[2024-01-24 14:19:32,033] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:32,040] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:32,041] [INFO] DQC Reference Directory: /var/lib/cwl/stgd61a89cc-d3dd-4766-a80f-2be4d0b1fba4/dqc_reference
[2024-01-24 14:19:33,435] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:33,436] [INFO] Task started: Prodigal
[2024-01-24 14:19:33,436] [INFO] Running command: gunzip -c /var/lib/cwl/stgd3770ad8-e6bf-48bd-9b14-c556b253b9a2/GCF_007992535.1_ASM799253v1_genomic.fna.gz | prodigal -d GCF_007992535.1_ASM799253v1_genomic.fna/cds.fna -a GCF_007992535.1_ASM799253v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:19:46,322] [INFO] Task succeeded: Prodigal
[2024-01-24 14:19:46,323] [INFO] Task started: HMMsearch
[2024-01-24 14:19:46,323] [INFO] Running command: hmmsearch --tblout GCF_007992535.1_ASM799253v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd61a89cc-d3dd-4766-a80f-2be4d0b1fba4/dqc_reference/reference_markers.hmm GCF_007992535.1_ASM799253v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:19:46,703] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:19:46,704] [INFO] Found 6/6 markers.
[2024-01-24 14:19:46,751] [INFO] Query marker FASTA was written to GCF_007992535.1_ASM799253v1_genomic.fna/markers.fasta
[2024-01-24 14:19:46,752] [INFO] Task started: Blastn
[2024-01-24 14:19:46,752] [INFO] Running command: blastn -query GCF_007992535.1_ASM799253v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd61a89cc-d3dd-4766-a80f-2be4d0b1fba4/dqc_reference/reference_markers.fasta -out GCF_007992535.1_ASM799253v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:19:48,244] [INFO] Task succeeded: Blastn
[2024-01-24 14:19:48,247] [INFO] Selected 16 target genomes.
[2024-01-24 14:19:48,248] [INFO] Target genome list was writen to GCF_007992535.1_ASM799253v1_genomic.fna/target_genomes.txt
[2024-01-24 14:19:48,252] [INFO] Task started: fastANI
[2024-01-24 14:19:48,252] [INFO] Running command: fastANI --query /var/lib/cwl/stgd3770ad8-e6bf-48bd-9b14-c556b253b9a2/GCF_007992535.1_ASM799253v1_genomic.fna.gz --refList GCF_007992535.1_ASM799253v1_genomic.fna/target_genomes.txt --output GCF_007992535.1_ASM799253v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:20:04,037] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:04,037] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd61a89cc-d3dd-4766-a80f-2be4d0b1fba4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:20:04,037] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd61a89cc-d3dd-4766-a80f-2be4d0b1fba4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:20:04,050] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:20:04,051] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:20:04,051] [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 soli	strain=DSM 24484	GCA_013409305.1	931535	931535	type	True	99.9997	1395	1396	95	conclusive
Cellulomonas fimi	strain=ATCC 484	GCA_000212695.1	1708	1708	type	True	81.4824	780	1396	95	below_threshold
Cellulomonas biazotea	strain=NBRC12680	GCA_004306155.1	1709	1709	type	True	81.4813	688	1396	95	below_threshold
Cellulomonas fimi	strain=NCTC7547	GCA_900637695.1	1708	1708	type	True	81.3807	779	1396	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	81.2052	689	1396	95	below_threshold
Cellulomonas terrae	strain=NBRC 100819	GCA_007990265.1	311234	311234	type	True	81.1945	694	1396	95	below_threshold
Cellulomonas persica	strain=NBRC 101101	GCA_007989825.1	76861	76861	type	True	81.0643	668	1396	95	below_threshold
Cellulomonas uda	strain=NBRC 3747	GCA_006538705.1	1714	1714	type	True	81.0058	656	1396	95	below_threshold
Cellulomonas massiliensis	strain=JC225	GCA_000312005.1	1465811	1465811	type	True	80.8656	671	1396	95	below_threshold
Cellulomonas fulva	strain=DKR-3	GCA_018531375.1	2835530	2835530	type	True	80.7834	676	1396	95	below_threshold
Cellulomonas cellasea	strain=NBRC 3753	GCA_006538745.1	43670	43670	type	True	80.638	731	1396	95	below_threshold
Cellulomonas flavigena	strain=DSM 20109	GCA_000092865.1	1711	1711	type	True	80.6229	675	1396	95	below_threshold
Cellulomonas telluris	strain=CPCC 204705	GCA_004886325.1	2306636	2306636	type	True	80.5697	706	1396	95	below_threshold
Cellulomonas avistercoris	strain=Sa3CUA2	GCA_014836445.1	2762242	2762242	type	True	80.5155	678	1396	95	below_threshold
Actinotalea solisilvae	strain=KACC 19191	GCA_016464425.1	2072922	2072922	type	True	79.2901	645	1396	95	below_threshold
Oerskovia rustica	strain=Sa4CUA1	GCA_014836555.1	2762237	2762237	type	True	79.0554	543	1396	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:20:04,052] [INFO] DFAST Taxonomy check result was written to GCF_007992535.1_ASM799253v1_genomic.fna/tc_result.tsv
