[2024-01-24 10:48:09,166] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:48:09,454] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:48:09,454] [INFO] DQC Reference Directory: /var/lib/cwl/stg75cc9217-6830-4379-9aed-c8c2642b21b2/dqc_reference
[2024-01-24 10:48:23,954] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:48:23,955] [INFO] Task started: Prodigal
[2024-01-24 10:48:23,955] [INFO] Running command: gunzip -c /var/lib/cwl/stgfa264741-f584-4ee0-9de6-47c8e4bd2fc4/GCF_012271785.1_ASM1227178v1_genomic.fna.gz | prodigal -d GCF_012271785.1_ASM1227178v1_genomic.fna/cds.fna -a GCF_012271785.1_ASM1227178v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:48:38,111] [INFO] Task succeeded: Prodigal
[2024-01-24 10:48:38,112] [INFO] Task started: HMMsearch
[2024-01-24 10:48:38,112] [INFO] Running command: hmmsearch --tblout GCF_012271785.1_ASM1227178v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg75cc9217-6830-4379-9aed-c8c2642b21b2/dqc_reference/reference_markers.hmm GCF_012271785.1_ASM1227178v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:48:38,390] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:48:38,391] [INFO] Found 6/6 markers.
[2024-01-24 10:48:38,427] [INFO] Query marker FASTA was written to GCF_012271785.1_ASM1227178v1_genomic.fna/markers.fasta
[2024-01-24 10:48:38,427] [INFO] Task started: Blastn
[2024-01-24 10:48:38,427] [INFO] Running command: blastn -query GCF_012271785.1_ASM1227178v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg75cc9217-6830-4379-9aed-c8c2642b21b2/dqc_reference/reference_markers.fasta -out GCF_012271785.1_ASM1227178v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:39,456] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:39,459] [INFO] Selected 13 target genomes.
[2024-01-24 10:48:39,459] [INFO] Target genome list was writen to GCF_012271785.1_ASM1227178v1_genomic.fna/target_genomes.txt
[2024-01-24 10:48:39,465] [INFO] Task started: fastANI
[2024-01-24 10:48:39,465] [INFO] Running command: fastANI --query /var/lib/cwl/stgfa264741-f584-4ee0-9de6-47c8e4bd2fc4/GCF_012271785.1_ASM1227178v1_genomic.fna.gz --refList GCF_012271785.1_ASM1227178v1_genomic.fna/target_genomes.txt --output GCF_012271785.1_ASM1227178v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:48:48,907] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:48,908] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg75cc9217-6830-4379-9aed-c8c2642b21b2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:48:48,908] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg75cc9217-6830-4379-9aed-c8c2642b21b2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:48:48,931] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:48:48,931] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:48:48,931] [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 terrestris	strain=ANT13_2	GCA_012271785.1	2723403	2723403	type	True	100.0	1433	1433	95	conclusive
Paeniglutamicibacter psychrophenolicus	strain=DSM 15454	GCA_017876575.1	257454	257454	type	True	82.0028	856	1433	95	below_threshold
Paeniglutamicibacter gangotriensis	strain=Lz1y	GCA_000348945.1	254787	254787	type	True	81.4665	729	1433	95	below_threshold
Paeniglutamicibacter kerguelensis	strain=DSM 15797	GCA_017876535.1	254788	254788	type	True	80.8541	659	1433	95	below_threshold
Paeniglutamicibacter cryotolerans	strain=DSM 22826	GCA_014190875.1	670079	670079	type	True	79.3724	408	1433	95	below_threshold
Zhihengliuella halotolerans	strain=DSM 17364	GCA_004217565.1	370736	370736	type	True	78.0535	224	1433	95	below_threshold
Zhihengliuella salsuginis	strain=KCTC 19466	GCA_014651715.1	578222	578222	type	True	77.9494	258	1433	95	below_threshold
Arthrobacter sunyaminii	strain=zg-ZUI122	GCA_017353495.1	2816859	2816859	type	True	77.9128	198	1433	95	below_threshold
Arthrobacter sunyaminii	strain=zg-ZUI122	GCA_018866305.1	2816859	2816859	type	True	77.8819	201	1433	95	below_threshold
