[2024-01-25 20:04:50,568] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:04:50,569] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:04:50,570] [INFO] DQC Reference Directory: /var/lib/cwl/stg1dc8f3af-47d9-4425-be9d-770a088a00e6/dqc_reference
[2024-01-25 20:04:51,715] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:04:51,716] [INFO] Task started: Prodigal
[2024-01-25 20:04:51,716] [INFO] Running command: gunzip -c /var/lib/cwl/stgeff75a05-2e5e-43cf-8218-dea9c4b160bd/GCF_002798015.1_ASM279801v1_genomic.fna.gz | prodigal -d GCF_002798015.1_ASM279801v1_genomic.fna/cds.fna -a GCF_002798015.1_ASM279801v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:05:00,521] [INFO] Task succeeded: Prodigal
[2024-01-25 20:05:00,522] [INFO] Task started: HMMsearch
[2024-01-25 20:05:00,522] [INFO] Running command: hmmsearch --tblout GCF_002798015.1_ASM279801v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1dc8f3af-47d9-4425-be9d-770a088a00e6/dqc_reference/reference_markers.hmm GCF_002798015.1_ASM279801v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:05:00,749] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:05:00,750] [INFO] Found 6/6 markers.
[2024-01-25 20:05:00,779] [INFO] Query marker FASTA was written to GCF_002798015.1_ASM279801v1_genomic.fna/markers.fasta
[2024-01-25 20:05:00,780] [INFO] Task started: Blastn
[2024-01-25 20:05:00,780] [INFO] Running command: blastn -query GCF_002798015.1_ASM279801v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1dc8f3af-47d9-4425-be9d-770a088a00e6/dqc_reference/reference_markers.fasta -out GCF_002798015.1_ASM279801v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:05:02,026] [INFO] Task succeeded: Blastn
[2024-01-25 20:05:02,029] [INFO] Selected 26 target genomes.
[2024-01-25 20:05:02,029] [INFO] Target genome list was writen to GCF_002798015.1_ASM279801v1_genomic.fna/target_genomes.txt
[2024-01-25 20:05:02,036] [INFO] Task started: fastANI
[2024-01-25 20:05:02,036] [INFO] Running command: fastANI --query /var/lib/cwl/stgeff75a05-2e5e-43cf-8218-dea9c4b160bd/GCF_002798015.1_ASM279801v1_genomic.fna.gz --refList GCF_002798015.1_ASM279801v1_genomic.fna/target_genomes.txt --output GCF_002798015.1_ASM279801v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:05:22,874] [INFO] Task succeeded: fastANI
[2024-01-25 20:05:22,875] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1dc8f3af-47d9-4425-be9d-770a088a00e6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:05:22,875] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1dc8f3af-47d9-4425-be9d-770a088a00e6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:05:22,890] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 20:05:22,890] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 20:05:22,890] [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	80.3009	605	1202	95	below_threshold
Sediminihabitans luteus	strain=DSM 25478	GCA_002797595.1	1138585	1138585	type	True	80.231	610	1202	95	below_threshold
Cellulosimicrobium funkei	strain=NBRC 104118	GCA_001570825.1	264251	264251	suspected-type	True	79.9674	621	1202	95	below_threshold
Cellulosimicrobium funkei	strain=JCM 14302	GCA_004519295.1	264251	264251	suspected-type	True	79.9397	631	1202	95	below_threshold
Cellulosimicrobium marinum	strain=NBRC 110994	GCA_020551945.1	1638992	1638992	type	True	79.8517	604	1202	95	below_threshold
Oerskovia turbata	strain=NRRL B-8019	GCA_000718325.1	1713	1713	type	True	79.7224	558	1202	95	below_threshold
Oerskovia enterophila	strain=DSM 43852	GCA_001692445.1	43678	43678	type	True	79.7115	571	1202	95	below_threshold
Oerskovia turbata	strain=JCM3160	GCA_004121315.1	1713	1713	type	True	79.6839	572	1202	95	below_threshold
