[2024-01-24 12:34:20,419] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:34:20,421] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:34:20,421] [INFO] DQC Reference Directory: /var/lib/cwl/stg81c8b047-f6bf-4af4-8670-a6bb80011158/dqc_reference
[2024-01-24 12:34:21,636] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:34:21,637] [INFO] Task started: Prodigal
[2024-01-24 12:34:21,637] [INFO] Running command: gunzip -c /var/lib/cwl/stg3829d295-4dcb-413c-b155-c2a68c9253ff/GCF_011759685.1_ASM1175968v1_genomic.fna.gz | prodigal -d GCF_011759685.1_ASM1175968v1_genomic.fna/cds.fna -a GCF_011759685.1_ASM1175968v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:34:31,513] [INFO] Task succeeded: Prodigal
[2024-01-24 12:34:31,514] [INFO] Task started: HMMsearch
[2024-01-24 12:34:31,514] [INFO] Running command: hmmsearch --tblout GCF_011759685.1_ASM1175968v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg81c8b047-f6bf-4af4-8670-a6bb80011158/dqc_reference/reference_markers.hmm GCF_011759685.1_ASM1175968v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:34:31,757] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:34:31,758] [INFO] Found 6/6 markers.
[2024-01-24 12:34:31,791] [INFO] Query marker FASTA was written to GCF_011759685.1_ASM1175968v1_genomic.fna/markers.fasta
[2024-01-24 12:34:31,792] [INFO] Task started: Blastn
[2024-01-24 12:34:31,792] [INFO] Running command: blastn -query GCF_011759685.1_ASM1175968v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg81c8b047-f6bf-4af4-8670-a6bb80011158/dqc_reference/reference_markers.fasta -out GCF_011759685.1_ASM1175968v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:34:33,066] [INFO] Task succeeded: Blastn
[2024-01-24 12:34:33,070] [INFO] Selected 13 target genomes.
[2024-01-24 12:34:33,071] [INFO] Target genome list was writen to GCF_011759685.1_ASM1175968v1_genomic.fna/target_genomes.txt
[2024-01-24 12:34:33,077] [INFO] Task started: fastANI
[2024-01-24 12:34:33,077] [INFO] Running command: fastANI --query /var/lib/cwl/stg3829d295-4dcb-413c-b155-c2a68c9253ff/GCF_011759685.1_ASM1175968v1_genomic.fna.gz --refList GCF_011759685.1_ASM1175968v1_genomic.fna/target_genomes.txt --output GCF_011759685.1_ASM1175968v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:34:46,238] [INFO] Task succeeded: fastANI
[2024-01-24 12:34:46,238] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg81c8b047-f6bf-4af4-8670-a6bb80011158/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:34:46,239] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg81c8b047-f6bf-4af4-8670-a6bb80011158/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:34:46,251] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:34:46,251] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:34:46,251] [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 uda	strain=NBRC 3747	GCA_006538705.1	1714	1714	type	True	99.9542	1125	1185	95	conclusive
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	90.5803	1030	1185	95	below_threshold
Cellulomonas persica	strain=NBRC 101101	GCA_007989825.1	76861	76861	type	True	85.7978	909	1185	95	below_threshold
Cellulomonas gelida	strain=NBRC 3748	GCA_006538725.1	1712	1712	type	True	85.5692	914	1185	95	below_threshold
Cellulomonas gelida	strain=JCM 1490	GCA_014647015.1	1712	1712	type	True	85.5088	944	1185	95	below_threshold
Cellulomonas gilvus	strain=ATCC 13127	GCA_000218545.1	11	11	type	True	84.1668	818	1185	95	below_threshold
Cellulomonas fulva	strain=DKR-3	GCA_018531375.1	2835530	2835530	type	True	83.8557	836	1185	95	below_threshold
Cellulomonas biazotea	strain=NBRC12680	GCA_004306155.1	1709	1709	type	True	82.1552	667	1185	95	below_threshold
Cellulomonas soli	strain=DSM 24484	GCA_013409305.1	931535	931535	type	True	81.0772	671	1185	95	below_threshold
Cellulomonas avistercoris	strain=Sa3CUA2	GCA_014836445.1	2762242	2762242	type	True	80.9026	720	1185	95	below_threshold
Cellulomonas xylanilytica	strain=NBRC 101102	GCA_007989805.1	233583	233583	type	True	80.8504	715	1185	95	below_threshold
