[2024-01-24 13:28:01,947] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:28:01,948] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:28:01,948] [INFO] DQC Reference Directory: /var/lib/cwl/stg46a330d0-a46c-4c48-a96d-fb7242026174/dqc_reference
[2024-01-24 13:28:03,249] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:28:03,255] [INFO] Task started: Prodigal
[2024-01-24 13:28:03,256] [INFO] Running command: gunzip -c /var/lib/cwl/stged35f117-0fa4-46ca-bf8d-1e07cb595f30/GCF_013376105.1_ASM1337610v1_genomic.fna.gz | prodigal -d GCF_013376105.1_ASM1337610v1_genomic.fna/cds.fna -a GCF_013376105.1_ASM1337610v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:17,115] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:17,115] [INFO] Task started: HMMsearch
[2024-01-24 13:28:17,115] [INFO] Running command: hmmsearch --tblout GCF_013376105.1_ASM1337610v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg46a330d0-a46c-4c48-a96d-fb7242026174/dqc_reference/reference_markers.hmm GCF_013376105.1_ASM1337610v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:17,382] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:17,383] [INFO] Found 6/6 markers.
[2024-01-24 13:28:17,423] [INFO] Query marker FASTA was written to GCF_013376105.1_ASM1337610v1_genomic.fna/markers.fasta
[2024-01-24 13:28:17,424] [INFO] Task started: Blastn
[2024-01-24 13:28:17,424] [INFO] Running command: blastn -query GCF_013376105.1_ASM1337610v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg46a330d0-a46c-4c48-a96d-fb7242026174/dqc_reference/reference_markers.fasta -out GCF_013376105.1_ASM1337610v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:18,529] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:18,534] [INFO] Selected 12 target genomes.
[2024-01-24 13:28:18,535] [INFO] Target genome list was writen to GCF_013376105.1_ASM1337610v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:18,544] [INFO] Task started: fastANI
[2024-01-24 13:28:18,544] [INFO] Running command: fastANI --query /var/lib/cwl/stged35f117-0fa4-46ca-bf8d-1e07cb595f30/GCF_013376105.1_ASM1337610v1_genomic.fna.gz --refList GCF_013376105.1_ASM1337610v1_genomic.fna/target_genomes.txt --output GCF_013376105.1_ASM1337610v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:29,102] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:29,103] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg46a330d0-a46c-4c48-a96d-fb7242026174/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:29,103] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg46a330d0-a46c-4c48-a96d-fb7242026174/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:29,114] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:28:29,114] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:28:29,115] [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
Arthrobacter wenxiniae	strain=AETb3-4	GCA_013376105.1	2713570	2713570	type	True	100.0	1395	1399	95	conclusive
Arthrobacter dokdonellae		GCA_003268655.1	2211210	2211210	type	True	87.048	1031	1399	95	below_threshold
Arthrobacter livingstonensis	strain=LI2	GCA_003219815.1	670078	670078	type	True	84.8149	1013	1399	95	below_threshold
Arthrobacter silviterrae	strain=DSM 27180	GCA_011045165.1	2026658	2026658	type	True	83.5091	884	1399	95	below_threshold
Arthrobacter stackebrandtii	strain=DSM 16005	GCA_017876675.1	272161	272161	type	True	82.0007	736	1399	95	below_threshold
Arthrobacter glacialis	strain=HLT2-12-2	GCA_002909445.1	1664	1664	type	True	80.4734	610	1399	95	below_threshold
Pseudarthrobacter enclensis	strain=NIO-1008	GCA_001457025.1	993070	993070	type	True	78.9848	472	1399	95	below_threshold
Pseudarthrobacter enclensis	strain=NIO-1008	GCA_900094675.1	993070	993070	type	True	78.9845	472	1399	95	below_threshold
Arthrobacter cryoconiti	strain=Cr6-08	GCA_020905375.1	748907	748907	type	True	78.6846	396	1399	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_018622995.1	2817475	2817475	type	True	78.6814	361	1399	95	below_threshold
Arthrobacter sedimenti	strain=MIC A30	GCA_011750795.2	2694931	2694931	type	True	78.6521	337	1399	95	below_threshold
Arthrobacter mobilis	strain=E918	GCA_012395835.1	2724944	2724944	type	True	78.5886	419	1399	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:29,116] [INFO] DFAST Taxonomy check result was written to GCF_013376105.1_ASM1337610v1_genomic.fna/tc_result.tsv
[2024-01-24 13:28:29,117] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:29,117] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:29,117] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg46a330d0-a46c-4c48-a96d-fb7242026174/dqc_reference/checkm_data
[2024-01-24 13:28:29,119] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:29,162] [INFO] Task started: CheckM
[2024-01-24 13:28:29,162] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013376105.1_ASM1337610v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013376105.1_ASM1337610v1_genomic.fna/checkm_input GCF_013376105.1_ASM1337610v1_genomic.fna/checkm_result
[2024-01-24 13:29:12,597] [INFO] Task succeeded: CheckM
[2024-01-24 13:29:12,598] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:29:12,620] [INFO] ===== Completeness check finished =====
[2024-01-24 13:29:12,620] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:29:12,621] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013376105.1_ASM1337610v1_genomic.fna/markers.fasta)
[2024-01-24 13:29:12,621] [INFO] Task started: Blastn
[2024-01-24 13:29:12,621] [INFO] Running command: blastn -query GCF_013376105.1_ASM1337610v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg46a330d0-a46c-4c48-a96d-fb7242026174/dqc_reference/reference_markers_gtdb.fasta -out GCF_013376105.1_ASM1337610v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:29:14,190] [INFO] Task succeeded: Blastn
[2024-01-24 13:29:14,195] [INFO] Selected 10 target genomes.
[2024-01-24 13:29:14,195] [INFO] Target genome list was writen to GCF_013376105.1_ASM1337610v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:29:14,203] [INFO] Task started: fastANI
[2024-01-24 13:29:14,203] [INFO] Running command: fastANI --query /var/lib/cwl/stged35f117-0fa4-46ca-bf8d-1e07cb595f30/GCF_013376105.1_ASM1337610v1_genomic.fna.gz --refList GCF_013376105.1_ASM1337610v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013376105.1_ASM1337610v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:29:23,825] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:23,834] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:29:23,834] [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_013376105.1	s__Specibacter sp013376105	100.0	1395	1399	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Specibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003268655.1	s__Specibacter dokdonellae	87.0357	1032	1399	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Specibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013376095.1	s__Specibacter sp013376095	85.8769	934	1399	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Specibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003219815.1	s__Specibacter livingstonensis	84.7945	1015	1399	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Specibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011045165.1	s__Specibacter silviterrae	83.5014	885	1399	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Specibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001281315.1	s__Specibacter sp001281315	82.9042	829	1399	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Specibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017876675.1	s__Specibacter stackebrandtii	82.0074	735	1399	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Specibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002929305.1	s__Specibacter sp002929305	80.7774	627	1399	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Specibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000482545.1	s__Specibacter sp000482545	80.7405	631	1399	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Specibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003946885.1	s__Specibacter cremeus	80.7141	699	1399	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Specibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:29:23,836] [INFO] GTDB search result was written to GCF_013376105.1_ASM1337610v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:29:23,836] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:29:23,844] [INFO] DFAST_QC result json was written to GCF_013376105.1_ASM1337610v1_genomic.fna/dqc_result.json
[2024-01-24 13:29:23,844] [INFO] DFAST_QC completed!
[2024-01-24 13:29:23,844] [INFO] Total running time: 0h1m22s