[2024-01-24 13:16:56,320] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:16:56,322] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:16:56,322] [INFO] DQC Reference Directory: /var/lib/cwl/stg72f02f4c-5fb4-4580-a3dd-fb932fc98787/dqc_reference
[2024-01-24 13:16:57,540] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:16:57,541] [INFO] Task started: Prodigal
[2024-01-24 13:16:57,541] [INFO] Running command: gunzip -c /var/lib/cwl/stgc3094204-fb0c-416b-b3c2-c3e7cbd6c1e2/GCF_031458355.1_ASM3145835v1_genomic.fna.gz | prodigal -d GCF_031458355.1_ASM3145835v1_genomic.fna/cds.fna -a GCF_031458355.1_ASM3145835v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:12,857] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:12,858] [INFO] Task started: HMMsearch
[2024-01-24 13:17:12,858] [INFO] Running command: hmmsearch --tblout GCF_031458355.1_ASM3145835v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg72f02f4c-5fb4-4580-a3dd-fb932fc98787/dqc_reference/reference_markers.hmm GCF_031458355.1_ASM3145835v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:13,172] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:13,174] [INFO] Found 6/6 markers.
[2024-01-24 13:17:13,218] [INFO] Query marker FASTA was written to GCF_031458355.1_ASM3145835v1_genomic.fna/markers.fasta
[2024-01-24 13:17:13,219] [INFO] Task started: Blastn
[2024-01-24 13:17:13,219] [INFO] Running command: blastn -query GCF_031458355.1_ASM3145835v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg72f02f4c-5fb4-4580-a3dd-fb932fc98787/dqc_reference/reference_markers.fasta -out GCF_031458355.1_ASM3145835v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:14,427] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:14,431] [INFO] Selected 13 target genomes.
[2024-01-24 13:17:14,432] [INFO] Target genome list was writen to GCF_031458355.1_ASM3145835v1_genomic.fna/target_genomes.txt
[2024-01-24 13:17:14,440] [INFO] Task started: fastANI
[2024-01-24 13:17:14,441] [INFO] Running command: fastANI --query /var/lib/cwl/stgc3094204-fb0c-416b-b3c2-c3e7cbd6c1e2/GCF_031458355.1_ASM3145835v1_genomic.fna.gz --refList GCF_031458355.1_ASM3145835v1_genomic.fna/target_genomes.txt --output GCF_031458355.1_ASM3145835v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:17:24,874] [INFO] Task succeeded: fastANI
[2024-01-24 13:17:24,874] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg72f02f4c-5fb4-4580-a3dd-fb932fc98787/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:17:24,874] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg72f02f4c-5fb4-4580-a3dd-fb932fc98787/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:17:24,885] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:17:24,886] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:17:24,886] [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	85.6008	1053	1520	95	below_threshold
Paeniglutamicibacter gangotriensis	strain=Lz1y	GCA_000348945.1	254787	254787	type	True	83.2629	892	1520	95	below_threshold
Paeniglutamicibacter kerguelensis	strain=DSM 15797	GCA_017876535.1	254788	254788	type	True	82.8274	822	1520	95	below_threshold
Paeniglutamicibacter terrestris	strain=ANT13_2	GCA_012271785.1	2723403	2723403	type	True	81.9282	822	1520	95	below_threshold
Paeniglutamicibacter cryotolerans	strain=DSM 22826	GCA_014190875.1	670079	670079	type	True	80.6821	587	1520	95	below_threshold
Glutamicibacter protophormiae	strain=JCM 1973	GCA_014647495.1	37930	37930	type	True	79.9344	500	1520	95	below_threshold
Zhihengliuella salsuginis	strain=KCTC 19466	GCA_014651715.1	578222	578222	type	True	78.8805	397	1520	95	below_threshold
Arthrobacter mobilis	strain=E918	GCA_012395835.1	2724944	2724944	type	True	78.8405	424	1520	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_018622995.1	2817475	2817475	type	True	78.8289	339	1520	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_017898065.1	2817475	2817475	type	True	78.5842	321	1520	95	below_threshold
Arthrobacter stackebrandtii	strain=DSM 16005	GCA_017876675.1	272161	272161	type	True	78.5337	375	1520	95	below_threshold
Arthrobacter citreus	strain=DSM 20133	GCA_009192745.1	1670	1670	type	True	78.2117	295	1520	95	below_threshold
Sinomonas notoginsengisoli	strain=KCTC 29237	GCA_021554725.1	1457311	1457311	type	True	77.7405	238	1520	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:17:24,887] [INFO] DFAST Taxonomy check result was written to GCF_031458355.1_ASM3145835v1_genomic.fna/tc_result.tsv
[2024-01-24 13:17:24,888] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:17:24,888] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:17:24,888] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg72f02f4c-5fb4-4580-a3dd-fb932fc98787/dqc_reference/checkm_data
[2024-01-24 13:17:24,889] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:17:24,933] [INFO] Task started: CheckM
[2024-01-24 13:17:24,934] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_031458355.1_ASM3145835v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_031458355.1_ASM3145835v1_genomic.fna/checkm_input GCF_031458355.1_ASM3145835v1_genomic.fna/checkm_result
[2024-01-24 13:18:11,208] [INFO] Task succeeded: CheckM
[2024-01-24 13:18:11,209] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:18:11,228] [INFO] ===== Completeness check finished =====
[2024-01-24 13:18:11,228] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:18:11,229] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_031458355.1_ASM3145835v1_genomic.fna/markers.fasta)
[2024-01-24 13:18:11,229] [INFO] Task started: Blastn
[2024-01-24 13:18:11,229] [INFO] Running command: blastn -query GCF_031458355.1_ASM3145835v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg72f02f4c-5fb4-4580-a3dd-fb932fc98787/dqc_reference/reference_markers_gtdb.fasta -out GCF_031458355.1_ASM3145835v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:13,048] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:13,051] [INFO] Selected 7 target genomes.
[2024-01-24 13:18:13,052] [INFO] Target genome list was writen to GCF_031458355.1_ASM3145835v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:18:13,056] [INFO] Task started: fastANI
[2024-01-24 13:18:13,056] [INFO] Running command: fastANI --query /var/lib/cwl/stgc3094204-fb0c-416b-b3c2-c3e7cbd6c1e2/GCF_031458355.1_ASM3145835v1_genomic.fna.gz --refList GCF_031458355.1_ASM3145835v1_genomic.fna/target_genomes_gtdb.txt --output GCF_031458355.1_ASM3145835v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:18:20,600] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:20,611] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:18:20,612] [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	88.7569	1137	1520	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	85.832	1077	1520	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	85.6043	1054	1520	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	85.5706	999	1520	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	83.2719	891	1520	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	82.8399	823	1520	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	82.2416	769	1520	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 13:18:20,614] [INFO] GTDB search result was written to GCF_031458355.1_ASM3145835v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:18:20,614] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:18:20,617] [INFO] DFAST_QC result json was written to GCF_031458355.1_ASM3145835v1_genomic.fna/dqc_result.json
[2024-01-24 13:18:20,618] [INFO] DFAST_QC completed!
[2024-01-24 13:18:20,618] [INFO] Total running time: 0h1m24s