[2024-01-24 14:20:14,982] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:20:14,985] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:20:14,986] [INFO] DQC Reference Directory: /var/lib/cwl/stg104f588f-2509-4073-bb63-6f1a07c6ee95/dqc_reference
[2024-01-24 14:20:16,283] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:20:16,284] [INFO] Task started: Prodigal
[2024-01-24 14:20:16,285] [INFO] Running command: gunzip -c /var/lib/cwl/stg0e027b53-9784-40d9-93b1-9fdd7b1a0dc3/GCF_030296575.1_ASM3029657v1_genomic.fna.gz | prodigal -d GCF_030296575.1_ASM3029657v1_genomic.fna/cds.fna -a GCF_030296575.1_ASM3029657v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:20:26,361] [INFO] Task succeeded: Prodigal
[2024-01-24 14:20:26,361] [INFO] Task started: HMMsearch
[2024-01-24 14:20:26,361] [INFO] Running command: hmmsearch --tblout GCF_030296575.1_ASM3029657v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg104f588f-2509-4073-bb63-6f1a07c6ee95/dqc_reference/reference_markers.hmm GCF_030296575.1_ASM3029657v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:20:26,597] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:20:26,598] [INFO] Found 6/6 markers.
[2024-01-24 14:20:26,642] [INFO] Query marker FASTA was written to GCF_030296575.1_ASM3029657v1_genomic.fna/markers.fasta
[2024-01-24 14:20:26,642] [INFO] Task started: Blastn
[2024-01-24 14:20:26,643] [INFO] Running command: blastn -query GCF_030296575.1_ASM3029657v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg104f588f-2509-4073-bb63-6f1a07c6ee95/dqc_reference/reference_markers.fasta -out GCF_030296575.1_ASM3029657v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:27,936] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:27,939] [INFO] Selected 16 target genomes.
[2024-01-24 14:20:27,940] [INFO] Target genome list was writen to GCF_030296575.1_ASM3029657v1_genomic.fna/target_genomes.txt
[2024-01-24 14:20:27,952] [INFO] Task started: fastANI
[2024-01-24 14:20:27,952] [INFO] Running command: fastANI --query /var/lib/cwl/stg0e027b53-9784-40d9-93b1-9fdd7b1a0dc3/GCF_030296575.1_ASM3029657v1_genomic.fna.gz --refList GCF_030296575.1_ASM3029657v1_genomic.fna/target_genomes.txt --output GCF_030296575.1_ASM3029657v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:20:41,314] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:41,314] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg104f588f-2509-4073-bb63-6f1a07c6ee95/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:20:41,315] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg104f588f-2509-4073-bb63-6f1a07c6ee95/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:20:41,328] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:20:41,329] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:20:41,329] [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=DSM 25478	GCA_002797595.1	1138585	1138585	type	True	81.8441	687	1171	95	below_threshold
Sediminihabitans luteus	strain=NBRC 108568	GCA_016863455.1	1138585	1138585	type	True	81.7859	674	1171	95	below_threshold
Paraoerskovia marina	strain=DSM 21750	GCA_000701465.1	545619	545619	type	True	80.4503	590	1171	95	below_threshold
Cellulosimicrobium funkei	strain=NBRC 104118	GCA_001570825.1	264251	264251	suspected-type	True	80.1756	627	1171	95	below_threshold
Cellulosimicrobium funkei	strain=JCM 14302	GCA_004519295.1	264251	264251	suspected-type	True	80.1273	642	1171	95	below_threshold
Oerskovia merdavium	strain=Sa2CUA9	GCA_014836755.1	2762227	2762227	type	True	80.0549	572	1171	95	below_threshold
Oerskovia douganii	strain=Sa1BUA8	GCA_015142735.1	2762210	2762210	type	True	80.0455	564	1171	95	below_threshold
Cellulosimicrobium marinum	strain=NBRC 110994	GCA_020551945.1	1638992	1638992	type	True	80.0197	620	1171	95	below_threshold
Oerskovia rustica	strain=Sa4CUA1	GCA_014836555.1	2762237	2762237	type	True	79.9486	584	1171	95	below_threshold
Oerskovia enterophila	strain=DSM 43852	GCA_001692445.1	43678	43678	type	True	79.9299	580	1171	95	below_threshold
Cellulosimicrobium arenosum	strain=KCTC 49039	GCA_014837295.1	2708133	2708133	type	True	79.8276	582	1171	95	below_threshold
Sanguibacter keddieii	strain=DSM 10542	GCA_000024925.1	60920	60920	type	True	79.2532	530	1171	95	below_threshold
Cellulomonas iranensis	strain=NBRC 101100	GCA_001552375.1	76862	76862	type	True	79.0816	488	1171	95	below_threshold
Actinotalea solisilvae	strain=KACC 19191	GCA_016464425.1	2072922	2072922	type	True	78.8424	505	1171	95	below_threshold
Cellulomonas avistercoris	strain=Sa3CUA2	GCA_014836445.1	2762242	2762242	type	True	78.7968	460	1171	95	below_threshold
Sanguibacter antarcticus	strain=DSM 18966	GCA_002564005.1	372484	372484	type	True	78.7606	422	1171	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:20:41,331] [INFO] DFAST Taxonomy check result was written to GCF_030296575.1_ASM3029657v1_genomic.fna/tc_result.tsv
[2024-01-24 14:20:41,331] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:20:41,332] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:20:41,332] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg104f588f-2509-4073-bb63-6f1a07c6ee95/dqc_reference/checkm_data
