[2024-01-24 14:02:51,382] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:02:51,385] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:02:51,385] [INFO] DQC Reference Directory: /var/lib/cwl/stgbce9a23a-ab35-4101-9830-3978071fbff8/dqc_reference
[2024-01-24 14:02:52,745] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:02:52,746] [INFO] Task started: Prodigal
[2024-01-24 14:02:52,746] [INFO] Running command: gunzip -c /var/lib/cwl/stg69925285-8ae5-40be-91b6-0d8673ee5541/GCF_014201805.1_ASM1420180v1_genomic.fna.gz | prodigal -d GCF_014201805.1_ASM1420180v1_genomic.fna/cds.fna -a GCF_014201805.1_ASM1420180v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:03:08,419] [INFO] Task succeeded: Prodigal
[2024-01-24 14:03:08,419] [INFO] Task started: HMMsearch
[2024-01-24 14:03:08,419] [INFO] Running command: hmmsearch --tblout GCF_014201805.1_ASM1420180v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbce9a23a-ab35-4101-9830-3978071fbff8/dqc_reference/reference_markers.hmm GCF_014201805.1_ASM1420180v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:03:08,725] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:03:08,727] [INFO] Found 6/6 markers.
[2024-01-24 14:03:08,774] [INFO] Query marker FASTA was written to GCF_014201805.1_ASM1420180v1_genomic.fna/markers.fasta
[2024-01-24 14:03:08,774] [INFO] Task started: Blastn
[2024-01-24 14:03:08,774] [INFO] Running command: blastn -query GCF_014201805.1_ASM1420180v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbce9a23a-ab35-4101-9830-3978071fbff8/dqc_reference/reference_markers.fasta -out GCF_014201805.1_ASM1420180v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:03:09,546] [INFO] Task succeeded: Blastn
[2024-01-24 14:03:09,549] [INFO] Selected 14 target genomes.
[2024-01-24 14:03:09,550] [INFO] Target genome list was writen to GCF_014201805.1_ASM1420180v1_genomic.fna/target_genomes.txt
[2024-01-24 14:03:09,562] [INFO] Task started: fastANI
[2024-01-24 14:03:09,563] [INFO] Running command: fastANI --query /var/lib/cwl/stg69925285-8ae5-40be-91b6-0d8673ee5541/GCF_014201805.1_ASM1420180v1_genomic.fna.gz --refList GCF_014201805.1_ASM1420180v1_genomic.fna/target_genomes.txt --output GCF_014201805.1_ASM1420180v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:03:23,432] [INFO] Task succeeded: fastANI
[2024-01-24 14:03:23,432] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbce9a23a-ab35-4101-9830-3978071fbff8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:03:23,433] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbce9a23a-ab35-4101-9830-3978071fbff8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:03:23,445] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:03:23,445] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:03:23,446] [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 metalli	strain=DSM 27521	GCA_014201805.1	1141878	1141878	type	True	100.0	1616	1621	95	conclusive
Deinococcus koreensis	strain=SJW1-2	GCA_002901445.1	2054903	2054903	type	True	82.5799	941	1621	95	below_threshold
Deinococcus actinosclerus	strain=BM2	GCA_001507665.1	1768108	1768108	type	True	81.9574	742	1621	95	below_threshold
Deinococcus kurensis	strain=KR-1	GCA_009687825.1	2662757	2662757	type	True	81.8853	821	1621	95	below_threshold
Deinococcus arenae	strain=JCM 31047	GCA_014647995.1	1452751	1452751	type	True	81.7676	808	1621	95	below_threshold
Deinococcus knuensis	strain=JCM 31406	GCA_014648155.1	1837380	1837380	type	True	81.7188	843	1621	95	below_threshold
Deinococcus seoulensis	strain=JCM 31404	GCA_014648115.1	1837379	1837379	type	True	81.6937	836	1621	95	below_threshold
Deinococcus daejeonensis	strain=JCM 16918	GCA_014647175.1	1007098	1007098	type	True	81.5711	809	1621	95	below_threshold
Deinococcus soli (ex Cha et al. 2016)	strain=N5	GCA_001007995.1	1309411	1309411	type	True	81.5604	728	1621	95	below_threshold
Deinococcus xianganensis	strain=Y35	GCA_009834985.1	1507289	1507289	type	True	81.5378	782	1621	95	below_threshold
Deinococcus saudiensis	strain=CGMCC 1.15089	GCA_014640655.1	1765963	1765963	type	True	81.369	810	1621	95	below_threshold
Deinococcus radiotolerans	strain=JCM 19173	GCA_014647435.1	1309407	1309407	type	True	81.215	820	1621	95	below_threshold
Deinococcus gobiensis	strain=I-0	GCA_000252445.1	502394	502394	type	True	80.7552	753	1621	95	below_threshold
