[2024-01-24 12:29:28,101] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:29:28,107] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:29:28,107] [INFO] DQC Reference Directory: /var/lib/cwl/stgbbd7a7e9-eab4-4c90-9f95-1e9c6063b8e7/dqc_reference
[2024-01-24 12:29:29,584] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:29:29,585] [INFO] Task started: Prodigal
[2024-01-24 12:29:29,586] [INFO] Running command: gunzip -c /var/lib/cwl/stg0e21c218-5cb5-4e9f-9bba-fa5c001bc1c2/GCF_008364845.1_ASM836484v1_genomic.fna.gz | prodigal -d GCF_008364845.1_ASM836484v1_genomic.fna/cds.fna -a GCF_008364845.1_ASM836484v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:29:41,400] [INFO] Task succeeded: Prodigal
[2024-01-24 12:29:41,400] [INFO] Task started: HMMsearch
[2024-01-24 12:29:41,401] [INFO] Running command: hmmsearch --tblout GCF_008364845.1_ASM836484v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbbd7a7e9-eab4-4c90-9f95-1e9c6063b8e7/dqc_reference/reference_markers.hmm GCF_008364845.1_ASM836484v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:29:41,762] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:29:41,764] [INFO] Found 6/6 markers.
[2024-01-24 12:29:41,815] [INFO] Query marker FASTA was written to GCF_008364845.1_ASM836484v1_genomic.fna/markers.fasta
[2024-01-24 12:29:41,816] [INFO] Task started: Blastn
[2024-01-24 12:29:41,816] [INFO] Running command: blastn -query GCF_008364845.1_ASM836484v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbbd7a7e9-eab4-4c90-9f95-1e9c6063b8e7/dqc_reference/reference_markers.fasta -out GCF_008364845.1_ASM836484v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:29:43,154] [INFO] Task succeeded: Blastn
[2024-01-24 12:29:43,158] [INFO] Selected 19 target genomes.
[2024-01-24 12:29:43,158] [INFO] Target genome list was writen to GCF_008364845.1_ASM836484v1_genomic.fna/target_genomes.txt
[2024-01-24 12:29:43,163] [INFO] Task started: fastANI
[2024-01-24 12:29:43,163] [INFO] Running command: fastANI --query /var/lib/cwl/stg0e21c218-5cb5-4e9f-9bba-fa5c001bc1c2/GCF_008364845.1_ASM836484v1_genomic.fna.gz --refList GCF_008364845.1_ASM836484v1_genomic.fna/target_genomes.txt --output GCF_008364845.1_ASM836484v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:30:00,266] [INFO] Task succeeded: fastANI
[2024-01-24 12:30:00,266] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbbd7a7e9-eab4-4c90-9f95-1e9c6063b8e7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:30:00,267] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbbd7a7e9-eab4-4c90-9f95-1e9c6063b8e7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:30:00,282] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:30:00,282] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:30:00,283] [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 subterranea	strain=HO-Ch2	GCA_008364845.1	2607497	2607497	type	True	100.0	1328	1330	95	conclusive
Actinotalea solisilvae	strain=KACC 19191	GCA_016464425.1	2072922	2072922	type	True	82.0145	816	1330	95	below_threshold
Cellulomonas carbonis	strain=T26	GCA_000767175.1	1386092	1386092	type	True	81.1298	678	1330	95	below_threshold
Cellulomonas carbonis	strain=CGMCC 1.10786	GCA_014636275.1	1386092	1386092	type	True	81.0848	725	1330	95	below_threshold
Cellulomonas cellasea	strain=NBRC 3753	GCA_006538745.1	43670	43670	type	True	80.0267	686	1330	95	below_threshold
Cellulomonas cellasea	strain=DSM 20118	GCA_000767135.1	43670	43670	type	True	79.9994	557	1330	95	below_threshold
Cellulomonas gilvus	strain=ATCC 13127	GCA_000218545.1	11	11	type	True	79.5871	584	1330	95	below_threshold
Cellulomonas iranensis	strain=NBRC 101100	GCA_001552375.1	76862	76862	type	True	79.5556	593	1330	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	79.4678	600	1330	95	below_threshold
Cellulomonas fulva	strain=DKR-3	GCA_018531375.1	2835530	2835530	type	True	79.3687	560	1330	95	below_threshold
Cellulomonas flavigena	strain=DSM 20109	GCA_000092865.1	1711	1711	type	True	79.31	615	1330	95	below_threshold
Oerskovia turbata	strain=JCM3160	GCA_004121315.1	1713	1713	type	True	79.2648	536	1330	95	below_threshold
Oerskovia turbata	strain=NRRL B-8019	GCA_000718325.1	1713	1713	type	True	79.242	535	1330	95	below_threshold
Cellulomonas avistercoris	strain=Sa3CUA2	GCA_014836445.1	2762242	2762242	type	True	79.0441	604	1330	95	below_threshold
Cellulosimicrobium funkei	strain=NBRC 104118	GCA_001570825.1	264251	264251	suspected-type	True	79.0296	632	1330	95	below_threshold
Cellulosimicrobium marinum	strain=NBRC 110994	GCA_020551945.1	1638992	1638992	type	True	78.9551	553	1330	95	below_threshold
Cellulomonas marina	strain=CGMCC 4.6945	GCA_900111925.1	988821	988821	type	True	78.788	560	1330	95	below_threshold
Sanguibacter suarezii	strain=NBRC 16159	GCA_001552735.1	60921	60921	type	True	78.422	444	1330	95	below_threshold
