[2024-01-24 13:55:19,688] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:55:19,690] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:55:19,691] [INFO] DQC Reference Directory: /var/lib/cwl/stgbf36fc1f-5da1-47e3-9c1e-cf346d320764/dqc_reference
[2024-01-24 13:55:21,049] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:55:21,050] [INFO] Task started: Prodigal
[2024-01-24 13:55:21,051] [INFO] Running command: gunzip -c /var/lib/cwl/stgfc5bb454-9484-48da-b62e-7cc521c6920b/GCF_000252445.1_ASM25244v1_genomic.fna.gz | prodigal -d GCF_000252445.1_ASM25244v1_genomic.fna/cds.fna -a GCF_000252445.1_ASM25244v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:55:33,520] [INFO] Task succeeded: Prodigal
[2024-01-24 13:55:33,521] [INFO] Task started: HMMsearch
[2024-01-24 13:55:33,521] [INFO] Running command: hmmsearch --tblout GCF_000252445.1_ASM25244v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbf36fc1f-5da1-47e3-9c1e-cf346d320764/dqc_reference/reference_markers.hmm GCF_000252445.1_ASM25244v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:55:33,823] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:55:33,824] [INFO] Found 6/6 markers.
[2024-01-24 13:55:33,864] [INFO] Query marker FASTA was written to GCF_000252445.1_ASM25244v1_genomic.fna/markers.fasta
[2024-01-24 13:55:33,865] [INFO] Task started: Blastn
[2024-01-24 13:55:33,865] [INFO] Running command: blastn -query GCF_000252445.1_ASM25244v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbf36fc1f-5da1-47e3-9c1e-cf346d320764/dqc_reference/reference_markers.fasta -out GCF_000252445.1_ASM25244v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:55:34,597] [INFO] Task succeeded: Blastn
[2024-01-24 13:55:34,601] [INFO] Selected 25 target genomes.
[2024-01-24 13:55:34,601] [INFO] Target genome list was writen to GCF_000252445.1_ASM25244v1_genomic.fna/target_genomes.txt
[2024-01-24 13:55:34,612] [INFO] Task started: fastANI
[2024-01-24 13:55:34,612] [INFO] Running command: fastANI --query /var/lib/cwl/stgfc5bb454-9484-48da-b62e-7cc521c6920b/GCF_000252445.1_ASM25244v1_genomic.fna.gz --refList GCF_000252445.1_ASM25244v1_genomic.fna/target_genomes.txt --output GCF_000252445.1_ASM25244v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:55:57,501] [INFO] Task succeeded: fastANI
[2024-01-24 13:55:57,502] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbf36fc1f-5da1-47e3-9c1e-cf346d320764/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:55:57,502] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbf36fc1f-5da1-47e3-9c1e-cf346d320764/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:55:57,522] [INFO] Found 25 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:55:57,523] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:55:57,523] [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
Deinococcus gobiensis	strain=I-0	GCA_000252445.1	502394	502394	type	True	100.0	1465	1466	95	conclusive
Deinococcus koreensis	strain=SJW1-2	GCA_002901445.1	2054903	2054903	type	True	81.0207	739	1466	95	below_threshold
Deinococcus budaensis	strain=DSM 101791	GCA_014201885.1	1665626	1665626	type	True	80.9014	670	1466	95	below_threshold
Deinococcus metalli	strain=DSM 27521	GCA_014201805.1	1141878	1141878	type	True	80.8897	737	1466	95	below_threshold
Deinococcus phoenicis	strain=1P10ME	GCA_000599865.1	1476583	1476583	type	True	80.8538	670	1466	95	below_threshold
Deinococcus actinosclerus	strain=BM2	GCA_001507665.1	1768108	1768108	type	True	80.7559	655	1466	95	below_threshold
Deinococcus kurensis	strain=KR-1	GCA_009687825.1	2662757	2662757	type	True	80.7	737	1466	95	below_threshold
Deinococcus radiodurans	strain=R1	GCA_000008565.1	1299	1299	type	True	80.459	607	1466	95	below_threshold
Deinococcus radiopugnans	strain=DSM 12027	GCA_014201625.1	57497	57497	type	True	80.3975	661	1466	95	below_threshold
Deinococcus terrestris	strain=SDU3-2	GCA_009377345.1	2651870	2651870	type	True	80.3887	631	1466	95	below_threshold
Deinococcus grandis	strain=ATCC 43672	GCA_001485435.1	57498	57498	type	True	80.3754	703	1466	95	below_threshold
Deinococcus aerophilus	strain=JCM 15443	GCA_014647075.1	522488	522488	type	True	80.37	657	1466	95	below_threshold
Deinococcus radiodurans	strain=DSM 20539	GCA_000685985.1	1299	1299	type	True	80.3623	611	1466	95	below_threshold
Deinococcus xianganensis	strain=Y35	GCA_009834985.1	1507289	1507289	type	True	80.2946	673	1466	95	below_threshold
Deinococcus saudiensis	strain=CGMCC 1.15089	GCA_014640655.1	1765963	1765963	type	True	80.1178	700	1466	95	below_threshold
Deinococcus radiotolerans	strain=JCM 19173	GCA_014647435.1	1309407	1309407	type	True	80.0835	662	1466	95	below_threshold
Deinococcus sedimenti	strain=JCM 31405	GCA_014648135.1	1867090	1867090	type	True	80.0204	685	1466	95	below_threshold
Deinococcus ficus	strain=CC-FR2-10	GCA_003444775.1	317577	317577	type	True	79.9886	611	1466	95	below_threshold
Deinococcus ficus	strain=DSM 19119	GCA_000430865.1	317577	317577	type	True	79.7575	617	1466	95	below_threshold
Deinococcus arcticus	strain=OD32	GCA_003028415.1	2136176	2136176	type	True	79.6935	659	1466	95	below_threshold
Deinococcus malanensis	strain=JCM 30331	GCA_014647655.1	1706855	1706855	type	True	78.8624	521	1466	95	below_threshold
Deinobacterium chartae	strain=DSM 21458	GCA_014202645.1	521158	521158	type	True	77.3896	332	1466	95	below_threshold