[2024-01-24 14:20:04,053] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:20:04,053] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:20:04,053] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd61a89cc-d3dd-4766-a80f-2be4d0b1fba4/dqc_reference/checkm_data
[2024-01-24 14:20:04,054] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:20:04,095] [INFO] Task started: CheckM
[2024-01-24 14:20:04,095] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007992535.1_ASM799253v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007992535.1_ASM799253v1_genomic.fna/checkm_input GCF_007992535.1_ASM799253v1_genomic.fna/checkm_result
[2024-01-24 14:21:16,146] [INFO] Task succeeded: CheckM
[2024-01-24 14:21:16,147] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:21:16,170] [INFO] ===== Completeness check finished =====
[2024-01-24 14:21:16,170] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:21:16,171] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007992535.1_ASM799253v1_genomic.fna/markers.fasta)
[2024-01-24 14:21:16,171] [INFO] Task started: Blastn
[2024-01-24 14:21:16,171] [INFO] Running command: blastn -query GCF_007992535.1_ASM799253v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd61a89cc-d3dd-4766-a80f-2be4d0b1fba4/dqc_reference/reference_markers_gtdb.fasta -out GCF_007992535.1_ASM799253v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:21:18,245] [INFO] Task succeeded: Blastn
[2024-01-24 14:21:18,248] [INFO] Selected 17 target genomes.
[2024-01-24 14:21:18,249] [INFO] Target genome list was writen to GCF_007992535.1_ASM799253v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:21:18,274] [INFO] Task started: fastANI
[2024-01-24 14:21:18,275] [INFO] Running command: fastANI --query /var/lib/cwl/stgd3770ad8-e6bf-48bd-9b14-c556b253b9a2/GCF_007992535.1_ASM799253v1_genomic.fna.gz --refList GCF_007992535.1_ASM799253v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007992535.1_ASM799253v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:21:34,445] [INFO] Task succeeded: fastANI
[2024-01-24 14:21:34,463] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:21:34,463] [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_013409305.1	s__Cellulomonas soli	99.9997	1395	1396	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_012396155.1	s__Cellulomonas septica	81.9734	471	1396	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003851725.1	s__Cellulomonas algicola	81.6209	658	1396	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	97.47	95.68	0.95	0.94	3	-
GCF_004306155.1	s__Cellulomonas biazotea	81.4889	689	1396	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000212695.1	s__Cellulomonas fimi	81.4327	786	1396	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	100.00	99.99	1.00	1.00	3	-
GCF_003470205.1	s__Cellulomonas rhizosphaerae	81.2852	632	1396	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862675.1	s__Cellulomonas chitinilytica	81.2672	762	1396	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003755175.1	s__Cellulomonas sp003755175	81.2062	707	1396	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007990265.1	s__Cellulomonas terrae	81.1985	694	1396	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	81.1478	715	1396	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001429255.1	s__Cellulomonas sp001429255	81.0991	749	1396	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	98.79	98.79	0.94	0.94	2	-
GCF_000708885.1	s__Cellulomonas sp000708885	81.0752	620	1396	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000312005.1	s__Cellulomonas massiliensis	80.8268	675	1396	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	99.99	99.99	0.99	0.99	2	-
GCF_009720485.1	s__Cellulomonas sp009720485	80.7481	688	1396	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005239125.1	s__Cellulomonas hominis_A	80.6608	631	1396	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862775.1	s__Cellulomonas phragmiteti	80.4812	666	1396	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014763765.1	s__Cellulomonas sp014763765	80.4109	612	1396	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 14:21:34,465] [INFO] GTDB search result was written to GCF_007992535.1_ASM799253v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:21:34,465] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:21:34,469] [INFO] DFAST_QC result json was written to GCF_007992535.1_ASM799253v1_genomic.fna/dqc_result.json
[2024-01-24 14:21:34,469] [INFO] DFAST_QC completed!
[2024-01-24 14:21:34,469] [INFO] Total running time: 0h2m2s