[2024-01-24 14:06:05,179] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:06:05,181] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:06:05,181] [INFO] DQC Reference Directory: /var/lib/cwl/stgf8fc4c9b-b2b7-419a-8e2d-761ec6427fce/dqc_reference
[2024-01-24 14:06:06,581] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:06:06,582] [INFO] Task started: Prodigal
[2024-01-24 14:06:06,582] [INFO] Running command: gunzip -c /var/lib/cwl/stgaff38234-ea83-479c-b51a-aad9e72c1c5a/GCF_001007995.1_ASM100799v1_genomic.fna.gz | prodigal -d GCF_001007995.1_ASM100799v1_genomic.fna/cds.fna -a GCF_001007995.1_ASM100799v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:16,522] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:16,523] [INFO] Task started: HMMsearch
[2024-01-24 14:06:16,523] [INFO] Running command: hmmsearch --tblout GCF_001007995.1_ASM100799v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf8fc4c9b-b2b7-419a-8e2d-761ec6427fce/dqc_reference/reference_markers.hmm GCF_001007995.1_ASM100799v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:16,788] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:16,790] [INFO] Found 6/6 markers.
[2024-01-24 14:06:16,820] [INFO] Query marker FASTA was written to GCF_001007995.1_ASM100799v1_genomic.fna/markers.fasta
[2024-01-24 14:06:16,820] [INFO] Task started: Blastn
[2024-01-24 14:06:16,820] [INFO] Running command: blastn -query GCF_001007995.1_ASM100799v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf8fc4c9b-b2b7-419a-8e2d-761ec6427fce/dqc_reference/reference_markers.fasta -out GCF_001007995.1_ASM100799v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:17,559] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:17,562] [INFO] Selected 9 target genomes.
[2024-01-24 14:06:17,562] [INFO] Target genome list was writen to GCF_001007995.1_ASM100799v1_genomic.fna/target_genomes.txt
[2024-01-24 14:06:17,579] [INFO] Task started: fastANI
[2024-01-24 14:06:17,579] [INFO] Running command: fastANI --query /var/lib/cwl/stgaff38234-ea83-479c-b51a-aad9e72c1c5a/GCF_001007995.1_ASM100799v1_genomic.fna.gz --refList GCF_001007995.1_ASM100799v1_genomic.fna/target_genomes.txt --output GCF_001007995.1_ASM100799v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:27,610] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:27,611] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf8fc4c9b-b2b7-419a-8e2d-761ec6427fce/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:27,611] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf8fc4c9b-b2b7-419a-8e2d-761ec6427fce/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:27,619] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:06:27,619] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 14:06:27,620] [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 soli (ex Cha et al. 2016)	strain=N5	GCA_001007995.1	1309411	1309411	type	True	100.0	1077	1078	95	inconclusive
Deinococcus saudiensis	strain=CGMCC 1.15089	GCA_014640655.1	1765963	1765963	type	True	98.027	1013	1078	95	inconclusive
Deinococcus grandis	strain=ATCC 43672	GCA_001485435.1	57498	57498	type	True	94.3701	978	1078	95	below_threshold
Deinococcus xianganensis	strain=Y35	GCA_009834985.1	1507289	1507289	type	True	94.3355	913	1078	95	below_threshold
Deinococcus daejeonensis	strain=JCM 16918	GCA_014647175.1	1007098	1007098	type	True	93.912	967	1078	95	below_threshold
Deinococcus arenae	strain=JCM 31047	GCA_014647995.1	1452751	1452751	type	True	92.1141	944	1078	95	below_threshold
Deinococcus kurensis	strain=KR-1	GCA_009687825.1	2662757	2662757	type	True	92.0716	962	1078	95	below_threshold
Deinococcus sedimenti	strain=JCM 31405	GCA_014648135.1	1867090	1867090	type	True	91.6372	957	1078	95	below_threshold
Deinococcus radiotolerans	strain=JCM 19173	GCA_014647435.1	1309407	1309407	type	True	90.616	934	1078	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:27,621] [INFO] DFAST Taxonomy check result was written to GCF_001007995.1_ASM100799v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:27,621] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:27,622] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:27,622] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf8fc4c9b-b2b7-419a-8e2d-761ec6427fce/dqc_reference/checkm_data
[2024-01-24 14:06:27,623] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:27,660] [INFO] Task started: CheckM
[2024-01-24 14:06:27,660] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001007995.1_ASM100799v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001007995.1_ASM100799v1_genomic.fna/checkm_input GCF_001007995.1_ASM100799v1_genomic.fna/checkm_result
[2024-01-24 14:07:05,599] [INFO] Task succeeded: CheckM
[2024-01-24 14:07:05,600] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:07:05,622] [INFO] ===== Completeness check finished =====
[2024-01-24 14:07:05,622] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:07:05,622] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001007995.1_ASM100799v1_genomic.fna/markers.fasta)
[2024-01-24 14:07:05,623] [INFO] Task started: Blastn
[2024-01-24 14:07:05,623] [INFO] Running command: blastn -query GCF_001007995.1_ASM100799v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf8fc4c9b-b2b7-419a-8e2d-761ec6427fce/dqc_reference/reference_markers_gtdb.fasta -out GCF_001007995.1_ASM100799v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:06,704] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:06,708] [INFO] Selected 7 target genomes.
[2024-01-24 14:07:06,708] [INFO] Target genome list was writen to GCF_001007995.1_ASM100799v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:07:06,725] [INFO] Task started: fastANI
[2024-01-24 14:07:06,726] [INFO] Running command: fastANI --query /var/lib/cwl/stgaff38234-ea83-479c-b51a-aad9e72c1c5a/GCF_001007995.1_ASM100799v1_genomic.fna.gz --refList GCF_001007995.1_ASM100799v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001007995.1_ASM100799v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:07:14,463] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:14,470] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:07:14,471] [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_001007995.1	s__Deinococcus soli	100.0	1077	1078	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	98.09	98.03	0.94	0.93	3	conclusive
GCF_001485435.1	s__Deinococcus grandis	94.3701	978	1078	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	92.9106	965	1078	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	92.6563	965	1078	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	96.26	96.21	0.94	0.94	4	-
GCF_014648135.1	s__Deinococcus sedimenti	91.6436	956	1078	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	90.6451	932	1078	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002198095.1	s__Deinococcus indicus	86.7835	837	1078	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	99.28	99.28	0.90	0.90	2	-
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[2024-01-24 14:07:14,472] [INFO] GTDB search result was written to GCF_001007995.1_ASM100799v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:07:14,479] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:07:14,483] [INFO] DFAST_QC result json was written to GCF_001007995.1_ASM100799v1_genomic.fna/dqc_result.json
[2024-01-24 14:07:14,483] [INFO] DFAST_QC completed!
[2024-01-24 14:07:14,483] [INFO] Total running time: 0h1m9s