Acidovorax caeni	strain=R-24608	GCA_001298675.1	343013	343013	type	True	75.0107	109	1466	95	below_threshold
Acidovorax caeni	strain=R-24608	GCA_900116825.1	343013	343013	type	True	74.9812	105	1466	95	below_threshold
Paucibacter toxinivorans	strain=DSM 16998	GCA_004362525.1	270368	270368	type	True	74.9692	138	1466	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:55:57,525] [INFO] DFAST Taxonomy check result was written to GCF_000252445.1_ASM25244v1_genomic.fna/tc_result.tsv
[2024-01-24 13:55:57,525] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:55:57,526] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:55:57,526] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbf36fc1f-5da1-47e3-9c1e-cf346d320764/dqc_reference/checkm_data
[2024-01-24 13:55:57,527] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:55:57,602] [INFO] Task started: CheckM
[2024-01-24 13:55:57,603] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000252445.1_ASM25244v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000252445.1_ASM25244v1_genomic.fna/checkm_input GCF_000252445.1_ASM25244v1_genomic.fna/checkm_result
[2024-01-24 13:56:50,593] [INFO] Task succeeded: CheckM
[2024-01-24 13:56:50,595] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:56:50,615] [INFO] ===== Completeness check finished =====
[2024-01-24 13:56:50,615] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:56:50,615] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000252445.1_ASM25244v1_genomic.fna/markers.fasta)
[2024-01-24 13:56:50,616] [INFO] Task started: Blastn
[2024-01-24 13:56:50,616] [INFO] Running command: blastn -query GCF_000252445.1_ASM25244v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbf36fc1f-5da1-47e3-9c1e-cf346d320764/dqc_reference/reference_markers_gtdb.fasta -out GCF_000252445.1_ASM25244v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:56:51,591] [INFO] Task succeeded: Blastn
[2024-01-24 13:56:51,595] [INFO] Selected 20 target genomes.
[2024-01-24 13:56:51,595] [INFO] Target genome list was writen to GCF_000252445.1_ASM25244v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:56:51,643] [INFO] Task started: fastANI
[2024-01-24 13:56:51,643] [INFO] Running command: fastANI --query /var/lib/cwl/stgfc5bb454-9484-48da-b62e-7cc521c6920b/GCF_000252445.1_ASM25244v1_genomic.fna.gz --refList GCF_000252445.1_ASM25244v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000252445.1_ASM25244v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:57:09,798] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:09,813] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:57:09,813] [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_000252445.1	s__Deinococcus gobiensis	100.0	1465	1466	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001424185.1	s__Deinococcus sp001424185	89.2937	1107	1466	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002901445.1	s__Deinococcus koreensis	80.9987	733	1466	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014201885.1	s__Deinococcus budaensis	80.8801	672	1466	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014201805.1	s__Deinococcus metalli	80.8582	740	1466	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000599865.1	s__Deinococcus phoenicis	80.8485	672	1466	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001507665.1	s__Deinococcus actinosclerus	80.7622	651	1466	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	96.26	96.21	0.94	0.94	4	-
GCF_009377345.1	s__Deinococcus sp009377345	80.4204	628	1466	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014647075.1	s__Deinococcus aerophilus	80.4094	654	1466	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001485435.1	s__Deinococcus grandis	80.378	707	1466	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	96.65	95.40	0.88	0.83	5	-
GCF_002198095.1	s__Deinococcus indicus	80.3009	706	1466	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	99.28	99.28	0.90	0.90	2	-
GCF_014647435.1	s__Deinococcus radiotolerans	80.0481	667	1466	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648135.1	s__Deinococcus sedimenti	80.0424	682	1466	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003028415.1	s__Deinococcus sp003028415	79.7275	655	1466	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014647655.1	s__Deinococcus malanensis	78.8585	522	1466	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014202645.1	s__Deinobacterium chartae	77.3793	333	1466	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015070875.1	s__Ramlibacter sp015070875	75.3691	126	1466	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015624425.1	s__Kinneretia sp015624425	75.2413	199	1466	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Kinneretia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018780645.1	s__Paucibacter sp018780645	74.9896	123	1466	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paucibacter	95.0	95.57	95.57	0.86	0.86	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:57:09,815] [INFO] GTDB search result was written to GCF_000252445.1_ASM25244v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:57:09,816] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:57:09,825] [INFO] DFAST_QC result json was written to GCF_000252445.1_ASM25244v1_genomic.fna/dqc_result.json
[2024-01-24 13:57:09,825] [INFO] DFAST_QC completed!
[2024-01-24 13:57:09,825] [INFO] Total running time: 0h1m50s