[2024-01-24 13:19:01,383] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:19:01,385] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:19:01,385] [INFO] DQC Reference Directory: /var/lib/cwl/stg9a372161-6d89-4636-9f00-9aa7f42ae726/dqc_reference
[2024-01-24 13:19:02,684] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:19:02,685] [INFO] Task started: Prodigal
[2024-01-24 13:19:02,685] [INFO] Running command: gunzip -c /var/lib/cwl/stga96f5d16-0a7f-4d37-bd33-433f6579af7f/GCF_013415325.1_ASM1341532v1_genomic.fna.gz | prodigal -d GCF_013415325.1_ASM1341532v1_genomic.fna/cds.fna -a GCF_013415325.1_ASM1341532v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:19:13,866] [INFO] Task succeeded: Prodigal
[2024-01-24 13:19:13,866] [INFO] Task started: HMMsearch
[2024-01-24 13:19:13,866] [INFO] Running command: hmmsearch --tblout GCF_013415325.1_ASM1341532v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9a372161-6d89-4636-9f00-9aa7f42ae726/dqc_reference/reference_markers.hmm GCF_013415325.1_ASM1341532v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:19:14,239] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:19:14,240] [INFO] Found 6/6 markers.
[2024-01-24 13:19:14,294] [INFO] Query marker FASTA was written to GCF_013415325.1_ASM1341532v1_genomic.fna/markers.fasta
[2024-01-24 13:19:14,294] [INFO] Task started: Blastn
[2024-01-24 13:19:14,294] [INFO] Running command: blastn -query GCF_013415325.1_ASM1341532v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9a372161-6d89-4636-9f00-9aa7f42ae726/dqc_reference/reference_markers.fasta -out GCF_013415325.1_ASM1341532v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:15,645] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:15,649] [INFO] Selected 20 target genomes.
[2024-01-24 13:19:15,650] [INFO] Target genome list was writen to GCF_013415325.1_ASM1341532v1_genomic.fna/target_genomes.txt
[2024-01-24 13:19:15,665] [INFO] Task started: fastANI
[2024-01-24 13:19:15,665] [INFO] Running command: fastANI --query /var/lib/cwl/stga96f5d16-0a7f-4d37-bd33-433f6579af7f/GCF_013415325.1_ASM1341532v1_genomic.fna.gz --refList GCF_013415325.1_ASM1341532v1_genomic.fna/target_genomes.txt --output GCF_013415325.1_ASM1341532v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:19:33,519] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:33,520] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9a372161-6d89-4636-9f00-9aa7f42ae726/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:19:33,521] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9a372161-6d89-4636-9f00-9aa7f42ae726/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:19:33,540] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:19:33,540] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:19:33,541] [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
Sanguibacter inulinus	strain=DSM 100099	GCA_013415325.1	60922	60922	type	True	100.0	1361	1365	95	conclusive
Sanguibacter keddieii	strain=DSM 10542	GCA_000024925.1	60920	60920	type	True	86.7153	1080	1365	95	below_threshold
Sanguibacter suarezii	strain=NBRC 16159	GCA_001552735.1	60921	60921	type	True	81.5163	703	1365	95	below_threshold
Sanguibacter gelidistatuariae	strain=ISLP-3	GCA_900096585.1	1814289	1814289	type	True	81.5129	684	1365	95	below_threshold
Sanguibacter suaedae	strain=YZGR15	GCA_016342785.1	2795737	2795737	type	True	80.5287	584	1365	95	below_threshold
Sanguibacter antarcticus	strain=DSM 18966	GCA_002564005.1	372484	372484	type	True	80.1536	588	1365	95	below_threshold
Oerskovia turbata	strain=JCM3160	GCA_004121315.1	1713	1713	type	True	79.9473	543	1365	95	below_threshold
Oerskovia douganii	strain=Sa1BUA8	GCA_015142735.1	2762210	2762210	type	True	79.7663	560	1365	95	below_threshold
Oerskovia rustica	strain=Sa4CUA1	GCA_014836555.1	2762237	2762237	type	True	79.7553	567	1365	95	below_threshold
Oerskovia enterophila	strain=DSM 43852	GCA_001692445.1	43678	43678	type	True	79.7475	567	1365	95	below_threshold
Flavimobilis marinus	strain=DSM 19083	GCA_900113055.1	285351	285351	type	True	79.6228	473	1365	95	below_threshold
Sediminihabitans luteus	strain=NBRC 108568	GCA_016863455.1	1138585	1138585	type	True	79.3326	521	1365	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	78.7407	470	1365	95	below_threshold
Actinotalea solisilvae	strain=KACC 19191	GCA_016464425.1	2072922	2072922	type	True	78.6213	545	1365	95	below_threshold
Cellulomonas carbonis	strain=T26	GCA_000767175.1	1386092	1386092	type	True	78.6145	458	1365	95	below_threshold
Cellulomonas hominis	strain=DSM 9581	GCA_014201095.1	156981	156981	suspected-type	True	78.5719	535	1365	95	below_threshold
Actinotalea subterranea	strain=HO-Ch2	GCA_008364845.1	2607497	2607497	type	True	78.5011	476	1365	95	below_threshold
Cellulomonas xylanilytica	strain=NBRC 101102	GCA_007989805.1	233583	233583	type	True	78.4804	478	1365	95	below_threshold
Cellulomonas persica	strain=NBRC 101101	GCA_007989825.1	76861	76861	type	True	78.3863	473	1365	95	below_threshold
Cellulomonas endophytica	strain=SYSUP0004	GCA_004123805.1	2494735	2494735	type	True	78.1365	463	1365	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:19:33,542] [INFO] DFAST Taxonomy check result was written to GCF_013415325.1_ASM1341532v1_genomic.fna/tc_result.tsv
