[2024-01-24 13:36:44,470] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:36:44,472] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:36:44,472] [INFO] DQC Reference Directory: /var/lib/cwl/stg99ad8680-227d-4ea9-8c39-cadffc754755/dqc_reference
[2024-01-24 13:36:45,749] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:36:45,750] [INFO] Task started: Prodigal
[2024-01-24 13:36:45,750] [INFO] Running command: gunzip -c /var/lib/cwl/stg95d249d9-8da2-428b-aacf-db40f6defc91/GCF_000186385.1_ASM18638v1_genomic.fna.gz | prodigal -d GCF_000186385.1_ASM18638v1_genomic.fna/cds.fna -a GCF_000186385.1_ASM18638v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:36:56,187] [INFO] Task succeeded: Prodigal
[2024-01-24 13:36:56,187] [INFO] Task started: HMMsearch
[2024-01-24 13:36:56,187] [INFO] Running command: hmmsearch --tblout GCF_000186385.1_ASM18638v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg99ad8680-227d-4ea9-8c39-cadffc754755/dqc_reference/reference_markers.hmm GCF_000186385.1_ASM18638v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:36:56,519] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:36:56,520] [INFO] Found 6/6 markers.
[2024-01-24 13:36:56,573] [INFO] Query marker FASTA was written to GCF_000186385.1_ASM18638v1_genomic.fna/markers.fasta
[2024-01-24 13:36:56,573] [INFO] Task started: Blastn
[2024-01-24 13:36:56,573] [INFO] Running command: blastn -query GCF_000186385.1_ASM18638v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg99ad8680-227d-4ea9-8c39-cadffc754755/dqc_reference/reference_markers.fasta -out GCF_000186385.1_ASM18638v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:36:57,338] [INFO] Task succeeded: Blastn
[2024-01-24 13:36:57,342] [INFO] Selected 19 target genomes.
[2024-01-24 13:36:57,343] [INFO] Target genome list was writen to GCF_000186385.1_ASM18638v1_genomic.fna/target_genomes.txt
[2024-01-24 13:36:57,365] [INFO] Task started: fastANI
[2024-01-24 13:36:57,365] [INFO] Running command: fastANI --query /var/lib/cwl/stg95d249d9-8da2-428b-aacf-db40f6defc91/GCF_000186385.1_ASM18638v1_genomic.fna.gz --refList GCF_000186385.1_ASM18638v1_genomic.fna/target_genomes.txt --output GCF_000186385.1_ASM18638v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:11,432] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:11,433] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg99ad8680-227d-4ea9-8c39-cadffc754755/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:11,433] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg99ad8680-227d-4ea9-8c39-cadffc754755/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:11,450] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:37:11,450] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:37:11,451] [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 maricopensis	strain=DSM 21211	GCA_000186385.1	309887	309887	type	True	100.0	1166	1166	95	conclusive
Deinococcus aquiradiocola	strain=JCM 14371	GCA_014646915.1	393059	393059	type	True	79.2392	567	1166	95	below_threshold
Deinococcus soli (ex Cha et al. 2016)	strain=N5	GCA_001007995.1	1309411	1309411	type	True	79.2078	474	1166	95	below_threshold
Deinococcus actinosclerus	strain=BM2	GCA_001507665.1	1768108	1768108	type	True	79.1369	490	1166	95	below_threshold
Deinococcus grandis	strain=ATCC 43672	GCA_001485435.1	57498	57498	type	True	79.0821	543	1166	95	below_threshold
Deinococcus arenae	strain=JCM 31047	GCA_014647995.1	1452751	1452751	type	True	79.0379	497	1166	95	below_threshold
Deinococcus xianganensis	strain=Y35	GCA_009834985.1	1507289	1507289	type	True	79.0018	517	1166	95	below_threshold
Deinococcus daejeonensis	strain=JCM 16918	GCA_014647175.1	1007098	1007098	type	True	78.9985	507	1166	95	below_threshold
Deinococcus sedimenti	strain=JCM 31405	GCA_014648135.1	1867090	1867090	type	True	78.9653	532	1166	95	below_threshold
Deinococcus ficus	strain=CC-FR2-10	GCA_003444775.1	317577	317577	type	True	78.9479	498	1166	95	below_threshold
Deinococcus kurensis	strain=KR-1	GCA_009687825.1	2662757	2662757	type	True	78.9347	544	1166	95	below_threshold
Deinococcus radiotolerans	strain=JCM 19173	GCA_014647435.1	1309407	1309407	type	True	78.8628	509	1166	95	below_threshold
Deinococcus phoenicis	strain=1P10ME	GCA_000599865.1	1476583	1476583	type	True	77.7811	387	1166	95	below_threshold
Deinococcus irradiatisoli	strain=17bor-2	GCA_003173015.1	2202254	2202254	type	True	77.7523	308	1166	95	below_threshold
Deinococcus metallilatus	strain=DSM 105434	GCA_014202095.1	1211322	1211322	type	True	77.7076	377	1166	95	below_threshold
Deinococcus radiodurans	strain=ATCC 13939 substr. R1	GCA_020546805.1	1299	1299	type	True	77.6104	285	1166	95	below_threshold
Deinococcus radiodurans	strain=R1	GCA_000008565.1	1299	1299	type	True	77.5664	285	1166	95	below_threshold
