[2024-01-25 17:34:07,125] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:34:07,128] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:34:07,128] [INFO] DQC Reference Directory: /var/lib/cwl/stgd7ad2e6a-2846-490a-8732-c361213ea637/dqc_reference
[2024-01-25 17:34:08,954] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:34:08,956] [INFO] Task started: Prodigal
[2024-01-25 17:34:08,956] [INFO] Running command: gunzip -c /var/lib/cwl/stge2f0e265-419f-494d-a1e3-f4f3ac67ed8a/GCF_017876575.1_ASM1787657v1_genomic.fna.gz | prodigal -d GCF_017876575.1_ASM1787657v1_genomic.fna/cds.fna -a GCF_017876575.1_ASM1787657v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:34:23,421] [INFO] Task succeeded: Prodigal
[2024-01-25 17:34:23,422] [INFO] Task started: HMMsearch
[2024-01-25 17:34:23,422] [INFO] Running command: hmmsearch --tblout GCF_017876575.1_ASM1787657v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd7ad2e6a-2846-490a-8732-c361213ea637/dqc_reference/reference_markers.hmm GCF_017876575.1_ASM1787657v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:34:23,776] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:34:23,777] [INFO] Found 6/6 markers.
[2024-01-25 17:34:23,815] [INFO] Query marker FASTA was written to GCF_017876575.1_ASM1787657v1_genomic.fna/markers.fasta
[2024-01-25 17:34:23,816] [INFO] Task started: Blastn
[2024-01-25 17:34:23,816] [INFO] Running command: blastn -query GCF_017876575.1_ASM1787657v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd7ad2e6a-2846-490a-8732-c361213ea637/dqc_reference/reference_markers.fasta -out GCF_017876575.1_ASM1787657v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:34:25,003] [INFO] Task succeeded: Blastn
[2024-01-25 17:34:25,007] [INFO] Selected 13 target genomes.
[2024-01-25 17:34:25,007] [INFO] Target genome list was writen to GCF_017876575.1_ASM1787657v1_genomic.fna/target_genomes.txt
[2024-01-25 17:34:25,012] [INFO] Task started: fastANI
[2024-01-25 17:34:25,012] [INFO] Running command: fastANI --query /var/lib/cwl/stge2f0e265-419f-494d-a1e3-f4f3ac67ed8a/GCF_017876575.1_ASM1787657v1_genomic.fna.gz --refList GCF_017876575.1_ASM1787657v1_genomic.fna/target_genomes.txt --output GCF_017876575.1_ASM1787657v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:34:36,220] [INFO] Task succeeded: fastANI
[2024-01-25 17:34:36,221] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd7ad2e6a-2846-490a-8732-c361213ea637/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:34:36,221] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd7ad2e6a-2846-490a-8732-c361213ea637/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:34:36,230] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:34:36,230] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:34:36,230] [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
Paeniglutamicibacter psychrophenolicus	strain=DSM 15454	GCA_017876575.1	257454	257454	type	True	100.0	1634	1634	95	conclusive
Paeniglutamicibacter gangotriensis	strain=Lz1y	GCA_000348945.1	254787	254787	type	True	84.2551	954	1634	95	below_threshold
Paeniglutamicibacter kerguelensis	strain=DSM 15797	GCA_017876535.1	254788	254788	type	True	83.4707	927	1634	95	below_threshold
Paeniglutamicibacter terrestris	strain=ANT13_2	GCA_012271785.1	2723403	2723403	type	True	81.9793	852	1634	95	below_threshold
Paeniglutamicibacter cryotolerans	strain=DSM 22826	GCA_014190875.1	670079	670079	type	True	80.8583	663	1634	95	below_threshold
Glutamicibacter protophormiae	strain=JCM 1973	GCA_014647495.1	37930	37930	type	True	80.0996	551	1634	95	below_threshold
Zhihengliuella salsuginis	strain=KCTC 19466	GCA_014651715.1	578222	578222	type	True	79.0203	427	1634	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_018622995.1	2817475	2817475	type	True	78.9259	351	1634	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_017898065.1	2817475	2817475	type	True	78.6767	338	1634	95	below_threshold
Arthrobacter mobilis	strain=E918	GCA_012395835.1	2724944	2724944	type	True	78.621	460	1634	95	below_threshold
Arthrobacter sunyaminii	strain=zg-ZUI122	GCA_018866305.1	2816859	2816859	type	True	78.3763	307	1634	95	below_threshold
Arthrobacter sunyaminii	strain=zg-ZUI122	GCA_017353495.1	2816859	2816859	type	True	78.1447	305	1634	95	below_threshold