[2024-01-24 13:19:33,543] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:19:33,543] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:19:33,543] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9a372161-6d89-4636-9f00-9aa7f42ae726/dqc_reference/checkm_data
[2024-01-24 13:19:33,544] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:19:33,589] [INFO] Task started: CheckM
[2024-01-24 13:19:33,590] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013415325.1_ASM1341532v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013415325.1_ASM1341532v1_genomic.fna/checkm_input GCF_013415325.1_ASM1341532v1_genomic.fna/checkm_result
[2024-01-24 13:20:28,752] [INFO] Task succeeded: CheckM
[2024-01-24 13:20:28,754] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:20:28,772] [INFO] ===== Completeness check finished =====
[2024-01-24 13:20:28,773] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:20:28,773] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013415325.1_ASM1341532v1_genomic.fna/markers.fasta)
[2024-01-24 13:20:28,774] [INFO] Task started: Blastn
[2024-01-24 13:20:28,774] [INFO] Running command: blastn -query GCF_013415325.1_ASM1341532v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9a372161-6d89-4636-9f00-9aa7f42ae726/dqc_reference/reference_markers_gtdb.fasta -out GCF_013415325.1_ASM1341532v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:20:30,686] [INFO] Task succeeded: Blastn
[2024-01-24 13:20:30,690] [INFO] Selected 19 target genomes.
[2024-01-24 13:20:30,690] [INFO] Target genome list was writen to GCF_013415325.1_ASM1341532v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:20:30,759] [INFO] Task started: fastANI
[2024-01-24 13:20:30,759] [INFO] Running command: fastANI --query /var/lib/cwl/stga96f5d16-0a7f-4d37-bd33-433f6579af7f/GCF_013415325.1_ASM1341532v1_genomic.fna.gz --refList GCF_013415325.1_ASM1341532v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013415325.1_ASM1341532v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:20:45,733] [INFO] Task succeeded: fastANI
[2024-01-24 13:20:45,755] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:20:45,755] [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_013415325.1	s__Sanguibacter inulinus	100.0	1361	1365	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Sanguibacter	95.0	98.94	97.89	0.97	0.94	3	conclusive
GCF_000024925.1	s__Sanguibacter keddieii	86.7132	1080	1365	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Sanguibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001552735.1	s__Sanguibacter suarezii	81.5395	701	1365	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Sanguibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900096585.1	s__Sanguibacter gelidistatuariae	81.499	686	1365	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Sanguibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016342785.1	s__Sanguibacter sp016342785	80.4999	587	1365	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Sanguibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002564005.1	s__Sanguibacter antarcticus	80.1834	585	1365	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Sanguibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003052455.1	s__Cellulosimicrobium cinnabarinum	79.1727	544	1365	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	96.0261	97.94	97.40	0.92	0.90	4	-
GCF_016907755.1	s__Cellulosimicrobium cellulans_D	79.1467	582	1365	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	79.1299	566	1365	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	98.64	98.58	0.94	0.93	3	-
GCF_006539945.1	s__Cellulosimicrobium cellulans	78.9988	577	1365	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003115775.1	s__Cellulomonas sp003115775	78.6996	455	1365	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	78.6797	465	1365	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	78.6256	463	1365	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	99.65	99.29	0.98	0.97	3	-
GCF_007989805.1	s__Cellulomonas xylanilytica	78.4979	476	1365	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	78.4765	472	1365	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000024965.1	s__Xylanimonas cellulosilytica	78.4603	442	1365	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Xylanimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000688475.1	s__Cellulomonas sp000688475	78.2363	426	1365	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004123805.1	s__Cellulomonas endophytica	78.1134	466	1365	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:20:45,757] [INFO] GTDB search result was written to GCF_013415325.1_ASM1341532v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:20:45,758] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:20:45,762] [INFO] DFAST_QC result json was written to GCF_013415325.1_ASM1341532v1_genomic.fna/dqc_result.json
[2024-01-24 13:20:45,762] [INFO] DFAST_QC completed!
[2024-01-24 13:20:45,762] [INFO] Total running time: 0h1m44s