[2024-01-24 14:03:08,570] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:03:08,572] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:03:08,572] [INFO] DQC Reference Directory: /var/lib/cwl/stgd91e5bbd-3aa6-43e7-8e5c-4898613a7a47/dqc_reference
[2024-01-24 14:03:10,040] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:03:10,041] [INFO] Task started: Prodigal
[2024-01-24 14:03:10,042] [INFO] Running command: gunzip -c /var/lib/cwl/stg9709b548-7434-455a-ab4b-0c3dd006fb85/GCF_000348945.1_ArGa1_genomic.fna.gz | prodigal -d GCF_000348945.1_ArGa1_genomic.fna/cds.fna -a GCF_000348945.1_ArGa1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:03:25,592] [INFO] Task succeeded: Prodigal
[2024-01-24 14:03:25,592] [INFO] Task started: HMMsearch
[2024-01-24 14:03:25,592] [INFO] Running command: hmmsearch --tblout GCF_000348945.1_ArGa1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd91e5bbd-3aa6-43e7-8e5c-4898613a7a47/dqc_reference/reference_markers.hmm GCF_000348945.1_ArGa1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:03:25,912] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:03:25,913] [INFO] Found 6/6 markers.
[2024-01-24 14:03:25,957] [INFO] Query marker FASTA was written to GCF_000348945.1_ArGa1_genomic.fna/markers.fasta
[2024-01-24 14:03:25,966] [INFO] Task started: Blastn
[2024-01-24 14:03:25,966] [INFO] Running command: blastn -query GCF_000348945.1_ArGa1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd91e5bbd-3aa6-43e7-8e5c-4898613a7a47/dqc_reference/reference_markers.fasta -out GCF_000348945.1_ArGa1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:03:26,978] [INFO] Task succeeded: Blastn
[2024-01-24 14:03:26,983] [INFO] Selected 13 target genomes.
[2024-01-24 14:03:26,983] [INFO] Target genome list was writen to GCF_000348945.1_ArGa1_genomic.fna/target_genomes.txt
[2024-01-24 14:03:26,988] [INFO] Task started: fastANI
[2024-01-24 14:03:26,988] [INFO] Running command: fastANI --query /var/lib/cwl/stg9709b548-7434-455a-ab4b-0c3dd006fb85/GCF_000348945.1_ArGa1_genomic.fna.gz --refList GCF_000348945.1_ArGa1_genomic.fna/target_genomes.txt --output GCF_000348945.1_ArGa1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:03:36,896] [INFO] Task succeeded: fastANI
[2024-01-24 14:03:36,897] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd91e5bbd-3aa6-43e7-8e5c-4898613a7a47/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:03:36,897] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd91e5bbd-3aa6-43e7-8e5c-4898613a7a47/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:03:36,908] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:03:36,908] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:03:36,908] [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 gangotriensis	strain=Lz1y	GCA_000348945.1	254787	254787	type	True	100.0	1429	1429	95	conclusive
Paeniglutamicibacter psychrophenolicus	strain=DSM 15454	GCA_017876575.1	257454	257454	type	True	84.3361	954	1429	95	below_threshold
Paeniglutamicibacter kerguelensis	strain=DSM 15797	GCA_017876535.1	254788	254788	type	True	81.43	712	1429	95	below_threshold
Paeniglutamicibacter terrestris	strain=ANT13_2	GCA_012271785.1	2723403	2723403	type	True	81.411	730	1429	95	below_threshold
Paeniglutamicibacter cryotolerans	strain=DSM 22826	GCA_014190875.1	670079	670079	type	True	79.6674	520	1429	95	below_threshold
Glutamicibacter halophytocola	strain=KLBMP 5180	GCA_001302565.1	1933880	1933880	type	True	78.6175	307	1429	95	below_threshold
Arthrobacter mobilis	strain=E918	GCA_012395835.1	2724944	2724944	type	True	78.0289	314	1429	95	below_threshold
Arthrobacter gallicola	strain=Sa2CUA1	GCA_014836775.1	2762225	2762225	type	True	77.8646	239	1429	95	below_threshold
Arthrobacter luteolus	strain=DSM 13067	GCA_008973725.1	98672	98672	type	True	77.8552	242	1429	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_017898065.1	2817475	2817475	type	True	77.7522	269	1429	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_018622995.1	2817475	2817475	type	True	77.7506	269	1429	95	below_threshold
Arthrobacter sunyaminii	strain=zg-ZUI122	GCA_017353495.1	2816859	2816859	type	True	77.6836	246	1429	95	below_threshold
Arthrobacter sunyaminii	strain=zg-ZUI122	GCA_018866305.1	2816859	2816859	type	True	77.664	245	1429	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:03:36,910] [INFO] DFAST Taxonomy check result was written to GCF_000348945.1_ArGa1_genomic.fna/tc_result.tsv
[2024-01-24 14:03:36,911] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:03:36,911] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:03:36,911] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd91e5bbd-3aa6-43e7-8e5c-4898613a7a47/dqc_reference/checkm_data
[2024-01-24 14:03:36,913] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:03:36,957] [INFO] Task started: CheckM
[2024-01-24 14:03:36,957] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000348945.1_ArGa1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000348945.1_ArGa1_genomic.fna/checkm_input GCF_000348945.1_ArGa1_genomic.fna/checkm_result
[2024-01-24 14:04:21,304] [INFO] Task succeeded: CheckM
[2024-01-24 14:04:21,305] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:04:21,328] [INFO] ===== Completeness check finished =====
[2024-01-24 14:04:21,328] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:04:21,329] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000348945.1_ArGa1_genomic.fna/markers.fasta)
[2024-01-24 14:04:21,329] [INFO] Task started: Blastn
[2024-01-24 14:04:21,329] [INFO] Running command: blastn -query GCF_000348945.1_ArGa1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd91e5bbd-3aa6-43e7-8e5c-4898613a7a47/dqc_reference/reference_markers_gtdb.fasta -out GCF_000348945.1_ArGa1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:04:22,818] [INFO] Task succeeded: Blastn
[2024-01-24 14:04:22,822] [INFO] Selected 6 target genomes.
[2024-01-24 14:04:22,822] [INFO] Target genome list was writen to GCF_000348945.1_ArGa1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:04:22,840] [INFO] Task started: fastANI
[2024-01-24 14:04:22,841] [INFO] Running command: fastANI --query /var/lib/cwl/stg9709b548-7434-455a-ab4b-0c3dd006fb85/GCF_000348945.1_ArGa1_genomic.fna.gz --refList GCF_000348945.1_ArGa1_genomic.fna/target_genomes_gtdb.txt --output GCF_000348945.1_ArGa1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:04:29,153] [INFO] Task succeeded: fastANI
[2024-01-24 14:04:29,163] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:04:29,163] [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_000348945.1	s__Paeniglutamicibacter gangotriensis	100.0	1429	1429	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Paeniglutamicibacter	95.0	97.63	97.63	0.86	0.86	2	conclusive
GCF_003287975.1	s__Paeniglutamicibacter sp003287975	84.5095	939	1429	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	84.4331	1013	1429	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	84.3558	952	1429	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	83.4055	885	1429	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	81.4127	715	1429	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 14:04:29,165] [INFO] GTDB search result was written to GCF_000348945.1_ArGa1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:04:29,166] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:04:29,169] [INFO] DFAST_QC result json was written to GCF_000348945.1_ArGa1_genomic.fna/dqc_result.json
[2024-01-24 14:04:29,169] [INFO] DFAST_QC completed!
[2024-01-24 14:04:29,169] [INFO] Total running time: 0h1m21s