[2024-01-24 11:21:07,406] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:21:07,408] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:21:07,408] [INFO] DQC Reference Directory: /var/lib/cwl/stg7b267434-5a14-4487-b43b-9f6fb16a8780/dqc_reference
[2024-01-24 11:21:11,964] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:21:11,965] [INFO] Task started: Prodigal
[2024-01-24 11:21:11,965] [INFO] Running command: gunzip -c /var/lib/cwl/stg8a25a810-2769-4e55-8203-bc311bcccb9f/GCF_007989825.1_ASM798982v1_genomic.fna.gz | prodigal -d GCF_007989825.1_ASM798982v1_genomic.fna/cds.fna -a GCF_007989825.1_ASM798982v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:21:21,815] [INFO] Task succeeded: Prodigal
[2024-01-24 11:21:21,815] [INFO] Task started: HMMsearch
[2024-01-24 11:21:21,816] [INFO] Running command: hmmsearch --tblout GCF_007989825.1_ASM798982v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7b267434-5a14-4487-b43b-9f6fb16a8780/dqc_reference/reference_markers.hmm GCF_007989825.1_ASM798982v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:21:22,062] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:21:22,064] [INFO] Found 6/6 markers.
[2024-01-24 11:21:22,099] [INFO] Query marker FASTA was written to GCF_007989825.1_ASM798982v1_genomic.fna/markers.fasta
[2024-01-24 11:21:22,099] [INFO] Task started: Blastn
[2024-01-24 11:21:22,099] [INFO] Running command: blastn -query GCF_007989825.1_ASM798982v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7b267434-5a14-4487-b43b-9f6fb16a8780/dqc_reference/reference_markers.fasta -out GCF_007989825.1_ASM798982v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:21:23,329] [INFO] Task succeeded: Blastn
[2024-01-24 11:21:23,333] [INFO] Selected 13 target genomes.
[2024-01-24 11:21:23,333] [INFO] Target genome list was writen to GCF_007989825.1_ASM798982v1_genomic.fna/target_genomes.txt
[2024-01-24 11:21:23,352] [INFO] Task started: fastANI
[2024-01-24 11:21:23,352] [INFO] Running command: fastANI --query /var/lib/cwl/stg8a25a810-2769-4e55-8203-bc311bcccb9f/GCF_007989825.1_ASM798982v1_genomic.fna.gz --refList GCF_007989825.1_ASM798982v1_genomic.fna/target_genomes.txt --output GCF_007989825.1_ASM798982v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:21:37,121] [INFO] Task succeeded: fastANI
[2024-01-24 11:21:37,122] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7b267434-5a14-4487-b43b-9f6fb16a8780/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:21:37,122] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7b267434-5a14-4487-b43b-9f6fb16a8780/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:21:37,133] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:21:37,134] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:21:37,134] [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 persica	strain=NBRC 101101	GCA_007989825.1	76861	76861	type	True	100.0	1196	1198	95	conclusive
Cellulomonas gelida	strain=NBRC 3748	GCA_006538725.1	1712	1712	type	True	88.5503	1032	1198	95	below_threshold
Cellulomonas gelida	strain=JCM 1490	GCA_014647015.1	1712	1712	type	True	88.4343	1080	1198	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	86.1083	972	1198	95	below_threshold
Cellulomonas uda	strain=NBRC 3747	GCA_006538705.1	1714	1714	type	True	85.6011	884	1198	95	below_threshold
Cellulomonas gilvus	strain=ATCC 13127	GCA_000218545.1	11	11	type	True	84.0077	851	1198	95	below_threshold
Cellulomonas fulva	strain=DKR-3	GCA_018531375.1	2835530	2835530	type	True	83.8823	868	1198	95	below_threshold
Cellulomonas rhizosphaerae	strain=NEAU-TCZ24	GCA_003470205.1	2293719	2293719	type	True	82.2186	675	1198	95	below_threshold
Cellulomonas biazotea	strain=NBRC12680	GCA_004306155.1	1709	1709	type	True	82.0231	684	1198	95	below_threshold
Cellulomonas massiliensis	strain=JC225	GCA_000312005.1	1465811	1465811	type	True	81.4962	742	1198	95	below_threshold
Cellulomonas avistercoris	strain=Sa3CUA2	GCA_014836445.1	2762242	2762242	type	True	80.7864	745	1198	95	below_threshold
