[2024-01-25 17:49:50,755] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:49:50,757] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:49:50,757] [INFO] DQC Reference Directory: /var/lib/cwl/stg26fd5a8f-4f1d-4e0a-a035-b7b2ecef83f7/dqc_reference
[2024-01-25 17:49:51,929] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:49:51,930] [INFO] Task started: Prodigal
[2024-01-25 17:49:51,930] [INFO] Running command: gunzip -c /var/lib/cwl/stg6760878e-bc9a-4a04-8b44-ff4ae4f51286/GCF_000767175.1_ASM76717v1_genomic.fna.gz | prodigal -d GCF_000767175.1_ASM76717v1_genomic.fna/cds.fna -a GCF_000767175.1_ASM76717v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:50:00,400] [INFO] Task succeeded: Prodigal
[2024-01-25 17:50:00,400] [INFO] Task started: HMMsearch
[2024-01-25 17:50:00,400] [INFO] Running command: hmmsearch --tblout GCF_000767175.1_ASM76717v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg26fd5a8f-4f1d-4e0a-a035-b7b2ecef83f7/dqc_reference/reference_markers.hmm GCF_000767175.1_ASM76717v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:50:00,636] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:50:00,637] [INFO] Found 6/6 markers.
[2024-01-25 17:50:00,671] [INFO] Query marker FASTA was written to GCF_000767175.1_ASM76717v1_genomic.fna/markers.fasta
[2024-01-25 17:50:00,672] [INFO] Task started: Blastn
[2024-01-25 17:50:00,672] [INFO] Running command: blastn -query GCF_000767175.1_ASM76717v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg26fd5a8f-4f1d-4e0a-a035-b7b2ecef83f7/dqc_reference/reference_markers.fasta -out GCF_000767175.1_ASM76717v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:50:01,968] [INFO] Task succeeded: Blastn
[2024-01-25 17:50:01,971] [INFO] Selected 15 target genomes.
[2024-01-25 17:50:01,972] [INFO] Target genome list was writen to GCF_000767175.1_ASM76717v1_genomic.fna/target_genomes.txt
[2024-01-25 17:50:01,979] [INFO] Task started: fastANI
[2024-01-25 17:50:01,979] [INFO] Running command: fastANI --query /var/lib/cwl/stg6760878e-bc9a-4a04-8b44-ff4ae4f51286/GCF_000767175.1_ASM76717v1_genomic.fna.gz --refList GCF_000767175.1_ASM76717v1_genomic.fna/target_genomes.txt --output GCF_000767175.1_ASM76717v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:50:16,334] [INFO] Task succeeded: fastANI
[2024-01-25 17:50:16,335] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg26fd5a8f-4f1d-4e0a-a035-b7b2ecef83f7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:50:16,335] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg26fd5a8f-4f1d-4e0a-a035-b7b2ecef83f7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:50:16,345] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 17:50:16,345] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:50:16,345] [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
Cellulomonas carbonis	strain=T26	GCA_000767175.1	1386092	1386092	type	True	100.0	1166	1175	95	conclusive
Cellulomonas carbonis	strain=CGMCC 1.10786	GCA_014636275.1	1386092	1386092	type	True	99.9991	1144	1175	95	conclusive
Actinotalea solisilvae	strain=KACC 19191	GCA_016464425.1	2072922	2072922	type	True	81.8501	747	1175	95	below_threshold
Actinotalea subterranea	strain=HO-Ch2	GCA_008364845.1	2607497	2607497	type	True	81.1005	678	1175	95	below_threshold
Cellulomonas cellasea	strain=DSM 20118	GCA_000767135.1	43670	43670	type	True	80.1159	574	1175	95	below_threshold
Cellulomonas hominis	strain=DSM 9581	GCA_014201095.1	156981	156981	suspected-type	True	79.6209	559	1175	95	below_threshold
Cellulomonas massiliensis	strain=JC225	GCA_000312005.1	1465811	1465811	type	True	79.6044	572	1175	95	below_threshold
Cellulomonas gilvus	strain=ATCC 13127	GCA_000218545.1	11	11	type	True	79.4104	553	1175	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	79.4002	586	1175	95	below_threshold
Cellulosimicrobium funkei	strain=NBRC 104118	GCA_001570825.1	264251	264251	suspected-type	True	79.3636	595	1175	95	below_threshold
Cellulomonas fulva	strain=DKR-3	GCA_018531375.1	2835530	2835530	type	True	79.311	549	1175	95	below_threshold
Cellulomonas soli	strain=DSM 24484	GCA_013409305.1	931535	931535	type	True	79.2181	545	1175	95	below_threshold
Cellulomonas avistercoris	strain=Sa3CUA2	GCA_014836445.1	2762242	2762242	type	True	79.0787	610	1175	95	below_threshold
Cellulomonas xylanilytica	strain=NBRC 101102	GCA_007989805.1	233583	233583	type	True	78.9328	547	1175	95	below_threshold
Sanguibacter inulinus	strain=DSM 100099	GCA_013415325.1	60922	60922	type	True	78.5746	462	1175	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:50:16,347] [INFO] DFAST Taxonomy check result was written to GCF_000767175.1_ASM76717v1_genomic.fna/tc_result.tsv
