[2024-01-25 18:10:35,602] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:10:35,603] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:10:35,603] [INFO] DQC Reference Directory: /var/lib/cwl/stg62cf96db-5520-4dfb-b9dc-f7af2bb7c30d/dqc_reference
[2024-01-25 18:10:36,768] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:10:36,769] [INFO] Task started: Prodigal
[2024-01-25 18:10:36,769] [INFO] Running command: gunzip -c /var/lib/cwl/stgb410f277-7f1c-425c-9c38-17590d8014b8/GCF_014646915.1_ASM1464691v1_genomic.fna.gz | prodigal -d GCF_014646915.1_ASM1464691v1_genomic.fna/cds.fna -a GCF_014646915.1_ASM1464691v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:10:57,551] [INFO] Task succeeded: Prodigal
[2024-01-25 18:10:57,552] [INFO] Task started: HMMsearch
[2024-01-25 18:10:57,552] [INFO] Running command: hmmsearch --tblout GCF_014646915.1_ASM1464691v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg62cf96db-5520-4dfb-b9dc-f7af2bb7c30d/dqc_reference/reference_markers.hmm GCF_014646915.1_ASM1464691v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:10:57,768] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:10:57,769] [INFO] Found 6/6 markers.
[2024-01-25 18:10:57,803] [INFO] Query marker FASTA was written to GCF_014646915.1_ASM1464691v1_genomic.fna/markers.fasta
[2024-01-25 18:10:57,803] [INFO] Task started: Blastn
[2024-01-25 18:10:57,803] [INFO] Running command: blastn -query GCF_014646915.1_ASM1464691v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg62cf96db-5520-4dfb-b9dc-f7af2bb7c30d/dqc_reference/reference_markers.fasta -out GCF_014646915.1_ASM1464691v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:10:58,552] [INFO] Task succeeded: Blastn
[2024-01-25 18:10:58,554] [INFO] Selected 21 target genomes.
[2024-01-25 18:10:58,555] [INFO] Target genome list was writen to GCF_014646915.1_ASM1464691v1_genomic.fna/target_genomes.txt
[2024-01-25 18:10:58,568] [INFO] Task started: fastANI
[2024-01-25 18:10:58,569] [INFO] Running command: fastANI --query /var/lib/cwl/stgb410f277-7f1c-425c-9c38-17590d8014b8/GCF_014646915.1_ASM1464691v1_genomic.fna.gz --refList GCF_014646915.1_ASM1464691v1_genomic.fna/target_genomes.txt --output GCF_014646915.1_ASM1464691v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:11:16,800] [INFO] Task succeeded: fastANI
[2024-01-25 18:11:16,800] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg62cf96db-5520-4dfb-b9dc-f7af2bb7c30d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:11:16,801] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg62cf96db-5520-4dfb-b9dc-f7af2bb7c30d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:11:16,813] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:11:16,814] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:11:16,814] [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 aquiradiocola	strain=JCM 14371	GCA_014646915.1	393059	393059	type	True	100.0	1364	1365	95	conclusive
Deinococcus knuensis	strain=JCM 31406	GCA_014648155.1	1837380	1837380	type	True	79.8399	659	1365	95	below_threshold
Deinococcus grandis	strain=ATCC 43672	GCA_001485435.1	57498	57498	type	True	79.7187	623	1365	95	below_threshold
Deinococcus seoulensis	strain=JCM 31404	GCA_014648115.1	1837379	1837379	type	True	79.7184	658	1365	95	below_threshold
Deinococcus arenae	strain=JCM 31047	GCA_014647995.1	1452751	1452751	type	True	79.5395	624	1365	95	below_threshold
Deinococcus sedimenti	strain=JCM 31405	GCA_014648135.1	1867090	1867090	type	True	79.5279	620	1365	95	below_threshold
Deinococcus kurensis	strain=KR-1	GCA_009687825.1	2662757	2662757	type	True	79.4935	622	1365	95	below_threshold
Deinococcus actinosclerus	strain=BM2	GCA_001507665.1	1768108	1768108	type	True	79.4925	567	1365	95	below_threshold
Deinococcus maricopensis	strain=DSM 21211	GCA_000186385.1	309887	309887	type	True	79.1384	587	1365	95	below_threshold
Deinococcus metalli	strain=DSM 27521	GCA_014201805.1	1141878	1141878	type	True	79.1243	618	1365	95	below_threshold
Deinococcus ficus	strain=DSM 19119	GCA_000430865.1	317577	317577	type	True	79.0777	525	1365	95	below_threshold
Deinococcus ficus	strain=CC-FR2-10	GCA_003444775.1	317577	317577	type	True	79.0324	525	1365	95	below_threshold
Deinococcus ruber	strain=JCM 31311	GCA_014648095.1	1848197	1848197	type	True	79.0233	589	1365	95	below_threshold
Deinococcus pimensis	strain=DSM 21231	GCA_000519345.1	309888	309888	type	True	78.5387	528	1365	95	below_threshold
Deinococcus gobiensis	strain=I-0	GCA_000252445.1	502394	502394	type	True	78.4097	541	1365	95	below_threshold
Deinococcus phoenicis	strain=1P10ME	GCA_000599865.1	1476583	1476583	type	True	78.0886	448	1365	95	below_threshold
Deinococcus irradiatisoli	strain=17bor-2	GCA_003173015.1	2202254	2202254	type	True	77.8753	391	1365	95	below_threshold
Deinococcus radiopugnans	strain=ATCC 19172	GCA_006335125.1	57497	57497	type	True	77.7969	461	1365	95	below_threshold
Deinococcus radiopugnans	strain=DSM 12027	GCA_014201625.1	57497	57497	type	True	77.7959	461	1365	95	below_threshold
Deinococcus radiodurans	strain=DSM 20539	GCA_000685985.1	1299	1299	type	True	77.2837	348	1365	95	below_threshold