Actinotalea solisilvae	strain=KACC 19191	GCA_016464425.1	2072922	2072922	type	True	79.5172	656	1198	95	below_threshold
Actinotalea subterranea	strain=HO-Ch2	GCA_008364845.1	2607497	2607497	type	True	79.3211	602	1198	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:21:37,135] [INFO] DFAST Taxonomy check result was written to GCF_007989825.1_ASM798982v1_genomic.fna/tc_result.tsv
[2024-01-24 11:21:37,136] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:21:37,136] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:21:37,136] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7b267434-5a14-4487-b43b-9f6fb16a8780/dqc_reference/checkm_data
[2024-01-24 11:21:37,137] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:21:37,172] [INFO] Task started: CheckM
[2024-01-24 11:21:37,173] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007989825.1_ASM798982v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007989825.1_ASM798982v1_genomic.fna/checkm_input GCF_007989825.1_ASM798982v1_genomic.fna/checkm_result
[2024-01-24 11:22:30,751] [INFO] Task succeeded: CheckM
[2024-01-24 11:22:30,753] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:22:30,770] [INFO] ===== Completeness check finished =====
[2024-01-24 11:22:30,770] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:22:30,771] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007989825.1_ASM798982v1_genomic.fna/markers.fasta)
[2024-01-24 11:22:30,771] [INFO] Task started: Blastn
[2024-01-24 11:22:30,771] [INFO] Running command: blastn -query GCF_007989825.1_ASM798982v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7b267434-5a14-4487-b43b-9f6fb16a8780/dqc_reference/reference_markers_gtdb.fasta -out GCF_007989825.1_ASM798982v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:22:32,809] [INFO] Task succeeded: Blastn
[2024-01-24 11:22:32,812] [INFO] Selected 10 target genomes.
[2024-01-24 11:22:32,813] [INFO] Target genome list was writen to GCF_007989825.1_ASM798982v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:22:32,820] [INFO] Task started: fastANI
[2024-01-24 11:22:32,820] [INFO] Running command: fastANI --query /var/lib/cwl/stg8a25a810-2769-4e55-8203-bc311bcccb9f/GCF_007989825.1_ASM798982v1_genomic.fna.gz --refList GCF_007989825.1_ASM798982v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007989825.1_ASM798982v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:22:42,514] [INFO] Task succeeded: fastANI
[2024-01-24 11:22:42,530] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:22:42,530] [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_007989825.1	s__Cellulomonas persica	100.0	1196	1198	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_006538725.1	s__Cellulomonas gelida	88.5391	1033	1198	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	99.61	99.23	0.96	0.91	3	-
GCF_006538705.1	s__Cellulomonas uda	85.5945	885	1198	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	98.69	98.01	0.94	0.90	4	-
GCF_000218545.1	s__Cellulomonas gilvus	83.9865	853	1198	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	83.8906	867	1198	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	83.1919	787	1198	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012396155.1	s__Cellulomonas septica	82.2718	506	1198	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	81.9521	690	1198	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	81.4802	744	1198	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	99.99	99.99	0.99	0.99	2	-
GCF_006715865.1	s__Cellulomonas sp006715865	80.6463	736	1198	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 11:22:42,531] [INFO] GTDB search result was written to GCF_007989825.1_ASM798982v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:22:42,532] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:22:42,535] [INFO] DFAST_QC result json was written to GCF_007989825.1_ASM798982v1_genomic.fna/dqc_result.json
[2024-01-24 11:22:42,536] [INFO] DFAST_QC completed!
[2024-01-24 11:22:42,536] [INFO] Total running time: 0h1m35s