Arthrobacter celericrescens	strain=NEAU-SA2	GCA_003614925.1	2320851	2320851	type	True	77.7959	234	1433	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_018622995.1	2817475	2817475	type	True	77.7554	230	1433	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_017898065.1	2817475	2817475	type	True	77.7264	231	1433	95	below_threshold
Arthrobacter mobilis	strain=E918	GCA_012395835.1	2724944	2724944	type	True	77.5217	257	1433	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:48:48,939] [INFO] DFAST Taxonomy check result was written to GCF_012271785.1_ASM1227178v1_genomic.fna/tc_result.tsv
[2024-01-24 10:48:48,940] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:48:48,940] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:48:48,940] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg75cc9217-6830-4379-9aed-c8c2642b21b2/dqc_reference/checkm_data
[2024-01-24 10:48:48,942] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:48:48,987] [INFO] Task started: CheckM
[2024-01-24 10:48:48,987] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_012271785.1_ASM1227178v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_012271785.1_ASM1227178v1_genomic.fna/checkm_input GCF_012271785.1_ASM1227178v1_genomic.fna/checkm_result
[2024-01-24 10:49:36,382] [INFO] Task succeeded: CheckM
[2024-01-24 10:49:36,384] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:49:36,404] [INFO] ===== Completeness check finished =====
[2024-01-24 10:49:36,405] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:49:36,405] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_012271785.1_ASM1227178v1_genomic.fna/markers.fasta)
[2024-01-24 10:49:36,405] [INFO] Task started: Blastn
[2024-01-24 10:49:36,406] [INFO] Running command: blastn -query GCF_012271785.1_ASM1227178v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg75cc9217-6830-4379-9aed-c8c2642b21b2/dqc_reference/reference_markers_gtdb.fasta -out GCF_012271785.1_ASM1227178v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:49:38,213] [INFO] Task succeeded: Blastn
[2024-01-24 10:49:38,218] [INFO] Selected 6 target genomes.
[2024-01-24 10:49:38,219] [INFO] Target genome list was writen to GCF_012271785.1_ASM1227178v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:49:38,225] [INFO] Task started: fastANI
[2024-01-24 10:49:38,225] [INFO] Running command: fastANI --query /var/lib/cwl/stgfa264741-f584-4ee0-9de6-47c8e4bd2fc4/GCF_012271785.1_ASM1227178v1_genomic.fna.gz --refList GCF_012271785.1_ASM1227178v1_genomic.fna/target_genomes_gtdb.txt --output GCF_012271785.1_ASM1227178v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:49:45,479] [INFO] Task succeeded: fastANI
[2024-01-24 10:49:45,491] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:49:45,491] [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_012271785.1	s__Paeniglutamicibacter terrestris	100.0	1433	1433	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Paeniglutamicibacter	95.0	98.96	98.96	0.92	0.92	2	conclusive
GCF_019084045.1	s__Paeniglutamicibacter sp019084045	82.4556	825	1433	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	82.0029	856	1433	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	81.9813	841	1433	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	81.9698	796	1433	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Paeniglutamicibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017876535.1	s__Paeniglutamicibacter kerguelensis	80.8547	658	1433	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 10:49:45,493] [INFO] GTDB search result was written to GCF_012271785.1_ASM1227178v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:49:45,494] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:49:45,497] [INFO] DFAST_QC result json was written to GCF_012271785.1_ASM1227178v1_genomic.fna/dqc_result.json
[2024-01-24 10:49:45,497] [INFO] DFAST_QC completed!
[2024-01-24 10:49:45,497] [INFO] Total running time: 0h1m36s