Deinococcus radiodurans	strain=R1	GCA_000008565.1	1299	1299	type	True	77.2584	352	1365	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:11:16,815] [INFO] DFAST Taxonomy check result was written to GCF_014646915.1_ASM1464691v1_genomic.fna/tc_result.tsv
[2024-01-25 18:11:16,816] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:11:16,816] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:11:16,816] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg62cf96db-5520-4dfb-b9dc-f7af2bb7c30d/dqc_reference/checkm_data
[2024-01-25 18:11:16,817] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:11:16,858] [INFO] Task started: CheckM
[2024-01-25 18:11:16,859] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014646915.1_ASM1464691v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014646915.1_ASM1464691v1_genomic.fna/checkm_input GCF_014646915.1_ASM1464691v1_genomic.fna/checkm_result
[2024-01-25 18:12:29,433] [INFO] Task succeeded: CheckM
[2024-01-25 18:12:29,434] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:12:29,454] [INFO] ===== Completeness check finished =====
[2024-01-25 18:12:29,454] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:12:29,455] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014646915.1_ASM1464691v1_genomic.fna/markers.fasta)
[2024-01-25 18:12:29,455] [INFO] Task started: Blastn
[2024-01-25 18:12:29,455] [INFO] Running command: blastn -query GCF_014646915.1_ASM1464691v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg62cf96db-5520-4dfb-b9dc-f7af2bb7c30d/dqc_reference/reference_markers_gtdb.fasta -out GCF_014646915.1_ASM1464691v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:12:30,664] [INFO] Task succeeded: Blastn
[2024-01-25 18:12:30,670] [INFO] Selected 19 target genomes.
[2024-01-25 18:12:30,670] [INFO] Target genome list was writen to GCF_014646915.1_ASM1464691v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:12:30,693] [INFO] Task started: fastANI
[2024-01-25 18:12:30,693] [INFO] Running command: fastANI --query /var/lib/cwl/stgb410f277-7f1c-425c-9c38-17590d8014b8/GCF_014646915.1_ASM1464691v1_genomic.fna.gz --refList GCF_014646915.1_ASM1464691v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014646915.1_ASM1464691v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:12:48,617] [INFO] Task succeeded: fastANI
[2024-01-25 18:12:48,628] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:12:48,629] [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_014646915.1	s__Deinococcus aquiradiocola	100.0	1364	1365	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_002017875.1	s__Deinococcus sp002017875	79.7084	652	1365	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	96.85	96.85	0.84	0.84	2	-
GCF_001485435.1	s__Deinococcus grandis	79.6938	627	1365	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	96.65	95.40	0.88	0.83	5	-
GCF_013337115.1	s__Deinococcus sp013337115	79.6894	631	1365	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648115.1	s__Deinococcus seoulensis	79.6518	667	1365	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	97.69	97.69	0.87	0.87	2	-
GCF_002198095.1	s__Deinococcus indicus	79.5746	644	1365	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	99.28	99.28	0.90	0.90	2	-
GCF_014648135.1	s__Deinococcus sedimenti	79.5536	617	1365	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	79.5063	565	1365	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	96.26	96.21	0.94	0.94	4	-
GCF_000186385.1	s__Deinococcus_B maricopensis	79.1418	586	1365	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014201805.1	s__Deinococcus metalli	79.1146	623	1365	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003444775.1	s__Deinococcus ficus	79.0334	526	1365	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	98.33	97.44	0.95	0.88	4	-
GCF_014648095.1	s__Deinococcus ruber	79.0191	588	1365	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000519345.1	s__Deinococcus_A pimensis	78.5761	523	1365	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000252445.1	s__Deinococcus gobiensis	78.4149	538	1365	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000599865.1	s__Deinococcus phoenicis	78.1143	444	1365	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003173015.1	s__Deinococcus irradiatisoli	77.852	392	1365	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006335125.1	s__Deinococcus radiopugnans	77.8281	457	1365	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	98.45	97.61	0.92	0.87	4	-
GCF_000008565.1	s__Deinococcus radiodurans	77.2593	351	1365	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	99.94	99.91	0.99	0.99	8	-
GCF_014202645.1	s__Deinobacterium chartae	76.9882	271	1365	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:12:48,630] [INFO] GTDB search result was written to GCF_014646915.1_ASM1464691v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:12:48,631] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:12:48,635] [INFO] DFAST_QC result json was written to GCF_014646915.1_ASM1464691v1_genomic.fna/dqc_result.json
[2024-01-25 18:12:48,635] [INFO] DFAST_QC completed!
[2024-01-25 18:12:48,635] [INFO] Total running time: 0h2m13s