-93c8-c85cb01dab7f/GCF_020686085.1_ASM2068608v1_genomic.fna.gz | prodigal -d GCF_020686085.1_ASM2068608v1_genomic.fna/cds.fna -a GCF_020686085.1_ASM2068608v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:42:15,809] [INFO] Task succeeded: Prodigal
[2024-01-25 17:42:15,809] [INFO] Task started: HMMsearch
[2024-01-25 17:42:15,809] [INFO] Running command: hmmsearch --tblout GCF_020686085.1_ASM2068608v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg098e5499-26d4-4397-b548-bbd14fe296a2/dqc_reference/reference_markers.hmm GCF_020686085.1_ASM2068608v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:42:16,030] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:42:16,031] [INFO] Found 6/6 markers.
[2024-01-25 17:42:16,060] [INFO] Query marker FASTA was written to GCF_020686085.1_ASM2068608v1_genomic.fna/markers.fasta
[2024-01-25 17:42:16,060] [INFO] Task started: Blastn
[2024-01-25 17:42:16,060] [INFO] Running command: blastn -query GCF_020686085.1_ASM2068608v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg098e5499-26d4-4397-b548-bbd14fe296a2/dqc_reference/reference_markers.fasta -out GCF_020686085.1_ASM2068608v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:42:17,269] [INFO] Task succeeded: Blastn
[2024-01-25 17:42:17,272] [INFO] Selected 22 target genomes.
[2024-01-25 17:42:17,272] [INFO] Target genome list was writen to GCF_020686085.1_ASM2068608v1_genomic.fna/target_genomes.txt
[2024-01-25 17:42:17,288] [INFO] Task started: fastANI
[2024-01-25 17:42:17,288] [INFO] Running command: fastANI --query /var/lib/cwl/stg97af4542-ae3b-4570-93c8-c85cb01dab7f/GCF_020686085.1_ASM2068608v1_genomic.fna.gz --refList GCF_020686085.1_ASM2068608v1_genomic.fna/target_genomes.txt --output GCF_020686085.1_ASM2068608v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:42:35,214] [INFO] Task succeeded: fastANI
[2024-01-25 17:42:35,214] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg098e5499-26d4-4397-b548-bbd14fe296a2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:42:35,214] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg098e5499-26d4-4397-b548-bbd14fe296a2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:42:35,231] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 17:42:35,231] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 17:42:35,231] [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
Cellulomonas timonensis	strain=SN7	GCA_900046455.1	1689271	1689271	type	True	86.8993	983	1170	95	below_threshold
Cellulomonas cellasea	strain=DSM 20118	GCA_000767135.1	43670	43670	type	True	81.1198	578	1170	95	below_threshold
Cellulomonas cellasea	strain=NBRC 3753	GCA_006538745.1	43670	43670	type	True	81.0723	708	1170	95	below_threshold
Cellulomonas biazotea	strain=NBRC12680	GCA_004306155.1	1709	1709	type	True	80.4802	596	1170	95	below_threshold
Cellulomonas terrae	strain=NBRC 100819	GCA_007990265.1	311234	311234	type	True	80.4774	603	1170	95	below_threshold
Cellulomonas soli	strain=DSM 24484	GCA_013409305.1	931535	931535	type	True	80.4213	607	1170	95	below_threshold
Cellulomonas hominis	strain=DSM 9581	GCA_014201095.1	156981	156981	suspected-type	True	80.3992	643	1170	95	below_threshold
Cellulomonas xylanilytica	strain=NBRC 101102	GCA_007989805.1	233583	233583	type	True	80.3548	624	1170	95	below_threshold
Cellulomonas hominis	strain=NBRC 16055	GCA_007989225.1	156981	156981	suspected-type	True	80.3237	623	1170	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	80.3063	593	1170	95	below_threshold
Cellulomonas fulva	strain=DKR-3	GCA_018531375.1	2835530	2835530	type	True	79.9835	599	1170	95	below_threshold
Cellulomonas oligotrophica	strain=DSM 24482	GCA_013409875.1	931536	931536	type	True	79.9735	629	1170	95	below_threshold
Cellulomonas telluris	strain=CPCC 204705	GCA_004886325.1	2306636	2306636	type	True	79.9686	612	1170	95	below_threshold
Cellulomonas avistercoris	strain=Sa3CUA2	GCA_014836445.1	2762242	2762242	type	True	79.8091	610	1170	95	below_threshold
Actinotalea solisilvae	strain=KACC 19191	GCA_016464425.1	2072922	2072922	type	True	79.4104	580	1170	95	below_threshold
Sanguibacter keddieii	strain=DSM 10542	GCA_000024925.1	60920	60920	type	True	79.3276	490	1170	95	below_threshold
Oerskovia turbata	strain=NRRL B-8019	GCA_000718325.1	1713	1713	type	True	79.312	487	1170	95	below_threshold
Oerskovia turbata	strain=JCM3160	GCA_004121315.1	1713	1713	type	True	79.308	488	1170	95	below_threshold
Cellulomonas carbonis	strain=T26	GCA_000767175.1	1386092	1386092	type	True	79.2728	491	1170	95	below_threshold
Oerskovia jenensis	strain=DSM 46000	GCA_016907235.1	162169	162169	type	True	79.2507	494	1170	95	below_threshold
Oerskovia merdavium	strain=Sa2CUA9	GCA_014836755.1	2762227	2762227	type	True	79.2461	512	1170	95	below_threshold
Sanguibacter suarezii	strain=NBRC 16159	GCA_001552735.1	60921	60921	type	True	79.0442	478	1170	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:42:35,237] [INFO] DFAST Taxonomy check result was written to GCF_020686085.1_ASM2068608v1_genomic.fna/tc_result.tsv
[2024-01-25 17:42:35,238] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:42:35,239] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:42:35,239] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg098e5499-26d4-4397-b548-bbd14fe296a2/dqc_reference/checkm_data
