[2024-01-24 14:14:32,041] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:14:32,043] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:14:32,043] [INFO] DQC Reference Directory: /var/lib/cwl/stg54dc065e-4e70-42aa-92a7-a041726e1f22/dqc_reference
[2024-01-24 14:14:33,282] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:14:33,283] [INFO] Task started: Prodigal
[2024-01-24 14:14:33,283] [INFO] Running command: gunzip -c /var/lib/cwl/stg60027f76-b639-4da4-b635-0cddced43c20/GCF_019084045.1_ASM1908404v1_genomic.fna.gz | prodigal -d GCF_019084045.1_ASM1908404v1_genomic.fna/cds.fna -a GCF_019084045.1_ASM1908404v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:14:47,593] [INFO] Task succeeded: Prodigal
[2024-01-24 14:14:47,594] [INFO] Task started: HMMsearch
[2024-01-24 14:14:47,594] [INFO] Running command: hmmsearch --tblout GCF_019084045.1_ASM1908404v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg54dc065e-4e70-42aa-92a7-a041726e1f22/dqc_reference/reference_markers.hmm GCF_019084045.1_ASM1908404v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:14:47,917] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:14:47,918] [INFO] Found 6/6 markers.
[2024-01-24 14:14:47,955] [INFO] Query marker FASTA was written to GCF_019084045.1_ASM1908404v1_genomic.fna/markers.fasta
[2024-01-24 14:14:47,956] [INFO] Task started: Blastn
[2024-01-24 14:14:47,956] [INFO] Running command: blastn -query GCF_019084045.1_ASM1908404v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg54dc065e-4e70-42aa-92a7-a041726e1f22/dqc_reference/reference_markers.fasta -out GCF_019084045.1_ASM1908404v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:49,136] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:49,140] [INFO] Selected 12 target genomes.
[2024-01-24 14:14:49,140] [INFO] Target genome list was writen to GCF_019084045.1_ASM1908404v1_genomic.fna/target_genomes.txt
[2024-01-24 14:14:49,148] [INFO] Task started: fastANI
[2024-01-24 14:14:49,148] [INFO] Running command: fastANI --query /var/lib/cwl/stg60027f76-b639-4da4-b635-0cddced43c20/GCF_019084045.1_ASM1908404v1_genomic.fna.gz --refList GCF_019084045.1_ASM1908404v1_genomic.fna/target_genomes.txt --output GCF_019084045.1_ASM1908404v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:14:58,487] [INFO] Task succeeded: fastANI
[2024-01-24 14:14:58,488] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg54dc065e-4e70-42aa-92a7-a041726e1f22/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:14:58,489] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg54dc065e-4e70-42aa-92a7-a041726e1f22/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:14:58,499] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:14:58,500] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:14:58,500] [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	86.4743	1080	1464	95	below_threshold
Paeniglutamicibacter gangotriensis	strain=Lz1y	GCA_000348945.1	254787	254787	type	True	83.4964	888	1464	95	below_threshold
Paeniglutamicibacter kerguelensis	strain=DSM 15797	GCA_017876535.1	254788	254788	type	True	83.3766	856	1464	95	below_threshold
Paeniglutamicibacter terrestris	strain=ANT13_2	GCA_012271785.1	2723403	2723403	type	True	82.2277	852	1464	95	below_threshold
Paeniglutamicibacter cryotolerans	strain=DSM 22826	GCA_014190875.1	670079	670079	type	True	80.6509	588	1464	95	below_threshold
Glutamicibacter protophormiae	strain=JCM 1973	GCA_014647495.1	37930	37930	type	True	80.128	530	1464	95	below_threshold
Arthrobacter mobilis	strain=E918	GCA_012395835.1	2724944	2724944	type	True	78.9962	456	1464	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_017898065.1	2817475	2817475	type	True	78.7951	349	1464	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_018622995.1	2817475	2817475	type	True	78.7742	351	1464	95	below_threshold
Arthrobacter sunyaminii	strain=zg-ZUI122	GCA_017353495.1	2816859	2816859	type	True	78.3622	295	1464	95	below_threshold
Arthrobacter sunyaminii	strain=zg-ZUI122	GCA_018866305.1	2816859	2816859	type	True	78.3411	297	1464	95	below_threshold
Arthrobacter sedimenti	strain=MIC A30	GCA_011750795.2	2694931	2694931	type	True	78.0345	305	1464	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:14:58,503] [INFO] DFAST Taxonomy check result was written to GCF_019084045.1_ASM1908404v1_genomic.fna/tc_result.tsv
[2024-01-24 14:14:58,503] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:14:58,504] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:14:58,504] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg54dc065e-4e70-42aa-92a7-a041726e1f22/dqc_reference/checkm_data
[2024-01-24 14:14:58,507] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:14:58,557] [INFO] Task started: CheckM
[2024-01-24 14:14:58,557] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019084045.1_ASM1908404v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019084045.1_ASM1908404v1_genomic.fna/checkm_input GCF_019084045.1_ASM1908404v1_genomic.fna/checkm_result
[2024-01-24 14:15:42,882] [INFO] Task succeeded: CheckM
[2024-01-24 14:15:42,884] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:15:42,909] [INFO] ===== Completeness check finished =====
[2024-01-24 14:15:42,909] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:15:42,910] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019084045.1_ASM1908404v1_genomic.fna/markers.fasta)
[2024-01-24 14:15:42,910] [INFO] Task started: Blastn
[2024-01-24 14:15:42,910] [INFO] Running command: blastn -query GCF_019084045.1_ASM1908404v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg54dc065e-4e70-42aa-92a7-a041726e1f22/dqc_reference/reference_markers_gtdb.fasta -out GCF_019084045.1_ASM1908404v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:44,946] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:44,950] [INFO] Selected 8 target genomes.
[2024-01-24 14:15:44,950] [INFO] Target genome list was writen to GCF_019084045.1_ASM1908404v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:15:44,959] [INFO] Task started: fastANI
[2024-01-24 14:15:44,959] [INFO] Running command: fastANI --query /var/lib/cwl/stg60027f76-b639-4da4-b635-0cddced43c20/GCF_019084045.1_ASM1908404v1_genomic.fna.gz --refList GCF_019084045.1_ASM1908404v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019084045.1_ASM1908404v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:15:54,200] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:54,208] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:15:54,208] [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_019084045.1	s__Paeniglutamicibacter sp019084045	100.0	1462	1464	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_001863355.1	s__Paeniglutamicibacter sp001863355	87.0131	1100	1464	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	86.4701	1081	1464	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	86.2673	1047	1464	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	83.5022	887	1464	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	83.3681	857	1464	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	82.5213	793	1464	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Paeniglutamicibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900010755.1	s__Paeniglutamicibacter antarcticus_A	82.1192	768	1464	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Paeniglutamicibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:15:54,210] [INFO] GTDB search result was written to GCF_019084045.1_ASM1908404v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:15:54,211] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:15:54,214] [INFO] DFAST_QC result json was written to GCF_019084045.1_ASM1908404v1_genomic.fna/dqc_result.json
[2024-01-24 14:15:54,214] [INFO] DFAST_QC completed!
[2024-01-24 14:15:54,214] [INFO] Total running time: 0h1m22s