[2024-01-24 13:40:43,774] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:43,777] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:43,777] [INFO] DQC Reference Directory: /var/lib/cwl/stgbeb48e5a-d7c3-40dd-a9fa-723ac6be021d/dqc_reference
[2024-01-24 13:40:45,154] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:45,155] [INFO] Task started: Prodigal
[2024-01-24 13:40:45,156] [INFO] Running command: gunzip -c /var/lib/cwl/stg45d7090e-96ce-40ca-a6ff-6bf3b50a596b/GCF_003217515.1_ASM321751v1_genomic.fna.gz | prodigal -d GCF_003217515.1_ASM321751v1_genomic.fna/cds.fna -a GCF_003217515.1_ASM321751v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:01,085] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:01,085] [INFO] Task started: HMMsearch
[2024-01-24 13:41:01,085] [INFO] Running command: hmmsearch --tblout GCF_003217515.1_ASM321751v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbeb48e5a-d7c3-40dd-a9fa-723ac6be021d/dqc_reference/reference_markers.hmm GCF_003217515.1_ASM321751v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:01,398] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:01,399] [INFO] Found 6/6 markers.
[2024-01-24 13:41:01,445] [INFO] Query marker FASTA was written to GCF_003217515.1_ASM321751v1_genomic.fna/markers.fasta
[2024-01-24 13:41:01,445] [INFO] Task started: Blastn
[2024-01-24 13:41:01,445] [INFO] Running command: blastn -query GCF_003217515.1_ASM321751v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbeb48e5a-d7c3-40dd-a9fa-723ac6be021d/dqc_reference/reference_markers.fasta -out GCF_003217515.1_ASM321751v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:02,142] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:02,145] [INFO] Selected 18 target genomes.
[2024-01-24 13:41:02,145] [INFO] Target genome list was writen to GCF_003217515.1_ASM321751v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:02,147] [INFO] Task started: fastANI
[2024-01-24 13:41:02,148] [INFO] Running command: fastANI --query /var/lib/cwl/stg45d7090e-96ce-40ca-a6ff-6bf3b50a596b/GCF_003217515.1_ASM321751v1_genomic.fna.gz --refList GCF_003217515.1_ASM321751v1_genomic.fna/target_genomes.txt --output GCF_003217515.1_ASM321751v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:15,467] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:15,468] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbeb48e5a-d7c3-40dd-a9fa-723ac6be021d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:15,468] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbeb48e5a-d7c3-40dd-a9fa-723ac6be021d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:15,517] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:41:15,517] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:15,517] [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 yavapaiensis	strain=DSM 18048	GCA_003217515.1	309889	309889	type	True	100.0	1553	1556	95	conclusive
Deinococcus pimensis	strain=DSM 21231	GCA_000519345.1	309888	309888	type	True	78.534	562	1556	95	below_threshold
Deinococcus maricopensis	strain=DSM 21211	GCA_000186385.1	309887	309887	type	True	77.2086	334	1556	95	below_threshold
Deinococcus peraridilitoris	strain=DSM 19664	GCA_000317835.1	432329	432329	type	True	77.1777	263	1556	95	below_threshold
Deinococcus aquiradiocola	strain=JCM 14371	GCA_014646915.1	393059	393059	type	True	76.962	314	1556	95	below_threshold
Deinococcus soli (ex Cha et al. 2016)	strain=N5	GCA_001007995.1	1309411	1309411	type	True	76.8347	220	1556	95	below_threshold
Deinobacterium chartae	strain=DSM 21458	GCA_014202645.1	521158	521158	type	True	76.7588	204	1556	95	below_threshold
Deinococcus actinosclerus	strain=BM2	GCA_001507665.1	1768108	1768108	type	True	76.7564	238	1556	95	below_threshold
Deinococcus metallilatus	strain=DSM 105434	GCA_014202095.1	1211322	1211322	type	True	76.6741	216	1556	95	below_threshold
Deinococcus metallilatus	strain=MA1002	GCA_004758605.1	1211322	1211322	type	True	76.6704	220	1556	95	below_threshold
Deinococcus metalli	strain=DSM 27521	GCA_014201805.1	1141878	1141878	type	True	76.6696	276	1556	95	below_threshold
Deinococcus saudiensis	strain=CGMCC 1.15089	GCA_014640655.1	1765963	1765963	type	True	76.6555	232	1556	95	below_threshold
Deinococcus gobiensis	strain=I-0	GCA_000252445.1	502394	502394	type	True	76.6539	239	1556	95	below_threshold
Deinococcus daejeonensis	strain=JCM 16918	GCA_014647175.1	1007098	1007098	type	True	76.6315	251	1556	95	below_threshold
Deinococcus seoulensis	strain=JCM 31404	GCA_014648115.1	1837379	1837379	type	True	76.6218	250	1556	95	below_threshold
Deinococcus knuensis	strain=JCM 31406	GCA_014648155.1	1837380	1837380	type	True	76.5772	246	1556	95	below_threshold
Deinococcus grandis	strain=ATCC 43672	GCA_001485435.1	57498	57498	type	True	76.4818	253	1556	95	below_threshold