[2024-01-25 17:50:16,348] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:50:16,348] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:50:16,348] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg26fd5a8f-4f1d-4e0a-a035-b7b2ecef83f7/dqc_reference/checkm_data
[2024-01-25 17:50:16,349] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:50:16,389] [INFO] Task started: CheckM
[2024-01-25 17:50:16,389] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000767175.1_ASM76717v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000767175.1_ASM76717v1_genomic.fna/checkm_input GCF_000767175.1_ASM76717v1_genomic.fna/checkm_result
[2024-01-25 17:51:05,795] [INFO] Task succeeded: CheckM
[2024-01-25 17:51:05,796] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:51:05,827] [INFO] ===== Completeness check finished =====
[2024-01-25 17:51:05,827] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:51:05,827] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000767175.1_ASM76717v1_genomic.fna/markers.fasta)
[2024-01-25 17:51:05,827] [INFO] Task started: Blastn
[2024-01-25 17:51:05,828] [INFO] Running command: blastn -query GCF_000767175.1_ASM76717v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg26fd5a8f-4f1d-4e0a-a035-b7b2ecef83f7/dqc_reference/reference_markers_gtdb.fasta -out GCF_000767175.1_ASM76717v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:51:07,898] [INFO] Task succeeded: Blastn
[2024-01-25 17:51:07,900] [INFO] Selected 15 target genomes.
[2024-01-25 17:51:07,901] [INFO] Target genome list was writen to GCF_000767175.1_ASM76717v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:51:07,915] [INFO] Task started: fastANI
[2024-01-25 17:51:07,915] [INFO] Running command: fastANI --query /var/lib/cwl/stg6760878e-bc9a-4a04-8b44-ff4ae4f51286/GCF_000767175.1_ASM76717v1_genomic.fna.gz --refList GCF_000767175.1_ASM76717v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000767175.1_ASM76717v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:51:21,242] [INFO] Task succeeded: fastANI
[2024-01-25 17:51:21,253] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:51:21,253] [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_014636275.1	s__Actinotalea carbonis	99.9991	1144	1175	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Actinotalea	95.0	100.00	100.00	0.97	0.97	2	conclusive
GCF_000603945.1	s__Actinotalea ferrariae	82.0439	620	1175	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	81.7836	754	1175	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	81.5492	476	1175	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Actinotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009996735.1	s__Actinotalea sp009996735	81.5036	673	1175	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	81.1736	620	1175	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Actinotalea	95.0	99.62	99.62	0.98	0.98	2	-
GCF_008364845.1	s__Actinotalea sp008364845	81.043	684	1175	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Actinotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000767215.1	s__Actinotalea fermentans	80.4826	466	1175	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Actinotalea	95.0	100.00	100.00	1.00	1.00	2	-
GCF_006538705.1	s__Cellulomonas uda	79.631	545	1175	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	98.69	98.01	0.94	0.90	4	-
GCA_014763765.1	s__Cellulomonas sp014763765	79.4695	516	1175	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000218545.1	s__Cellulomonas gilvus	79.4367	550	1175	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013409305.1	s__Cellulomonas soli	79.301	534	1175	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_018388465.1	s__Cellulomonas sp018388465	79.1452	510	1175	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	99.65	99.29	0.98	0.97	3	-
GCF_016862675.1	s__Cellulomonas chitinilytica	79.1413	615	1175	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013415325.1	s__Sanguibacter inulinus	78.6027	459	1175	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Sanguibacter	95.0	98.94	97.89	0.97	0.94	3	-
--------------------------------------------------------------------------------
[2024-01-25 17:51:21,254] [INFO] GTDB search result was written to GCF_000767175.1_ASM76717v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:51:21,255] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:51:21,258] [INFO] DFAST_QC result json was written to GCF_000767175.1_ASM76717v1_genomic.fna/dqc_result.json
[2024-01-25 17:51:21,258] [INFO] DFAST_QC completed!
[2024-01-25 17:51:21,258] [INFO] Total running time: 0h1m31s