[2024-01-24 10:57:39,015] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:39,021] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:39,022] [INFO] DQC Reference Directory: /var/lib/cwl/stgcbc3c625-6da0-41e5-b946-815d7fea9b8f/dqc_reference
[2024-01-24 10:57:40,367] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:40,367] [INFO] Task started: Prodigal
[2024-01-24 10:57:40,368] [INFO] Running command: gunzip -c /var/lib/cwl/stgf51760a5-a856-4679-9e9a-c1642153750e/GCF_017565425.1_ASM1756542v1_genomic.fna.gz | prodigal -d GCF_017565425.1_ASM1756542v1_genomic.fna/cds.fna -a GCF_017565425.1_ASM1756542v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:50,252] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:50,253] [INFO] Task started: HMMsearch
[2024-01-24 10:57:50,253] [INFO] Running command: hmmsearch --tblout GCF_017565425.1_ASM1756542v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcbc3c625-6da0-41e5-b946-815d7fea9b8f/dqc_reference/reference_markers.hmm GCF_017565425.1_ASM1756542v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:50,540] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:50,542] [INFO] Found 6/6 markers.
[2024-01-24 10:57:50,579] [INFO] Query marker FASTA was written to GCF_017565425.1_ASM1756542v1_genomic.fna/markers.fasta
[2024-01-24 10:57:50,579] [INFO] Task started: Blastn
[2024-01-24 10:57:50,579] [INFO] Running command: blastn -query GCF_017565425.1_ASM1756542v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcbc3c625-6da0-41e5-b946-815d7fea9b8f/dqc_reference/reference_markers.fasta -out GCF_017565425.1_ASM1756542v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:51,993] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:51,996] [INFO] Selected 23 target genomes.
[2024-01-24 10:57:51,997] [INFO] Target genome list was writen to GCF_017565425.1_ASM1756542v1_genomic.fna/target_genomes.txt
[2024-01-24 10:57:52,004] [INFO] Task started: fastANI
[2024-01-24 10:57:52,004] [INFO] Running command: fastANI --query /var/lib/cwl/stgf51760a5-a856-4679-9e9a-c1642153750e/GCF_017565425.1_ASM1756542v1_genomic.fna.gz --refList GCF_017565425.1_ASM1756542v1_genomic.fna/target_genomes.txt --output GCF_017565425.1_ASM1756542v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:58:09,357] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:09,358] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcbc3c625-6da0-41e5-b946-815d7fea9b8f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:58:09,358] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcbc3c625-6da0-41e5-b946-815d7fea9b8f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:58:09,376] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 10:58:09,377] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 10:58:09,377] [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
Actinotalea solisilvae	strain=KACC 19191	GCA_016464425.1	2072922	2072922	type	True	80.3695	641	1200	95	below_threshold
Actinotalea subterranea	strain=HO-Ch2	GCA_008364845.1	2607497	2607497	type	True	80.3189	650	1200	95	below_threshold
Cellulomonas carbonis	strain=T26	GCA_000767175.1	1386092	1386092	type	True	80.2714	576	1200	95	below_threshold
Cellulomonas carbonis	strain=CGMCC 1.10786	GCA_014636275.1	1386092	1386092	type	True	80.149	617	1200	95	below_threshold
Cellulomonas timonensis	strain=SN7	GCA_900046455.1	1689271	1689271	type	True	79.2852	486	1200	95	below_threshold
Cellulomonas cellasea	strain=DSM 20118	GCA_000767135.1	43670	43670	type	True	79.2128	492	1200	95	below_threshold
Cellulomonas cellasea	strain=NBRC 3753	GCA_006538745.1	43670	43670	type	True	79.1559	589	1200	95	below_threshold
Cellulomonas soli	strain=DSM 24484	GCA_013409305.1	931535	931535	type	True	79.0423	516	1200	95	below_threshold
Sanguibacter suarezii	strain=NBRC 16159	GCA_001552735.1	60921	60921	type	True	79.0294	464	1200	95	below_threshold
Cellulomonas fulva	strain=DKR-3	GCA_018531375.1	2835530	2835530	type	True	78.9001	477	1200	95	below_threshold
Cellulomonas taurus	strain=P40-2	GCA_012931845.1	2729175	2729175	type	True	78.7606	432	1200	95	below_threshold
Oerskovia rustica	strain=Sa4CUA1	GCA_014836555.1	2762237	2762237	type	True	78.7394	461	1200	95	below_threshold
Cellulomonas hominis	strain=NBRC 16055	GCA_007989225.1	156981	156981	suspected-type	True	78.7278	539	1200	95	below_threshold
Cellulomonas iranensis	strain=NBRC 101100	GCA_001552375.1	76862	76862	type	True	78.6993	511	1200	95	below_threshold
Cellulomonas hominis	strain=DSM 9581	GCA_014201095.1	156981	156981	suspected-type	True	78.6972	549	1200	95	below_threshold
Cellulomonas biazotea	strain=NBRC12680	GCA_004306155.1	1709	1709	type	True	78.6938	497	1200	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	78.668	499	1200	95	below_threshold
Oerskovia douganii	strain=Sa1BUA8	GCA_015142735.1	2762210	2762210	type	True	78.6483	461	1200	95	below_threshold
Oerskovia jenensis	strain=DSM 46000	GCA_016907235.1	162169	162169	type	True	78.6337	480	1200	95	below_threshold
Cellulosimicrobium funkei	strain=JCM 14302	GCA_004519295.1	264251	264251	suspected-type	True	78.4031	504	1200	95	below_threshold
Cellulosimicrobium funkei	strain=NBRC 104118	GCA_001570825.1	264251	264251	suspected-type	True	78.3804	499	1200	95	below_threshold
Paraoerskovia marina	strain=DSM 21750	GCA_000701465.1	545619	545619	type	True	78.1715	374	1200	95	below_threshold
