[2024-01-24 11:27:04,740] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:27:04,742] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:27:04,743] [INFO] DQC Reference Directory: /var/lib/cwl/stgfdd4c840-6e82-4452-bd3a-f5397279b507/dqc_reference
[2024-01-24 11:27:05,922] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:27:05,923] [INFO] Task started: Prodigal
[2024-01-24 11:27:05,923] [INFO] Running command: gunzip -c /var/lib/cwl/stg7ff6acca-5813-4bd3-8eeb-a23aa32a2465/GCF_017368795.1_ASM1736879v1_genomic.fna.gz | prodigal -d GCF_017368795.1_ASM1736879v1_genomic.fna/cds.fna -a GCF_017368795.1_ASM1736879v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:27:18,228] [INFO] Task succeeded: Prodigal
[2024-01-24 11:27:18,229] [INFO] Task started: HMMsearch
[2024-01-24 11:27:18,229] [INFO] Running command: hmmsearch --tblout GCF_017368795.1_ASM1736879v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfdd4c840-6e82-4452-bd3a-f5397279b507/dqc_reference/reference_markers.hmm GCF_017368795.1_ASM1736879v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:27:18,471] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:27:18,472] [INFO] Found 6/6 markers.
[2024-01-24 11:27:18,508] [INFO] Query marker FASTA was written to GCF_017368795.1_ASM1736879v1_genomic.fna/markers.fasta
[2024-01-24 11:27:18,508] [INFO] Task started: Blastn
[2024-01-24 11:27:18,508] [INFO] Running command: blastn -query GCF_017368795.1_ASM1736879v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfdd4c840-6e82-4452-bd3a-f5397279b507/dqc_reference/reference_markers.fasta -out GCF_017368795.1_ASM1736879v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:19,608] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:19,611] [INFO] Selected 18 target genomes.
[2024-01-24 11:27:19,612] [INFO] Target genome list was writen to GCF_017368795.1_ASM1736879v1_genomic.fna/target_genomes.txt
[2024-01-24 11:27:19,622] [INFO] Task started: fastANI
[2024-01-24 11:27:19,622] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ff6acca-5813-4bd3-8eeb-a23aa32a2465/GCF_017368795.1_ASM1736879v1_genomic.fna.gz --refList GCF_017368795.1_ASM1736879v1_genomic.fna/target_genomes.txt --output GCF_017368795.1_ASM1736879v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:27:33,404] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:33,405] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfdd4c840-6e82-4452-bd3a-f5397279b507/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:27:33,405] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfdd4c840-6e82-4452-bd3a-f5397279b507/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:27:33,430] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:27:33,431] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:27:33,431] [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 celericrescens	strain=NEAU-SA2	GCA_003614925.1	2320851	2320851	type	True	82.5737	770	1299	95	below_threshold
Arthrobacter cupressi	strain=DSM 24664	GCA_013409905.1	1045773	1045773	type	True	82.4845	785	1299	95	below_threshold
Arthrobacter cupressi	strain=CGMCC 1.10783	GCA_900099975.1	1045773	1045773	type	True	82.4823	768	1299	95	below_threshold
Arthrobacter silvisoli	strain=NEAU-SA1	GCA_003369445.1	2291022	2291022	type	True	82.3311	766	1299	95	below_threshold
Paenarthrobacter nicotinovorans	strain=JCM 3874	GCA_014648735.1	29320	29320	suspected-type	True	82.1494	715	1299	95	below_threshold
Paenarthrobacter nicotinovorans	strain=ATCC 49919	GCA_021919345.1	29320	29320	suspected-type	True	82.1192	726	1299	95	below_threshold
Paenarthrobacter nicotinovorans	strain=DSM 420	GCA_017876445.1	29320	29320	suspected-type	True	82.0927	743	1299	95	below_threshold
Paenarthrobacter histidinolovorans	strain=JCM 2520	GCA_014647595.1	43664	43664	type	True	81.9597	737	1299	95	below_threshold
Arthrobacter ipis	strain=IA7	GCA_014694315.1	2716202	2716202	type	True	81.5747	660	1299	95	below_threshold
Paenarthrobacter aurescens	strain=NBRC 12136	GCA_006538985.1	43663	43663	type	True	81.5183	675	1299	95	below_threshold
Arthrobacter pascens	strain=DSM 20545	GCA_017052465.1	1677	1677	type	True	81.4638	656	1299	95	below_threshold
Pseudarthrobacter enclensis	strain=NIO-1008	GCA_900094675.1	993070	993070	type	True	81.3574	649	1299	95	below_threshold
Arthrobacter mobilis	strain=E918	GCA_012395835.1	2724944	2724944	type	True	79.3455	448	1299	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_018622995.1	2817475	2817475	type	True	79.2899	354	1299	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_017898065.1	2817475	2817475	type	True	79.2706	353	1299	95	below_threshold
Arthrobacter sunyaminii	strain=zg-ZUI122	GCA_018866305.1	2816859	2816859	type	True	78.9131	318	1299	95	below_threshold
Arthrobacter sunyaminii	strain=zg-ZUI122	GCA_017353495.1	2816859	2816859	type	True	78.8024	318	1299	95	below_threshold
Arthrobacter silviterrae	strain=DSM 27180	GCA_011045165.1	2026658	2026658	type	True	78.7854	456	1299	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:27:33,432] [INFO] DFAST Taxonomy check result was written to GCF_017368795.1_ASM1736879v1_genomic.fna/tc_result.tsv
[2024-01-24 11:27:33,433] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:27:33,433] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:27:33,434] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfdd4c840-6e82-4452-bd3a-f5397279b507/dqc_reference/checkm_data
[2024-01-24 11:27:33,436] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:27:33,489] [INFO] Task started: CheckM
[2024-01-24 11:27:33,489] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017368795.1_ASM1736879v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017368795.1_ASM1736879v1_genomic.fna/checkm_input GCF_017368795.1_ASM1736879v1_genomic.fna/checkm_result