Citricoccus zhacaiensis	strain=CGMCC 1.7064	GCA_014645315.1	489142	489142	type	True	77.7627	317	1634	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:34:36,231] [INFO] DFAST Taxonomy check result was written to GCF_017876575.1_ASM1787657v1_genomic.fna/tc_result.tsv
[2024-01-25 17:34:36,232] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:34:36,232] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:34:36,232] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd7ad2e6a-2846-490a-8732-c361213ea637/dqc_reference/checkm_data
[2024-01-25 17:34:36,233] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:34:36,280] [INFO] Task started: CheckM
[2024-01-25 17:34:36,280] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017876575.1_ASM1787657v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017876575.1_ASM1787657v1_genomic.fna/checkm_input GCF_017876575.1_ASM1787657v1_genomic.fna/checkm_result
[2024-01-25 17:35:30,538] [INFO] Task succeeded: CheckM
[2024-01-25 17:35:30,539] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:35:30,555] [INFO] ===== Completeness check finished =====
[2024-01-25 17:35:30,555] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:35:30,556] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017876575.1_ASM1787657v1_genomic.fna/markers.fasta)
[2024-01-25 17:35:30,556] [INFO] Task started: Blastn
[2024-01-25 17:35:30,556] [INFO] Running command: blastn -query GCF_017876575.1_ASM1787657v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd7ad2e6a-2846-490a-8732-c361213ea637/dqc_reference/reference_markers_gtdb.fasta -out GCF_017876575.1_ASM1787657v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:35:32,524] [INFO] Task succeeded: Blastn
[2024-01-25 17:35:32,527] [INFO] Selected 8 target genomes.
[2024-01-25 17:35:32,527] [INFO] Target genome list was writen to GCF_017876575.1_ASM1787657v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:35:32,532] [INFO] Task started: fastANI
[2024-01-25 17:35:32,532] [INFO] Running command: fastANI --query /var/lib/cwl/stge2f0e265-419f-494d-a1e3-f4f3ac67ed8a/GCF_017876575.1_ASM1787657v1_genomic.fna.gz --refList GCF_017876575.1_ASM1787657v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017876575.1_ASM1787657v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:35:41,736] [INFO] Task succeeded: fastANI
[2024-01-25 17:35:41,742] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:35:41,743] [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_017876575.1	s__Paeniglutamicibacter psychrophenolicus	100.0	1634	1634	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Paeniglutamicibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003287975.1	s__Paeniglutamicibacter sp003287975	93.6817	1246	1634	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Paeniglutamicibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001863355.1	s__Paeniglutamicibacter sp001863355	92.1906	1253	1634	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Paeniglutamicibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019084045.1	s__Paeniglutamicibacter sp019084045	86.47	1079	1634	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Paeniglutamicibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000348945.1	s__Paeniglutamicibacter gangotriensis	84.2508	955	1634	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Paeniglutamicibacter	95.0	97.63	97.63	0.86	0.86	2	-
GCF_017876535.1	s__Paeniglutamicibacter kerguelensis	83.4933	928	1634	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Paeniglutamicibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017876735.1	s__Paeniglutamicibacter antarcticus	83.0295	878	1634	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Paeniglutamicibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012271785.1	s__Paeniglutamicibacter terrestris	81.9733	853	1634	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Paeniglutamicibacter	95.0	98.96	98.96	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2024-01-25 17:35:41,745] [INFO] GTDB search result was written to GCF_017876575.1_ASM1787657v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:35:41,745] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:35:41,748] [INFO] DFAST_QC result json was written to GCF_017876575.1_ASM1787657v1_genomic.fna/dqc_result.json
[2024-01-25 17:35:41,748] [INFO] DFAST_QC completed!
[2024-01-25 17:35:41,748] [INFO] Total running time: 0h1m35s