Deinococcus radiodurans	strain=ATCC 13939 substr. R2	GCA_020547025.1	1299	1299	type	True	77.5221	283	1166	95	below_threshold
Deinococcus radiodurans	strain=DSM 20539	GCA_000685985.1	1299	1299	type	True	77.3308	280	1166	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:11,452] [INFO] DFAST Taxonomy check result was written to GCF_000186385.1_ASM18638v1_genomic.fna/tc_result.tsv
[2024-01-24 13:37:11,453] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:11,453] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:11,454] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg99ad8680-227d-4ea9-8c39-cadffc754755/dqc_reference/checkm_data
[2024-01-24 13:37:11,455] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:11,497] [INFO] Task started: CheckM
[2024-01-24 13:37:11,497] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000186385.1_ASM18638v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000186385.1_ASM18638v1_genomic.fna/checkm_input GCF_000186385.1_ASM18638v1_genomic.fna/checkm_result
[2024-01-24 13:37:52,157] [INFO] Task succeeded: CheckM
[2024-01-24 13:37:52,159] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:37:52,187] [INFO] ===== Completeness check finished =====
[2024-01-24 13:37:52,187] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:37:52,188] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000186385.1_ASM18638v1_genomic.fna/markers.fasta)
[2024-01-24 13:37:52,188] [INFO] Task started: Blastn
[2024-01-24 13:37:52,188] [INFO] Running command: blastn -query GCF_000186385.1_ASM18638v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg99ad8680-227d-4ea9-8c39-cadffc754755/dqc_reference/reference_markers_gtdb.fasta -out GCF_000186385.1_ASM18638v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:53,269] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:53,273] [INFO] Selected 17 target genomes.
[2024-01-24 13:37:53,273] [INFO] Target genome list was writen to GCF_000186385.1_ASM18638v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:37:53,295] [INFO] Task started: fastANI
[2024-01-24 13:37:53,295] [INFO] Running command: fastANI --query /var/lib/cwl/stg95d249d9-8da2-428b-aacf-db40f6defc91/GCF_000186385.1_ASM18638v1_genomic.fna.gz --refList GCF_000186385.1_ASM18638v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000186385.1_ASM18638v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:38:06,579] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:06,599] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:38:06,599] [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_000186385.1	s__Deinococcus_B maricopensis	100.0	1166	1166	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus_B	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014646915.1	s__Deinococcus aquiradiocola	79.2753	563	1166	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	79.2387	475	1166	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	98.09	98.03	0.94	0.93	3	-
GCF_002017875.1	s__Deinococcus sp002017875	79.0718	504	1166	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	79.0432	547	1166	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	96.65	95.40	0.88	0.83	5	-
GCF_001507665.1	s__Deinococcus actinosclerus	79.0243	497	1166	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	79.0096	529	1166	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	78.9737	533	1166	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003444775.1	s__Deinococcus ficus	78.9143	505	1166	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	98.33	97.44	0.95	0.88	4	-
GCF_013337115.1	s__Deinococcus sp013337115	78.908	544	1166	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	78.8551	508	1166	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	77.8109	309	1166	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	77.7538	391	1166	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002869765.1	s__Deinococcus planocerae	77.6554	358	1166	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	77.5377	283	1166	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	99.94	99.91	0.99	0.99	8	-
GCF_018863415.1	s__Deinococcus sp018863415	77.4867	378	1166	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000745175.1	s__Deinococcus sp000745175	77.4053	256	1166	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 13:38:06,601] [INFO] GTDB search result was written to GCF_000186385.1_ASM18638v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:38:06,602] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:38:06,606] [INFO] DFAST_QC result json was written to GCF_000186385.1_ASM18638v1_genomic.fna/dqc_result.json
[2024-01-24 13:38:06,606] [INFO] DFAST_QC completed!
[2024-01-24 13:38:06,606] [INFO] Total running time: 0h1m22s