[2024-01-24 12:29:28,798] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:29:28,803] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:29:28,803] [INFO] DQC Reference Directory: /var/lib/cwl/stg52a118f2-810f-4a0f-bf19-77a16839980c/dqc_reference
[2024-01-24 12:29:30,149] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:29:30,150] [INFO] Task started: Prodigal
[2024-01-24 12:29:30,150] [INFO] Running command: gunzip -c /var/lib/cwl/stg6c3dcadc-a961-4d37-9cc4-8fce2b57d9d5/GCF_030161595.1_ASM3016159v1_genomic.fna.gz | prodigal -d GCF_030161595.1_ASM3016159v1_genomic.fna/cds.fna -a GCF_030161595.1_ASM3016159v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:29:40,955] [INFO] Task succeeded: Prodigal
[2024-01-24 12:29:40,956] [INFO] Task started: HMMsearch
[2024-01-24 12:29:40,956] [INFO] Running command: hmmsearch --tblout GCF_030161595.1_ASM3016159v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg52a118f2-810f-4a0f-bf19-77a16839980c/dqc_reference/reference_markers.hmm GCF_030161595.1_ASM3016159v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:29:41,350] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:29:41,352] [INFO] Found 6/6 markers.
[2024-01-24 12:29:41,393] [INFO] Query marker FASTA was written to GCF_030161595.1_ASM3016159v1_genomic.fna/markers.fasta
[2024-01-24 12:29:41,394] [INFO] Task started: Blastn
[2024-01-24 12:29:41,394] [INFO] Running command: blastn -query GCF_030161595.1_ASM3016159v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg52a118f2-810f-4a0f-bf19-77a16839980c/dqc_reference/reference_markers.fasta -out GCF_030161595.1_ASM3016159v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:29:42,781] [INFO] Task succeeded: Blastn
[2024-01-24 12:29:42,785] [INFO] Selected 30 target genomes.
[2024-01-24 12:29:42,786] [INFO] Target genome list was writen to GCF_030161595.1_ASM3016159v1_genomic.fna/target_genomes.txt
[2024-01-24 12:29:42,806] [INFO] Task started: fastANI
[2024-01-24 12:29:42,806] [INFO] Running command: fastANI --query /var/lib/cwl/stg6c3dcadc-a961-4d37-9cc4-8fce2b57d9d5/GCF_030161595.1_ASM3016159v1_genomic.fna.gz --refList GCF_030161595.1_ASM3016159v1_genomic.fna/target_genomes.txt --output GCF_030161595.1_ASM3016159v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:30:08,621] [INFO] Task succeeded: fastANI
[2024-01-24 12:30:08,622] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg52a118f2-810f-4a0f-bf19-77a16839980c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:30:08,622] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg52a118f2-810f-4a0f-bf19-77a16839980c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:30:08,644] [INFO] Found 30 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:30:08,644] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:30:08,644] [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
Sediminihabitans luteus	strain=NBRC 108568	GCA_016863455.1	1138585	1138585	type	True	78.3111	437	1280	95	below_threshold
Beutenbergia cavernae	strain=DSM 12333	GCA_000023105.1	84757	84757	type	True	78.2036	561	1280	95	below_threshold
Sediminihabitans luteus	strain=DSM 25478	GCA_002797595.1	1138585	1138585	type	True	78.2007	445	1280	95	below_threshold
Cellulomonas cellasea	strain=DSM 20118	GCA_000767135.1	43670	43670	type	True	78.1355	428	1280	95	below_threshold
Cellulomonas biazotea	strain=NBRC12680	GCA_004306155.1	1709	1709	type	True	78.1294	444	1280	95	below_threshold
Cellulomonas shaoxiangyii	strain=Z28	GCA_004798685.1	2566013	2566013	type	True	78.0866	470	1280	95	below_threshold
Cellulomonas uda	strain=NBRC 3747	GCA_006538705.1	1714	1714	type	True	78.0858	440	1280	95	below_threshold
Cellulomonas oligotrophica	strain=DSM 24482	GCA_013409875.1	931536	931536	type	True	78.0638	503	1280	95	below_threshold
Cellulomonas hominis	strain=DSM 9581	GCA_014201095.1	156981	156981	suspected-type	True	78.0557	498	1280	95	below_threshold
Cellulomonas cellasea	strain=NBRC 3753	GCA_006538745.1	43670	43670	type	True	78.0142	509	1280	95	below_threshold