Oerskovia douganii	strain=Sa1BUA8	GCA_015142735.1	2762210	2762210	type	True	79.5845	583	1202	95	below_threshold
Oerskovia merdavium	strain=Sa2CUA9	GCA_014836755.1	2762227	2762227	type	True	79.5204	575	1202	95	below_threshold
Cellulomonas uda	strain=NBRC 3747	GCA_006538705.1	1714	1714	type	True	79.4106	524	1202	95	below_threshold
Cellulosimicrobium arenosum	strain=KCTC 49039	GCA_014837295.1	2708133	2708133	type	True	79.403	580	1202	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	79.3794	566	1202	95	below_threshold
Cellulomonas massiliensis	strain=JC225	GCA_000312005.1	1465811	1465811	type	True	79.3278	521	1202	95	below_threshold
Cellulomonas soli	strain=DSM 24484	GCA_013409305.1	931535	931535	type	True	79.2084	491	1202	95	below_threshold
Cellulomonas cellasea	strain=DSM 20118	GCA_000767135.1	43670	43670	type	True	79.0802	477	1202	95	below_threshold
Cellulomonas fulva	strain=DKR-3	GCA_018531375.1	2835530	2835530	type	True	79.0639	536	1202	95	below_threshold
Cellulomonas cellasea	strain=NBRC 3753	GCA_006538745.1	43670	43670	type	True	79.0222	602	1202	95	below_threshold
Sanguibacter suaedae	strain=YZGR15	GCA_016342785.1	2795737	2795737	type	True	78.9059	440	1202	95	below_threshold
Cellulomonas terrae	strain=NBRC 100819	GCA_007990265.1	311234	311234	type	True	78.8778	508	1202	95	below_threshold
Cellulomonas avistercoris	strain=Sa3CUA2	GCA_014836445.1	2762242	2762242	type	True	78.8322	543	1202	95	below_threshold
Cellulomonas hominis	strain=DSM 9581	GCA_014201095.1	156981	156981	suspected-type	True	78.8126	569	1202	95	below_threshold
Cellulomonas hominis	strain=NBRC 16055	GCA_007989225.1	156981	156981	suspected-type	True	78.7973	543	1202	95	below_threshold
Cellulomonas xylanilytica	strain=NBRC 101102	GCA_007989805.1	233583	233583	type	True	78.7057	528	1202	95	below_threshold
Actinotalea subterranea	strain=HO-Ch2	GCA_008364845.1	2607497	2607497	type	True	78.647	498	1202	95	below_threshold
Promicromonospora sukumoe	strain=DSM 44121	GCA_014137995.1	88382	88382	type	True	78.5475	580	1202	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:05:22,892] [INFO] DFAST Taxonomy check result was written to GCF_002798015.1_ASM279801v1_genomic.fna/tc_result.tsv
[2024-01-25 20:05:22,892] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:05:22,893] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:05:22,893] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1dc8f3af-47d9-4425-be9d-770a088a00e6/dqc_reference/checkm_data
[2024-01-25 20:05:22,893] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:05:22,931] [INFO] Task started: CheckM
[2024-01-25 20:05:22,931] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002798015.1_ASM279801v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002798015.1_ASM279801v1_genomic.fna/checkm_input GCF_002798015.1_ASM279801v1_genomic.fna/checkm_result
[2024-01-25 20:06:20,027] [INFO] Task succeeded: CheckM
[2024-01-25 20:06:20,029] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:06:20,053] [INFO] ===== Completeness check finished =====
[2024-01-25 20:06:20,053] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:06:20,054] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002798015.1_ASM279801v1_genomic.fna/markers.fasta)
[2024-01-25 20:06:20,055] [INFO] Task started: Blastn
[2024-01-25 20:06:20,055] [INFO] Running command: blastn -query GCF_002798015.1_ASM279801v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1dc8f3af-47d9-4425-be9d-770a088a00e6/dqc_reference/reference_markers_gtdb.fasta -out GCF_002798015.1_ASM279801v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:06:22,117] [INFO] Task succeeded: Blastn
[2024-01-25 20:06:22,120] [INFO] Selected 20 target genomes.
