[2024-01-24 15:17:48,929] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:17:48,931] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:17:48,931] [INFO] DQC Reference Directory: /var/lib/cwl/stg1053f842-47d8-43de-aad4-58be03cf2409/dqc_reference
[2024-01-24 15:17:51,533] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:17:51,534] [INFO] Task started: Prodigal
[2024-01-24 15:17:51,535] [INFO] Running command: gunzip -c /var/lib/cwl/stg8a81962f-e516-40f8-bdcf-e1a7fa9079f4/GCF_014648095.1_ASM1464809v1_genomic.fna.gz | prodigal -d GCF_014648095.1_ASM1464809v1_genomic.fna/cds.fna -a GCF_014648095.1_ASM1464809v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:18:08,706] [INFO] Task succeeded: Prodigal
[2024-01-24 15:18:08,706] [INFO] Task started: HMMsearch
[2024-01-24 15:18:08,706] [INFO] Running command: hmmsearch --tblout GCF_014648095.1_ASM1464809v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1053f842-47d8-43de-aad4-58be03cf2409/dqc_reference/reference_markers.hmm GCF_014648095.1_ASM1464809v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:18:09,028] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:18:09,030] [INFO] Found 6/6 markers.
[2024-01-24 15:18:09,078] [INFO] Query marker FASTA was written to GCF_014648095.1_ASM1464809v1_genomic.fna/markers.fasta
[2024-01-24 15:18:09,079] [INFO] Task started: Blastn
[2024-01-24 15:18:09,079] [INFO] Running command: blastn -query GCF_014648095.1_ASM1464809v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1053f842-47d8-43de-aad4-58be03cf2409/dqc_reference/reference_markers.fasta -out GCF_014648095.1_ASM1464809v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:18:09,783] [INFO] Task succeeded: Blastn
[2024-01-24 15:18:09,786] [INFO] Selected 22 target genomes.
[2024-01-24 15:18:09,786] [INFO] Target genome list was writen to GCF_014648095.1_ASM1464809v1_genomic.fna/target_genomes.txt
[2024-01-24 15:18:09,796] [INFO] Task started: fastANI
[2024-01-24 15:18:09,797] [INFO] Running command: fastANI --query /var/lib/cwl/stg8a81962f-e516-40f8-bdcf-e1a7fa9079f4/GCF_014648095.1_ASM1464809v1_genomic.fna.gz --refList GCF_014648095.1_ASM1464809v1_genomic.fna/target_genomes.txt --output GCF_014648095.1_ASM1464809v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:18:25,710] [INFO] Task succeeded: fastANI
[2024-01-24 15:18:25,710] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1053f842-47d8-43de-aad4-58be03cf2409/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:18:25,711] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1053f842-47d8-43de-aad4-58be03cf2409/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:18:25,726] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:18:25,726] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:18:25,727] [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 ruber	strain=JCM 31311	GCA_014648095.1	1848197	1848197	type	True	100.0	1937	1943	95	conclusive
Deinococcus aquiradiocola	strain=JCM 14371	GCA_014646915.1	393059	393059	type	True	78.9725	596	1943	95	below_threshold
Deinococcus irradiatisoli	strain=17bor-2	GCA_003173015.1	2202254	2202254	type	True	78.3989	415	1943	95	below_threshold
Deinococcus alpinitundrae	strain=LMG 24283	GCA_009982895.1	468913	468913	type	True	78.2975	516	1943	95	below_threshold
Deinococcus rubellus	strain=Ant6	GCA_025244745.1	1889240	1889240	type	True	78.272	406	1943	95	below_threshold
Deinococcus gobiensis	strain=I-0	GCA_000252445.1	502394	502394	type	True	78.1241	445	1943	95	below_threshold
Deinococcus phoenicis	strain=1P10ME	GCA_000599865.1	1476583	1476583	type	True	78.049	410	1943	95	below_threshold
Deinococcus radiopugnans	strain=DSM 12027	GCA_014201625.1	57497	57497	type	True	78.0021	467	1943	95	below_threshold
Deinococcus aerolatus	strain=JCM 15442	GCA_014647055.1	522487	522487	type	True	77.9658	408	1943	95	below_threshold
Deinococcus aerophilus	strain=JCM 15443	GCA_014647075.1	522488	522488	type	True	77.7839	393	1943	95	below_threshold
Deinococcus radiodurans	strain=ATCC 13939	GCA_020546685.1	1299	1299	type	True	77.6308	327	1943	95	below_threshold
Deinococcus radiodurans	strain=ATCC 13939	GCA_000687895.1	1299	1299	type	True	77.6037	324	1943	95	below_threshold
Deinococcus multiflagellatus	strain=KACC 19287	GCA_020166415.1	1656887	1656887	type	True	77.5816	379	1943	95	below_threshold
Deinococcus radiodurans	strain=DSM 20539	GCA_000685985.1	1299	1299	type	True	77.5678	330	1943	95	below_threshold
Deinococcus radiodurans	strain=R1	GCA_000008565.1	1299	1299	type	True	77.5589	328	1943	95	below_threshold
Deinococcus actinosclerus	strain=BM2	GCA_001507665.1	1768108	1768108	type	True	77.4916	346	1943	95	below_threshold