Cellulomonas hominis	strain=NBRC 16055	GCA_007989225.1	156981	156981	suspected-type	True	77.9963	478	1280	95	below_threshold
Georgenia wutianyii	strain=Z294	GCA_006349365.1	2585135	2585135	type	True	77.9889	462	1280	95	below_threshold
Ruania suaedae	strain=LR1S40	GCA_021049265.1	2897774	2897774	type	True	77.9115	337	1280	95	below_threshold
Cellulosimicrobium funkei	strain=JCM 14302	GCA_004519295.1	264251	264251	suspected-type	True	77.898	526	1280	95	below_threshold
Cellulomonas telluris	strain=CPCC 204705	GCA_004886325.1	2306636	2306636	type	True	77.8977	514	1280	95	below_threshold
Cellulomonas carbonis	strain=T26	GCA_000767175.1	1386092	1386092	type	True	77.8892	418	1280	95	below_threshold
Cellulomonas timonensis	strain=SN7	GCA_900046455.1	1689271	1689271	type	True	77.8773	410	1280	95	below_threshold
Oceanitalea stevensii	strain=Sa1BUA1	GCA_014837105.1	2763072	2763072	type	True	77.8701	441	1280	95	below_threshold
Cellulosimicrobium funkei	strain=NBRC 104118	GCA_001570825.1	264251	264251	suspected-type	True	77.8668	506	1280	95	below_threshold
Cellulosimicrobium marinum	strain=NBRC 110994	GCA_020551945.1	1638992	1638992	type	True	77.8185	489	1280	95	below_threshold
Cellulomonas terrae	strain=NBRC 100819	GCA_007990265.1	311234	311234	type	True	77.8001	424	1280	95	below_threshold
Georgenia thermotolerans	strain=DSM 21501	GCA_009299305.1	527326	527326	type	True	77.7653	420	1280	95	below_threshold
Georgenia thermotolerans	strain=NBRC 104148	GCA_009193185.1	527326	527326	type	True	77.7279	438	1280	95	below_threshold
Actinotalea solisilvae	strain=KACC 19191	GCA_016464425.1	2072922	2072922	type	True	77.6388	508	1280	95	below_threshold
Occultella kanbiaonis	strain=HY164	GCA_009708215.1	2675754	2675754	type	True	77.6006	422	1280	95	below_threshold
Occultella aeris	strain=CIP 111667	GCA_902703175.1	2761496	2761496	type	True	77.5933	388	1280	95	below_threshold
Georgenia ruanii	strain=JCM 15130	GCA_009193175.1	348442	348442	type	True	77.4978	463	1280	95	below_threshold
Occultella gossypii	strain=N2-46	GCA_019947135.1	2800820	2800820	type	True	77.454	420	1280	95	below_threshold
Ruania alba	strain=DSM 21368	GCA_900105765.1	648782	648782	type	True	77.3614	285	1280	95	below_threshold
Embleya hyalina	strain=NBRC 13850	GCA_003967355.1	516124	516124	type	True	75.9889	387	1280	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:30:08,646] [INFO] DFAST Taxonomy check result was written to GCF_030161595.1_ASM3016159v1_genomic.fna/tc_result.tsv
[2024-01-24 12:30:08,647] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:30:08,647] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:30:08,647] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg52a118f2-810f-4a0f-bf19-77a16839980c/dqc_reference/checkm_data
[2024-01-24 12:30:08,649] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:30:08,693] [INFO] Task started: CheckM
[2024-01-24 12:30:08,693] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030161595.1_ASM3016159v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030161595.1_ASM3016159v1_genomic.fna/checkm_input GCF_030161595.1_ASM3016159v1_genomic.fna/checkm_result
[2024-01-24 12:31:12,798] [INFO] Task succeeded: CheckM
[2024-01-24 12:31:12,800] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:31:12,825] [INFO] ===== Completeness check finished =====
[2024-01-24 12:31:12,826] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:31:12,826] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030161595.1_ASM3016159v1_genomic.fna/markers.fasta)
[2024-01-24 12:31:12,826] [INFO] Task started: Blastn
[2024-01-24 12:31:12,827] [INFO] Running command: blastn -query GCF_030161595.1_ASM3016159v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg52a118f2-810f-4a0f-bf19-77a16839980c/dqc_reference/reference_markers_gtdb.fasta -out GCF_030161595.1_ASM3016159v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:14,729] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:14,733] [INFO] Selected 14 target genomes.