[2024-01-25 20:06:22,120] [INFO] Target genome list was writen to GCF_002798015.1_ASM279801v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:06:22,129] [INFO] Task started: fastANI
[2024-01-25 20:06:22,129] [INFO] Running command: fastANI --query /var/lib/cwl/stgeff75a05-2e5e-43cf-8218-dea9c4b160bd/GCF_002798015.1_ASM279801v1_genomic.fna.gz --refList GCF_002798015.1_ASM279801v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002798015.1_ASM279801v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:06:39,711] [INFO] Task succeeded: fastANI
[2024-01-25 20:06:39,724] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:06:39,724] [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_002798015.1	s__Luteimicrobium subarcticum	100.0	1201	1202	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Luteimicrobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009429125.1	s__Luteimicrobium xylanilyticum	81.7491	779	1202	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Luteimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002797595.1	s__Sediminihabitans luteus	80.2397	610	1202	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Sediminihabitans	95.0	100.00	100.00	1.00	1.00	2	-
GCF_010287905.1	s__Cellulosimicrobium fucosivorans	80.004	622	1202	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	98.84	98.55	0.94	0.90	6	-
GCA_003052455.1	s__Cellulosimicrobium cinnabarinum	79.9667	633	1202	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	96.0261	97.94	97.40	0.92	0.90	4	-
GCF_004519295.1	s__Cellulosimicrobium funkei	79.9176	633	1202	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	96.0261	98.03	96.84	0.93	0.88	18	-
GCF_016907755.1	s__Cellulosimicrobium cellulans_D	79.8979	667	1202	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	99.18	99.18	0.97	0.97	2	-
GCF_001019615.1	s__Cellulosimicrobium cellulans_E	79.7549	656	1202	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	98.64	98.58	0.94	0.93	3	-
GCF_000215105.1	s__Isoptericola variabilis_A	79.7392	569	1202	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Isoptericola	95.0	99.96	99.96	0.98	0.98	2	-
GCF_009708005.2	s__Cellulosimicrobium sp009708005	79.6741	675	1202	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016921195.1	s__Cellulosimicrobium cellulans_F	79.6667	654	1202	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014836755.1	s__Oerskovia sp014836755	79.5425	572	1202	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Oerskovia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006538705.1	s__Cellulomonas uda	79.4605	517	1202	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	98.69	98.01	0.94	0.90	4	-
GCF_000212695.1	s__Cellulomonas fimi	79.3786	588	1202	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	100.00	99.99	1.00	1.00	3	-
GCF_000312005.1	s__Cellulomonas massiliensis	79.3096	523	1202	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	99.99	99.99	0.99	0.99	2	-
GCF_006538745.1	s__Cellulomonas cellasea	79.0076	604	1202	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	97.79	95.59	0.95	0.91	3	-
GCF_011603975.1	s__Cellulomonas sp011603975	78.9964	496	1202	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	78.9053	508	1202	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018388445.1	s__Cellulomonas sp018388445	78.8848	510	1202	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	99.55	99.30	0.98	0.97	4	-
GCF_007679345.1	s__Cellulomonas cellulans_A	78.8382	557	1202	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:06:39,726] [INFO] GTDB search result was written to GCF_002798015.1_ASM279801v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:06:39,727] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:06:39,730] [INFO] DFAST_QC result json was written to GCF_002798015.1_ASM279801v1_genomic.fna/dqc_result.json
[2024-01-25 20:06:39,730] [INFO] DFAST_QC completed!
[2024-01-25 20:06:39,731] [INFO] Total running time: 0h1m49s