Deinococcus arenae	strain=JCM 31047	GCA_014647995.1	1452751	1452751	type	True	77.4225	392	1943	95	below_threshold
Deinococcus saudiensis	strain=CGMCC 1.15089	GCA_014640655.1	1765963	1765963	type	True	77.3081	346	1943	95	below_threshold
Deinococcus soli (ex Cha et al. 2016)	strain=N5	GCA_001007995.1	1309411	1309411	type	True	77.2581	329	1943	95	below_threshold
Deinococcus maricopensis	strain=DSM 21211	GCA_000186385.1	309887	309887	type	True	76.9873	261	1943	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:18:25,728] [INFO] DFAST Taxonomy check result was written to GCF_014648095.1_ASM1464809v1_genomic.fna/tc_result.tsv
[2024-01-24 15:18:25,729] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:18:25,729] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:18:25,729] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1053f842-47d8-43de-aad4-58be03cf2409/dqc_reference/checkm_data
[2024-01-24 15:18:25,730] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:18:25,797] [INFO] Task started: CheckM
[2024-01-24 15:18:25,797] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014648095.1_ASM1464809v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014648095.1_ASM1464809v1_genomic.fna/checkm_input GCF_014648095.1_ASM1464809v1_genomic.fna/checkm_result
[2024-01-24 15:19:17,053] [INFO] Task succeeded: CheckM
[2024-01-24 15:19:17,056] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:19:17,082] [INFO] ===== Completeness check finished =====
[2024-01-24 15:19:17,082] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:19:17,083] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014648095.1_ASM1464809v1_genomic.fna/markers.fasta)
[2024-01-24 15:19:17,084] [INFO] Task started: Blastn
[2024-01-24 15:19:17,084] [INFO] Running command: blastn -query GCF_014648095.1_ASM1464809v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1053f842-47d8-43de-aad4-58be03cf2409/dqc_reference/reference_markers_gtdb.fasta -out GCF_014648095.1_ASM1464809v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:18,022] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:18,026] [INFO] Selected 15 target genomes.
[2024-01-24 15:19:18,027] [INFO] Target genome list was writen to GCF_014648095.1_ASM1464809v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:19:18,040] [INFO] Task started: fastANI
[2024-01-24 15:19:18,040] [INFO] Running command: fastANI --query /var/lib/cwl/stg8a81962f-e516-40f8-bdcf-e1a7fa9079f4/GCF_014648095.1_ASM1464809v1_genomic.fna.gz --refList GCF_014648095.1_ASM1464809v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014648095.1_ASM1464809v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:19:30,660] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:30,674] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:19:30,675] [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_014648095.1	s__Deinococcus ruber	100.0	1937	1943	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_014646915.1	s__Deinococcus aquiradiocola	78.9724	596	1943	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	78.3986	415	1943	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009982895.1	s__Deinococcus alpinitundrae	78.2922	516	1943	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	78.1196	443	1943	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	78.0317	411	1943	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014647055.1	s__Deinococcus aerolatus	77.9563	409	1943	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	77.7541	398	1943	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000008565.1	s__Deinococcus radiodurans	77.5583	328	1943	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	99.94	99.91	0.99	0.99	8	-
GCF_002017875.1	s__Deinococcus sp002017875	77.342	386	1943	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	96.85	96.85	0.84	0.84	2	-
GCF_000186385.1	s__Deinococcus_B maricopensis	76.9876	261	1943	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016790695.1	s__JAEUOS01 sp016790695	75.0071	58	1943	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__JAEUOS01;g__JAEUOS01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013366375.1	s__Schlegelella_A koreensis	74.9798	61	1943	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Schlegelella_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:19:30,677] [INFO] GTDB search result was written to GCF_014648095.1_ASM1464809v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:19:30,678] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:19:30,686] [INFO] DFAST_QC result json was written to GCF_014648095.1_ASM1464809v1_genomic.fna/dqc_result.json
[2024-01-24 15:19:30,687] [INFO] DFAST_QC completed!
[2024-01-24 15:19:30,687] [INFO] Total running time: 0h1m42s