Actinotalea solisilvae	strain=KACC 19191	GCA_016464425.1	2072922	2072922	type	True	79.5243	654	1185	95	below_threshold
Oerskovia rustica	strain=Sa4CUA1	GCA_014836555.1	2762237	2762237	type	True	79.3662	562	1185	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:34:46,253] [INFO] DFAST Taxonomy check result was written to GCF_011759685.1_ASM1175968v1_genomic.fna/tc_result.tsv
[2024-01-24 12:34:46,254] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:34:46,255] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:34:46,255] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg81c8b047-f6bf-4af4-8670-a6bb80011158/dqc_reference/checkm_data
[2024-01-24 12:34:46,256] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:34:46,292] [INFO] Task started: CheckM
[2024-01-24 12:34:46,293] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_011759685.1_ASM1175968v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_011759685.1_ASM1175968v1_genomic.fna/checkm_input GCF_011759685.1_ASM1175968v1_genomic.fna/checkm_result
[2024-01-24 12:35:42,278] [INFO] Task succeeded: CheckM
[2024-01-24 12:35:42,279] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:35:42,302] [INFO] ===== Completeness check finished =====
[2024-01-24 12:35:42,302] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:35:42,303] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_011759685.1_ASM1175968v1_genomic.fna/markers.fasta)
[2024-01-24 12:35:42,303] [INFO] Task started: Blastn
[2024-01-24 12:35:42,303] [INFO] Running command: blastn -query GCF_011759685.1_ASM1175968v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg81c8b047-f6bf-4af4-8670-a6bb80011158/dqc_reference/reference_markers_gtdb.fasta -out GCF_011759685.1_ASM1175968v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:35:44,376] [INFO] Task succeeded: Blastn
[2024-01-24 12:35:44,381] [INFO] Selected 9 target genomes.
[2024-01-24 12:35:44,381] [INFO] Target genome list was writen to GCF_011759685.1_ASM1175968v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:35:44,389] [INFO] Task started: fastANI
[2024-01-24 12:35:44,390] [INFO] Running command: fastANI --query /var/lib/cwl/stg3829d295-4dcb-413c-b155-c2a68c9253ff/GCF_011759685.1_ASM1175968v1_genomic.fna.gz --refList GCF_011759685.1_ASM1175968v1_genomic.fna/target_genomes_gtdb.txt --output GCF_011759685.1_ASM1175968v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:35:53,281] [INFO] Task succeeded: fastANI
[2024-01-24 12:35:53,296] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:35:53,296] [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_006538705.1	s__Cellulomonas uda	99.9542	1125	1185	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	98.69	98.01	0.94	0.90	4	conclusive
GCF_007989825.1	s__Cellulomonas persica	85.8106	908	1185	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006538725.1	s__Cellulomonas gelida	85.5943	911	1185	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	99.61	99.23	0.96	0.91	3	-
GCF_000218545.1	s__Cellulomonas gilvus	84.1463	820	1185	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018531375.1	s__Cellulomonas sp018531375	83.8924	832	1185	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007990245.1	s__Cellulomonas composti	83.1162	777	1185	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000708885.1	s__Cellulomonas sp000708885	82.3929	658	1185	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004306155.1	s__Cellulomonas biazotea	82.108	672	1185	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	80.9583	693	1185	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 12:35:53,297] [INFO] GTDB search result was written to GCF_011759685.1_ASM1175968v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:35:53,298] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:35:53,303] [INFO] DFAST_QC result json was written to GCF_011759685.1_ASM1175968v1_genomic.fna/dqc_result.json
[2024-01-24 12:35:53,303] [INFO] DFAST_QC completed!
[2024-01-24 12:35:53,303] [INFO] Total running time: 0h1m33s