[2024-01-24 15:26:04,580] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:26:04,582] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:26:04,582] [INFO] DQC Reference Directory: /var/lib/cwl/stgbbe4dafc-6b0f-495a-aa95-cf1cc29c34a3/dqc_reference
[2024-01-24 15:26:07,021] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:26:07,022] [INFO] Task started: Prodigal
[2024-01-24 15:26:07,023] [INFO] Running command: gunzip -c /var/lib/cwl/stg41bed709-19d5-4bdb-ab25-8eea5e358345/GCF_017876535.1_ASM1787653v1_genomic.fna.gz | prodigal -d GCF_017876535.1_ASM1787653v1_genomic.fna/cds.fna -a GCF_017876535.1_ASM1787653v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:26:23,025] [INFO] Task succeeded: Prodigal
[2024-01-24 15:26:23,026] [INFO] Task started: HMMsearch
[2024-01-24 15:26:23,026] [INFO] Running command: hmmsearch --tblout GCF_017876535.1_ASM1787653v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbbe4dafc-6b0f-495a-aa95-cf1cc29c34a3/dqc_reference/reference_markers.hmm GCF_017876535.1_ASM1787653v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:26:23,321] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:26:23,323] [INFO] Found 6/6 markers.
[2024-01-24 15:26:23,371] [INFO] Query marker FASTA was written to GCF_017876535.1_ASM1787653v1_genomic.fna/markers.fasta
[2024-01-24 15:26:23,371] [INFO] Task started: Blastn
[2024-01-24 15:26:23,371] [INFO] Running command: blastn -query GCF_017876535.1_ASM1787653v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbbe4dafc-6b0f-495a-aa95-cf1cc29c34a3/dqc_reference/reference_markers.fasta -out GCF_017876535.1_ASM1787653v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:26:24,484] [INFO] Task succeeded: Blastn
[2024-01-24 15:26:24,488] [INFO] Selected 14 target genomes.
[2024-01-24 15:26:24,489] [INFO] Target genome list was writen to GCF_017876535.1_ASM1787653v1_genomic.fna/target_genomes.txt
[2024-01-24 15:26:24,505] [INFO] Task started: fastANI
[2024-01-24 15:26:24,506] [INFO] Running command: fastANI --query /var/lib/cwl/stg41bed709-19d5-4bdb-ab25-8eea5e358345/GCF_017876535.1_ASM1787653v1_genomic.fna.gz --refList GCF_017876535.1_ASM1787653v1_genomic.fna/target_genomes.txt --output GCF_017876535.1_ASM1787653v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:26:37,102] [INFO] Task succeeded: fastANI
[2024-01-24 15:26:37,103] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbbe4dafc-6b0f-495a-aa95-cf1cc29c34a3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:26:37,103] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbbe4dafc-6b0f-495a-aa95-cf1cc29c34a3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:26:37,121] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:26:37,121] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:26:37,121] [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 kerguelensis	strain=DSM 15797	GCA_017876535.1	254788	254788	type	True	100.0	1598	1600	95	conclusive
Paeniglutamicibacter psychrophenolicus	strain=DSM 15454	GCA_017876575.1	257454	257454	type	True	83.4877	927	1600	95	below_threshold
Paeniglutamicibacter gangotriensis	strain=Lz1y	GCA_000348945.1	254787	254787	type	True	81.339	725	1600	95	below_threshold
Paeniglutamicibacter cryotolerans	strain=DSM 22826	GCA_014190875.1	670079	670079	type	True	80.825	588	1600	95	below_threshold
Paeniglutamicibacter terrestris	strain=ANT13_2	GCA_012271785.1	2723403	2723403	type	True	80.7023	672	1600	95	below_threshold
Glutamicibacter protophormiae	strain=JCM 1973	GCA_014647495.1	37930	37930	type	True	80.161	500	1600	95	below_threshold
Glutamicibacter halophytocola	strain=KLBMP 5180	GCA_001302565.1	1933880	1933880	type	True	79.6302	360	1600	95	below_threshold
Zhihengliuella salsuginis	strain=KCTC 19466	GCA_014651715.1	578222	578222	type	True	79.0887	393	1600	95	below_threshold
Arthrobacter mobilis	strain=E918	GCA_012395835.1	2724944	2724944	type	True	78.8923	380	1600	95	below_threshold
Arthrobacter stackebrandtii	strain=DSM 16005	GCA_017876675.1	272161	272161	type	True	78.8871	386	1600	95	below_threshold
Arthrobacter sunyaminii	strain=zg-ZUI122	GCA_018866305.1	2816859	2816859	type	True	78.4171	270	1600	95	below_threshold