[2024-01-24 11:28:11,165] [INFO] Task succeeded: CheckM
[2024-01-24 11:28:11,167] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:28:11,185] [INFO] ===== Completeness check finished =====
[2024-01-24 11:28:11,186] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:28:11,186] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017368795.1_ASM1736879v1_genomic.fna/markers.fasta)
[2024-01-24 11:28:11,187] [INFO] Task started: Blastn
[2024-01-24 11:28:11,187] [INFO] Running command: blastn -query GCF_017368795.1_ASM1736879v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfdd4c840-6e82-4452-bd3a-f5397279b507/dqc_reference/reference_markers_gtdb.fasta -out GCF_017368795.1_ASM1736879v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:28:12,932] [INFO] Task succeeded: Blastn
[2024-01-24 11:28:12,936] [INFO] Selected 22 target genomes.
[2024-01-24 11:28:12,936] [INFO] Target genome list was writen to GCF_017368795.1_ASM1736879v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:28:12,985] [INFO] Task started: fastANI
[2024-01-24 11:28:12,985] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ff6acca-5813-4bd3-8eeb-a23aa32a2465/GCF_017368795.1_ASM1736879v1_genomic.fna.gz --refList GCF_017368795.1_ASM1736879v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017368795.1_ASM1736879v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:28:34,300] [INFO] Task succeeded: fastANI
[2024-01-24 11:28:34,317] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:28:34,317] [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_017368795.1	s__PO-11 sp017368795	100.0	1295	1299	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__PO-11	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001766675.1	s__Arthrobacter_G sp001766675	82.596	762	1299	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_G	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003614925.1	s__Arthrobacter_G celericrescens	82.5696	770	1299	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_G	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900099975.1	s__Arthrobacter_G cupressi	82.4724	769	1299	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_G	95.0	99.99	99.99	1.00	1.00	2	-
GCF_003369445.1	s__Arthrobacter_G silvisoli	82.3453	764	1299	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_G	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648735.1	s__Paenarthrobacter nicotinovorans	82.15	716	1299	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Paenarthrobacter	95.0	98.78	98.50	0.92	0.90	10	-
GCF_002009585.1	s__Arthrobacter_K sp002009585	82.0487	726	1299	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_K	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902706295.1	s__Paenarthrobacter sp902706295	81.9994	755	1299	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Paenarthrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014647595.1	s__Paenarthrobacter histidinolovorans	81.9367	740	1299	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Paenarthrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000514015.1	s__Paenarthrobacter nicotinovorans_A	81.8777	715	1299	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Paenarthrobacter	95.0	98.33	98.25	0.94	0.92	3	-
GCF_018215265.1	s__Paenarthrobacter sp018215265	81.8513	737	1299	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Paenarthrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014207375.1	s__Arthrobacter_K sp014207375	81.8485	754	1299	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_K	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018224015.1	s__Arthrobacter_I sp018224015	81.8121	672	1299	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_I	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000014925.1	s__Paenarthrobacter aurescens_A	81.8022	733	1299	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Paenarthrobacter	95.0	98.88	98.80	0.86	0.86	3	-
GCF_013179505.1	s__Paenarthrobacter sp013179505	81.7618	652	1299	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Paenarthrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001512305.1	s__Arthrobacter_I sp001512305	81.7356	691	1299	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_I	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000876655.1	s__Arthrobacter_I sp000876655	81.6488	689	1299	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_I	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003097355.1	s__Arthrobacter_I sp003097355	81.6185	694	1299	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_I	95.0	95.72	95.72	0.82	0.82	2	-
GCF_004798705.1	s__Arthrobacter_I sp004798705	81.5602	653	1299	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_I	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902506095.1	s__Pseudarthrobacter sp902506095	81.1071	642	1299	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Pseudarthrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012395835.1	s__Arthrobacter_F mobilis	79.3505	448	1299	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_F	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011045165.1	s__Specibacter silviterrae	78.8044	454	1299	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 11:28:34,319] [INFO] GTDB search result was written to GCF_017368795.1_ASM1736879v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:28:34,319] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:28:34,323] [INFO] DFAST_QC result json was written to GCF_017368795.1_ASM1736879v1_genomic.fna/dqc_result.json
[2024-01-24 11:28:34,323] [INFO] DFAST_QC completed!
[2024-01-24 11:28:34,323] [INFO] Total running time: 0h1m30s