Georgenia faecalis	strain=ZLJ0423	GCA_003710105.1	2483799	2483799	type	True	78.1395	417	1200	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:58:09,381] [INFO] DFAST Taxonomy check result was written to GCF_017565425.1_ASM1756542v1_genomic.fna/tc_result.tsv
[2024-01-24 10:58:09,382] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:58:09,382] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:58:09,383] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcbc3c625-6da0-41e5-b946-815d7fea9b8f/dqc_reference/checkm_data
[2024-01-24 10:58:09,384] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:58:09,425] [INFO] Task started: CheckM
[2024-01-24 10:58:09,426] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017565425.1_ASM1756542v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017565425.1_ASM1756542v1_genomic.fna/checkm_input GCF_017565425.1_ASM1756542v1_genomic.fna/checkm_result
[2024-01-24 10:59:03,963] [INFO] Task succeeded: CheckM
[2024-01-24 10:59:03,965] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:59:03,996] [INFO] ===== Completeness check finished =====
[2024-01-24 10:59:03,997] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:59:03,997] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017565425.1_ASM1756542v1_genomic.fna/markers.fasta)
[2024-01-24 10:59:03,998] [INFO] Task started: Blastn
[2024-01-24 10:59:03,998] [INFO] Running command: blastn -query GCF_017565425.1_ASM1756542v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcbc3c625-6da0-41e5-b946-815d7fea9b8f/dqc_reference/reference_markers_gtdb.fasta -out GCF_017565425.1_ASM1756542v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:59:06,148] [INFO] Task succeeded: Blastn
[2024-01-24 10:59:06,152] [INFO] Selected 15 target genomes.
[2024-01-24 10:59:06,152] [INFO] Target genome list was writen to GCF_017565425.1_ASM1756542v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:59:06,179] [INFO] Task started: fastANI
[2024-01-24 10:59:06,179] [INFO] Running command: fastANI --query /var/lib/cwl/stgf51760a5-a856-4679-9e9a-c1642153750e/GCF_017565425.1_ASM1756542v1_genomic.fna.gz --refList GCF_017565425.1_ASM1756542v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017565425.1_ASM1756542v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:59:18,283] [INFO] Task succeeded: fastANI
[2024-01-24 10:59:18,301] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:59:18,302] [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_017565425.1	s__Actinotalea sp017565425	100.0	1199	1200	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Actinotalea	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009996735.1	s__Actinotalea sp009996735	81.0728	657	1200	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Actinotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000767165.1	s__Actinotalea bogoriensis	80.6689	455	1200	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Actinotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016464425.1	s__Actinotalea solisilvae	80.3829	640	1200	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Actinotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008364845.1	s__Actinotalea sp008364845	80.3612	645	1200	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Actinotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014042015.1	s__Actinotalea sp014042015	80.3526	618	1200	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Actinotalea	95.0	99.62	99.62	0.98	0.98	2	-
GCF_000526515.1	s__Actinotalea sp000526515	80.2173	608	1200	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Actinotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014360395.1	s__Actinotalea sp014360395	80.1697	402	1200	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Actinotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000603945.1	s__Actinotalea ferrariae	80.0669	508	1200	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Actinotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013409305.1	s__Cellulomonas soli	79.033	517	1200	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCA_012514545.1	s__Actinotalea sp012514545	79.0315	394	1200	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Actinotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014763765.1	s__Cellulomonas sp014763765	78.8461	468	1200	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907365.1	s__Oerskovia paurometabola	78.7093	475	1200	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Oerskovia	95.0	99.20	99.20	0.97	0.97	2	-
GCF_016907235.1	s__Oerskovia jenensis	78.6207	481	1200	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Oerskovia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004519295.1	s__Cellulosimicrobium funkei	78.4044	504	1200	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	96.0261	98.03	96.84	0.93	0.88	18	-
--------------------------------------------------------------------------------
[2024-01-24 10:59:18,304] [INFO] GTDB search result was written to GCF_017565425.1_ASM1756542v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:59:18,305] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:59:18,308] [INFO] DFAST_QC result json was written to GCF_017565425.1_ASM1756542v1_genomic.fna/dqc_result.json
[2024-01-24 10:59:18,308] [INFO] DFAST_QC completed!
[2024-01-24 10:59:18,309] [INFO] Total running time: 0h1m39s