[2024-01-24 14:20:41,333] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:20:41,370] [INFO] Task started: CheckM
[2024-01-24 14:20:41,370] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030296575.1_ASM3029657v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030296575.1_ASM3029657v1_genomic.fna/checkm_input GCF_030296575.1_ASM3029657v1_genomic.fna/checkm_result
[2024-01-24 14:21:27,535] [INFO] Task succeeded: CheckM
[2024-01-24 14:21:27,536] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:21:27,552] [INFO] ===== Completeness check finished =====
[2024-01-24 14:21:27,552] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:21:27,553] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030296575.1_ASM3029657v1_genomic.fna/markers.fasta)
[2024-01-24 14:21:27,553] [INFO] Task started: Blastn
[2024-01-24 14:21:27,553] [INFO] Running command: blastn -query GCF_030296575.1_ASM3029657v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg104f588f-2509-4073-bb63-6f1a07c6ee95/dqc_reference/reference_markers_gtdb.fasta -out GCF_030296575.1_ASM3029657v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:21:29,416] [INFO] Task succeeded: Blastn
[2024-01-24 14:21:29,419] [INFO] Selected 18 target genomes.
[2024-01-24 14:21:29,419] [INFO] Target genome list was writen to GCF_030296575.1_ASM3029657v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:21:29,440] [INFO] Task started: fastANI
[2024-01-24 14:21:29,441] [INFO] Running command: fastANI --query /var/lib/cwl/stg0e027b53-9784-40d9-93b1-9fdd7b1a0dc3/GCF_030296575.1_ASM3029657v1_genomic.fna.gz --refList GCF_030296575.1_ASM3029657v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030296575.1_ASM3029657v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:21:43,827] [INFO] Task succeeded: fastANI
[2024-01-24 14:21:43,842] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 14:21:43,842] [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_003752595.1	s__Sediminihabitans sp003752595	82.1402	714	1171	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Sediminihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002797595.1	s__Sediminihabitans luteus	81.8208	690	1171	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Sediminihabitans	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000701465.1	s__Paraoerskovia marina	80.4717	587	1171	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Paraoerskovia	95.0	98.25	98.25	0.95	0.95	2	-
GCF_005937995.2	s__Oerskovia sp005937995	80.2457	556	1171	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Oerskovia	95.0	96.13	96.13	0.91	0.91	2	-
GCF_009708005.2	s__Cellulosimicrobium sp009708005	80.2305	653	1171	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001722485.1	s__Cellulosimicrobium cellulans_A	80.2278	522	1171	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004519295.1	s__Cellulosimicrobium funkei	80.1849	636	1171	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	96.0261	98.03	96.84	0.93	0.88	18	-
GCF_016907365.1	s__Oerskovia paurometabola	80.1722	587	1171	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Oerskovia	95.0	99.20	99.20	0.97	0.97	2	-
GCF_016907755.1	s__Cellulosimicrobium cellulans_D	80.1714	673	1171	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	80.1496	633	1171	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	98.64	98.58	0.94	0.93	3	-
GCF_010287905.1	s__Cellulosimicrobium fucosivorans	80.1318	623	1171	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	98.84	98.55	0.94	0.90	6	-
GCF_006539945.1	s__Cellulosimicrobium cellulans	80.0923	638	1171	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	80.0799	632	1171	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015142735.1	s__Oerskovia sp015142735	79.9777	571	1171	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Oerskovia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001692445.1	s__Oerskovia enterophila	79.9224	581	1171	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Oerskovia	95.0	98.35	97.89	0.90	0.89	4	-
GCF_014837295.1	s__Cellulosimicrobium arenosum	79.8556	579	1171	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000024925.1	s__Sanguibacter keddieii	79.2051	535	1171	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Sanguibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001552375.1	s__Cellulomonas iranensis	79.0272	494	1171	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	98.21	97.89	0.91	0.88	6	-
--------------------------------------------------------------------------------
[2024-01-24 14:21:43,844] [INFO] GTDB search result was written to GCF_030296575.1_ASM3029657v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:21:43,844] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:21:43,848] [INFO] DFAST_QC result json was written to GCF_030296575.1_ASM3029657v1_genomic.fna/dqc_result.json
[2024-01-24 14:21:43,848] [INFO] DFAST_QC completed!
[2024-01-24 14:21:43,848] [INFO] Total running time: 0h1m29s