[2024-01-25 17:42:35,244] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:42:35,282] [INFO] Task started: CheckM
[2024-01-25 17:42:35,282] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020686085.1_ASM2068608v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020686085.1_ASM2068608v1_genomic.fna/checkm_input GCF_020686085.1_ASM2068608v1_genomic.fna/checkm_result
[2024-01-25 17:43:15,371] [INFO] Task succeeded: CheckM
[2024-01-25 17:43:15,372] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:43:15,390] [INFO] ===== Completeness check finished =====
[2024-01-25 17:43:15,390] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:43:15,391] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020686085.1_ASM2068608v1_genomic.fna/markers.fasta)
[2024-01-25 17:43:15,391] [INFO] Task started: Blastn
[2024-01-25 17:43:15,391] [INFO] Running command: blastn -query GCF_020686085.1_ASM2068608v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg098e5499-26d4-4397-b548-bbd14fe296a2/dqc_reference/reference_markers_gtdb.fasta -out GCF_020686085.1_ASM2068608v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:43:17,497] [INFO] Task succeeded: Blastn
[2024-01-25 17:43:17,500] [INFO] Selected 23 target genomes.
[2024-01-25 17:43:17,500] [INFO] Target genome list was writen to GCF_020686085.1_ASM2068608v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:43:17,543] [INFO] Task started: fastANI
[2024-01-25 17:43:17,543] [INFO] Running command: fastANI --query /var/lib/cwl/stg97af4542-ae3b-4570-93c8-c85cb01dab7f/GCF_020686085.1_ASM2068608v1_genomic.fna.gz --refList GCF_020686085.1_ASM2068608v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020686085.1_ASM2068608v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:43:37,280] [INFO] Task succeeded: fastANI
[2024-01-25 17:43:37,294] [INFO] Found 23 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 17:43:37,294] [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_900046455.1	s__Cellulomonas timonensis	86.8939	985	1170	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	100.00	100.00	0.99	0.99	2	-
GCF_006538745.1	s__Cellulomonas cellasea	81.0909	706	1170	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	97.79	95.59	0.95	0.91	3	-
GCF_003115775.1	s__Cellulomonas sp003115775	80.7281	587	1170	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003470205.1	s__Cellulomonas rhizosphaerae	80.6327	536	1170	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011603975.1	s__Cellulomonas sp011603975	80.5543	567	1170	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013409475.1	s__Cellulomonas hominis_B	80.5208	630	1170	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005239125.1	s__Cellulomonas hominis_A	80.4457	573	1170	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862755.1	s__Cellulomonas pakistanensis	80.4353	621	1170	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007990265.1	s__Cellulomonas terrae	80.4298	607	1170	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001424125.1	s__Cellulomonas sp001424125	80.4031	575	1170	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_901521055.1	s__Cellulomonas hominis_C	80.3958	602	1170	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008033115.1	s__Cellulomonas sp008033115	80.3192	648	1170	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	96.34	96.34	0.91	0.91	2	-
GCF_001426705.1	s__Cellulomonas sp001426705	80.31	621	1170	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018388465.1	s__Cellulomonas sp018388465	80.2885	628	1170	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	99.65	99.29	0.98	0.97	3	-
GCF_016862675.1	s__Cellulomonas chitinilytica	80.2623	644	1170	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007679345.1	s__Cellulomonas cellulans_A	80.2377	650	1170	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014763765.1	s__Cellulomonas sp014763765	80.2315	551	1170	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017744555.1	s__Cellulomonas sp017744555	80.0473	629	1170	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006386485.1	s__Cellulomonas oligotrophica	79.9602	634	1170	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	100.00	100.00	1.00	1.00	3	-
GCF_001722485.1	s__Cellulosimicrobium cellulans_A	79.2813	467	1170	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003052455.1	s__Cellulosimicrobium cinnabarinum	79.1818	516	1170	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	96.0261	97.94	97.40	0.92	0.90	4	-
GCF_001552735.1	s__Sanguibacter suarezii	79.0473	477	1170	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Sanguibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009708005.2	s__Cellulosimicrobium sp009708005	78.9026	543	1170	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:43:37,296] [INFO] GTDB search result was written to GCF_020686085.1_ASM2068608v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:43:37,297] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:43:37,300] [INFO] DFAST_QC result json was written to GCF_020686085.1_ASM2068608v1_genomic.fna/dqc_result.json
[2024-01-25 17:43:37,301] [INFO] DFAST_QC completed!
[2024-01-25 17:43:37,301] [INFO] Total running time: 0h1m32s