Arthrobacter sunyaminii	strain=zg-ZUI122	GCA_017353495.1	2816859	2816859	type	True	78.2812	271	1600	95	below_threshold
Arthrobacter citreus	strain=DSM 20133	GCA_009192745.1	1670	1670	type	True	78.1377	318	1600	95	below_threshold
Sinomonas notoginsengisoli	strain=KCTC 29237	GCA_021554725.1	1457311	1457311	type	True	77.608	232	1600	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:26:37,124] [INFO] DFAST Taxonomy check result was written to GCF_017876535.1_ASM1787653v1_genomic.fna/tc_result.tsv
[2024-01-24 15:26:37,125] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:26:37,125] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:26:37,125] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbbe4dafc-6b0f-495a-aa95-cf1cc29c34a3/dqc_reference/checkm_data
[2024-01-24 15:26:37,127] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:26:37,194] [INFO] Task started: CheckM
[2024-01-24 15:26:37,195] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017876535.1_ASM1787653v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017876535.1_ASM1787653v1_genomic.fna/checkm_input GCF_017876535.1_ASM1787653v1_genomic.fna/checkm_result
[2024-01-24 15:27:26,984] [INFO] Task succeeded: CheckM
[2024-01-24 15:27:26,985] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:27:27,008] [INFO] ===== Completeness check finished =====
[2024-01-24 15:27:27,009] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:27:27,009] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017876535.1_ASM1787653v1_genomic.fna/markers.fasta)
[2024-01-24 15:27:27,010] [INFO] Task started: Blastn
[2024-01-24 15:27:27,010] [INFO] Running command: blastn -query GCF_017876535.1_ASM1787653v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbbe4dafc-6b0f-495a-aa95-cf1cc29c34a3/dqc_reference/reference_markers_gtdb.fasta -out GCF_017876535.1_ASM1787653v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:28,724] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:28,729] [INFO] Selected 8 target genomes.
[2024-01-24 15:27:28,730] [INFO] Target genome list was writen to GCF_017876535.1_ASM1787653v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:27:28,738] [INFO] Task started: fastANI
[2024-01-24 15:27:28,738] [INFO] Running command: fastANI --query /var/lib/cwl/stg41bed709-19d5-4bdb-ab25-8eea5e358345/GCF_017876535.1_ASM1787653v1_genomic.fna.gz --refList GCF_017876535.1_ASM1787653v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017876535.1_ASM1787653v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:27:37,248] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:37,261] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:27:37,261] [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_017876535.1	s__Paeniglutamicibacter kerguelensis	100.0	1596	1600	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_900010755.1	s__Paeniglutamicibacter antarcticus_A	84.1088	899	1600	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Paeniglutamicibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017876575.1	s__Paeniglutamicibacter psychrophenolicus	83.4672	924	1600	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	83.2847	898	1600	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	83.253	868	1600	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Paeniglutamicibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003287975.1	s__Paeniglutamicibacter sp003287975	83.083	892	1600	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Paeniglutamicibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002975435.1	s__Paeniglutamicibacter sp002975435	80.9726	620	1600	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	80.7201	668	1600	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Paeniglutamicibacter	95.0	98.96	98.96	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2024-01-24 15:27:37,263] [INFO] GTDB search result was written to GCF_017876535.1_ASM1787653v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:27:37,263] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:27:37,267] [INFO] DFAST_QC result json was written to GCF_017876535.1_ASM1787653v1_genomic.fna/dqc_result.json
[2024-01-24 15:27:37,267] [INFO] DFAST_QC completed!
[2024-01-24 15:27:37,267] [INFO] Total running time: 0h1m33s