[2024-01-24 12:31:14,734] [INFO] Target genome list was writen to GCF_030161595.1_ASM3016159v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:31:14,745] [INFO] Task started: fastANI
[2024-01-24 12:31:14,745] [INFO] Running command: fastANI --query /var/lib/cwl/stg6c3dcadc-a961-4d37-9cc4-8fce2b57d9d5/GCF_030161595.1_ASM3016159v1_genomic.fna.gz --refList GCF_030161595.1_ASM3016159v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030161595.1_ASM3016159v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:31:26,425] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:26,444] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:31:26,444] [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_004786095.1	s__Serinibacter_A arcticus	84.4473	840	1280	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Beutenbergiaceae;g__Serinibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003121705.1	s__Serinibacter_A sp003121705	83.018	835	1280	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Beutenbergiaceae;g__Serinibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006351005.1	s__Miniimonas arenae	80.4982	612	1280	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Beutenbergiaceae;g__Miniimonas	95.0	98.18	97.40	0.91	0.83	3	-
GCF_003751805.1	s__Salana multivorans	79.7992	566	1280	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Beutenbergiaceae;g__Salana	95.0	99.05	99.05	0.93	0.93	2	-
GCF_002563925.1	s__Serinibacter salmoneus	79.2382	482	1280	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Beutenbergiaceae;g__Serinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009733795.1	s__Pseudactinotalea caeni	78.3565	485	1280	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Beutenbergiaceae;g__Pseudactinotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002797595.1	s__Sediminihabitans luteus	78.2103	444	1280	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Sediminihabitans	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004306155.1	s__Cellulomonas biazotea	78.1439	443	1280	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003851725.1	s__Cellulomonas algicola	77.9962	444	1280	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	97.47	95.68	0.95	0.94	3	-
GCA_014837105.1	s__Oceanitalea sp014837105	77.8564	443	1280	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Oceanitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009846865.1	s__Xylanimonas puerhi	77.8043	479	1280	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Xylanimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009193185.1	s__Georgenia thermotolerans	77.726	440	1280	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Georgenia	95.0	99.99	99.99	1.00	1.00	2	-
GCF_016464425.1	s__Actinotalea solisilvae	77.6594	506	1280	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Actinotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003222205.1	s__40CM-2-70-7 sp003222205	74.7211	73	1280	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__GWC2-71-9;g__40CM-2-70-7	95.0	97.54	95.75	0.87	0.83	8	-
--------------------------------------------------------------------------------
[2024-01-24 12:31:26,448] [INFO] GTDB search result was written to GCF_030161595.1_ASM3016159v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:31:26,448] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:31:26,454] [INFO] DFAST_QC result json was written to GCF_030161595.1_ASM3016159v1_genomic.fna/dqc_result.json
[2024-01-24 12:31:26,454] [INFO] DFAST_QC completed!
[2024-01-24 12:31:26,454] [INFO] Total running time: 0h1m58s