Cellulomonas endophytica	strain=SYSUP0004	GCA_004123805.1	2494735	2494735	type	True	78.3886	568	1330	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:30:00,284] [INFO] DFAST Taxonomy check result was written to GCF_008364845.1_ASM836484v1_genomic.fna/tc_result.tsv
[2024-01-24 12:30:00,285] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:30:00,285] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:30:00,285] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbbd7a7e9-eab4-4c90-9f95-1e9c6063b8e7/dqc_reference/checkm_data
[2024-01-24 12:30:00,287] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:30:00,332] [INFO] Task started: CheckM
[2024-01-24 12:30:00,332] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008364845.1_ASM836484v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008364845.1_ASM836484v1_genomic.fna/checkm_input GCF_008364845.1_ASM836484v1_genomic.fna/checkm_result
[2024-01-24 12:31:06,593] [INFO] Task succeeded: CheckM
[2024-01-24 12:31:06,595] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:31:06,616] [INFO] ===== Completeness check finished =====
[2024-01-24 12:31:06,616] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:31:06,617] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008364845.1_ASM836484v1_genomic.fna/markers.fasta)
[2024-01-24 12:31:06,617] [INFO] Task started: Blastn
[2024-01-24 12:31:06,617] [INFO] Running command: blastn -query GCF_008364845.1_ASM836484v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbbd7a7e9-eab4-4c90-9f95-1e9c6063b8e7/dqc_reference/reference_markers_gtdb.fasta -out GCF_008364845.1_ASM836484v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:08,599] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:08,603] [INFO] Selected 14 target genomes.
[2024-01-24 12:31:08,604] [INFO] Target genome list was writen to GCF_008364845.1_ASM836484v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:31:08,615] [INFO] Task started: fastANI
[2024-01-24 12:31:08,615] [INFO] Running command: fastANI --query /var/lib/cwl/stg0e21c218-5cb5-4e9f-9bba-fa5c001bc1c2/GCF_008364845.1_ASM836484v1_genomic.fna.gz --refList GCF_008364845.1_ASM836484v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008364845.1_ASM836484v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:31:21,198] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:21,218] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:31:21,218] [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_008364845.1	s__Actinotalea sp008364845	100.0	1328	1330	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_016464425.1	s__Actinotalea solisilvae	82.0231	813	1330	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	81.5539	723	1330	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Actinotalea	95.0	99.62	99.62	0.98	0.98	2	-
GCF_009996735.1	s__Actinotalea sp009996735	81.096	734	1330	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Actinotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014636275.1	s__Actinotalea carbonis	81.0794	725	1330	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Actinotalea	95.0	100.00	100.00	0.97	0.97	2	-
GCF_000526515.1	s__Actinotalea sp000526515	80.862	734	1330	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Actinotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017565425.1	s__Actinotalea sp017565425	80.4846	638	1330	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Actinotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012514545.1	s__Actinotalea sp012514545	80.1368	471	1330	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Actinotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006538745.1	s__Cellulomonas cellasea	80.067	681	1330	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	97.79	95.59	0.95	0.91	3	-
GCF_001552375.1	s__Cellulomonas iranensis	79.5826	590	1330	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	98.21	97.89	0.91	0.88	6	-
GCF_000092865.1	s__Cellulomonas flavigena	79.3351	613	1330	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001462455.1	s__Cellulomonas sp001462455	79.3224	614	1330	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005937995.2	s__Oerskovia sp005937995	79.0579	551	1330	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Oerskovia	95.0	96.13	96.13	0.91	0.91	2	-
GCF_018388465.1	s__Cellulomonas sp018388465	79.0089	560	1330	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	99.65	99.29	0.98	0.97	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:31:21,223] [INFO] GTDB search result was written to GCF_008364845.1_ASM836484v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:31:21,224] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:31:21,228] [INFO] DFAST_QC result json was written to GCF_008364845.1_ASM836484v1_genomic.fna/dqc_result.json
[2024-01-24 12:31:21,228] [INFO] DFAST_QC completed!
[2024-01-24 12:31:21,229] [INFO] Total running time: 0h1m53s