Paenibacillus artemisiicola	strain=MWE-103	GCA_017652985.1	1172618	1172618	type	True	74.7037	69	1556	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:15,519] [INFO] DFAST Taxonomy check result was written to GCF_003217515.1_ASM321751v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:15,519] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:15,519] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:15,519] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbeb48e5a-d7c3-40dd-a9fa-723ac6be021d/dqc_reference/checkm_data
[2024-01-24 13:41:15,520] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:15,568] [INFO] Task started: CheckM
[2024-01-24 13:41:15,568] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003217515.1_ASM321751v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003217515.1_ASM321751v1_genomic.fna/checkm_input GCF_003217515.1_ASM321751v1_genomic.fna/checkm_result
[2024-01-24 13:42:09,096] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:09,097] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:09,119] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:09,119] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:09,120] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003217515.1_ASM321751v1_genomic.fna/markers.fasta)
[2024-01-24 13:42:09,120] [INFO] Task started: Blastn
[2024-01-24 13:42:09,120] [INFO] Running command: blastn -query GCF_003217515.1_ASM321751v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbeb48e5a-d7c3-40dd-a9fa-723ac6be021d/dqc_reference/reference_markers_gtdb.fasta -out GCF_003217515.1_ASM321751v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:10,029] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:10,032] [INFO] Selected 17 target genomes.
[2024-01-24 13:42:10,032] [INFO] Target genome list was writen to GCF_003217515.1_ASM321751v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:10,040] [INFO] Task started: fastANI
[2024-01-24 13:42:10,040] [INFO] Running command: fastANI --query /var/lib/cwl/stg45d7090e-96ce-40ca-a6ff-6bf3b50a596b/GCF_003217515.1_ASM321751v1_genomic.fna.gz --refList GCF_003217515.1_ASM321751v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003217515.1_ASM321751v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:21,941] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:21,958] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:21,959] [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_003217515.1	s__Deinococcus_A yavapaiensis	100.0	1553	1556	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000519345.1	s__Deinococcus_A pimensis	78.5518	560	1556	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_000186385.1	s__Deinococcus_B maricopensis	77.208	335	1556	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_000317835.1	s__Deinococcus_A peraridilitoris	77.1876	262	1556	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_014646915.1	s__Deinococcus aquiradiocola	76.9116	321	1556	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001007995.1	s__Deinococcus soli	76.8468	220	1556	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	98.09	98.03	0.94	0.93	3	-
GCF_002953415.1	s__Deinococcus sp002953415	76.7954	216	1556	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	76.7588	204	1556	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001507665.1	s__Deinococcus actinosclerus	76.7564	238	1556	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	96.26	96.21	0.94	0.94	4	-
GCF_004758605.1	s__Deinococcus metallilatus	76.6704	220	1556	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	100.00	100.00	0.98	0.98	4	-
GCF_014201805.1	s__Deinococcus metalli	76.6615	277	1556	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000252445.1	s__Deinococcus gobiensis	76.6539	239	1556	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	76.6221	247	1556	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	99.28	99.28	0.90	0.90	2	-
GCF_004801415.1	s__Deinococcus sp004801415	76.6193	207	1556	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	76.6139	251	1556	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	76.4733	254	1556	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	96.65	95.40	0.88	0.83	5	-
GCF_002017875.1	s__Deinococcus sp002017875	76.4674	240	1556	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	96.85	96.85	0.84	0.84	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:21,961] [INFO] GTDB search result was written to GCF_003217515.1_ASM321751v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:21,962] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:21,966] [INFO] DFAST_QC result json was written to GCF_003217515.1_ASM321751v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:21,966] [INFO] DFAST_QC completed!
[2024-01-24 13:42:21,966] [INFO] Total running time: 0h1m38s