Deinococcus malanensis	strain=JCM 30331	GCA_014647655.1	1706855	1706855	type	True	79.1966	498	1621	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:03:23,448] [INFO] DFAST Taxonomy check result was written to GCF_014201805.1_ASM1420180v1_genomic.fna/tc_result.tsv
[2024-01-24 14:03:23,448] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:03:23,448] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:03:23,449] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbce9a23a-ab35-4101-9830-3978071fbff8/dqc_reference/checkm_data
[2024-01-24 14:03:23,450] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:03:23,498] [INFO] Task started: CheckM
[2024-01-24 14:03:23,498] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014201805.1_ASM1420180v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014201805.1_ASM1420180v1_genomic.fna/checkm_input GCF_014201805.1_ASM1420180v1_genomic.fna/checkm_result
[2024-01-24 14:04:37,302] [INFO] Task succeeded: CheckM
[2024-01-24 14:04:37,304] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:04:37,326] [INFO] ===== Completeness check finished =====
[2024-01-24 14:04:37,326] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:04:37,327] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014201805.1_ASM1420180v1_genomic.fna/markers.fasta)
[2024-01-24 14:04:37,327] [INFO] Task started: Blastn
[2024-01-24 14:04:37,327] [INFO] Running command: blastn -query GCF_014201805.1_ASM1420180v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbce9a23a-ab35-4101-9830-3978071fbff8/dqc_reference/reference_markers_gtdb.fasta -out GCF_014201805.1_ASM1420180v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:04:38,425] [INFO] Task succeeded: Blastn
[2024-01-24 14:04:38,430] [INFO] Selected 14 target genomes.
[2024-01-24 14:04:38,430] [INFO] Target genome list was writen to GCF_014201805.1_ASM1420180v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:04:38,492] [INFO] Task started: fastANI
[2024-01-24 14:04:38,492] [INFO] Running command: fastANI --query /var/lib/cwl/stg69925285-8ae5-40be-91b6-0d8673ee5541/GCF_014201805.1_ASM1420180v1_genomic.fna.gz --refList GCF_014201805.1_ASM1420180v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014201805.1_ASM1420180v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:04:52,743] [INFO] Task succeeded: fastANI
[2024-01-24 14:04:52,766] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:04:52,766] [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_014201805.1	s__Deinococcus metalli	100.0	1616	1621	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_004801415.1	s__Deinococcus sp004801415	85.2343	1134	1621	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	82.5929	939	1621	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	81.9556	745	1621	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	96.26	96.21	0.94	0.94	4	-
GCF_002198095.1	s__Deinococcus indicus	81.8739	820	1621	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	99.28	99.28	0.90	0.90	2	-
GCF_002017875.1	s__Deinococcus sp002017875	81.803	831	1621	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	96.85	96.85	0.84	0.84	2	-
GCF_014648115.1	s__Deinococcus seoulensis	81.6564	841	1621	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	97.69	97.69	0.87	0.87	2	-
GCF_001485435.1	s__Deinococcus grandis	81.6087	824	1621	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	96.65	95.40	0.88	0.83	5	-
GCF_001007995.1	s__Deinococcus soli	81.5302	730	1621	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	98.09	98.03	0.94	0.93	3	-
GCF_013337115.1	s__Deinococcus sp013337115	81.4533	791	1621	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	81.3672	815	1621	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014647435.1	s__Deinococcus radiotolerans	81.2076	821	1621	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000252445.1	s__Deinococcus gobiensis	80.7771	750	1621	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	79.177	500	1621	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:04:52,768] [INFO] GTDB search result was written to GCF_014201805.1_ASM1420180v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:04:52,769] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:04:52,773] [INFO] DFAST_QC result json was written to GCF_014201805.1_ASM1420180v1_genomic.fna/dqc_result.json
[2024-01-24 14:04:52,774] [INFO] DFAST_QC completed!
[2024-01-24 14:04:52,774] [INFO] Total running time: 0h2m1s