[2024-01-25 19:54:35,423] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:54:35,425] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:54:35,425] [INFO] DQC Reference Directory: /var/lib/cwl/stg04d21189-fd24-4a07-90df-3dcd9052013c/dqc_reference
[2024-01-25 19:54:36,589] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:54:36,590] [INFO] Task started: Prodigal
[2024-01-25 19:54:36,590] [INFO] Running command: gunzip -c /var/lib/cwl/stgfd33f5f9-82b5-43e3-8826-90c4a4fead62/GCF_020166415.1_ASM2016641v1_genomic.fna.gz | prodigal -d GCF_020166415.1_ASM2016641v1_genomic.fna/cds.fna -a GCF_020166415.1_ASM2016641v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:54:49,294] [INFO] Task succeeded: Prodigal
[2024-01-25 19:54:49,294] [INFO] Task started: HMMsearch
[2024-01-25 19:54:49,295] [INFO] Running command: hmmsearch --tblout GCF_020166415.1_ASM2016641v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg04d21189-fd24-4a07-90df-3dcd9052013c/dqc_reference/reference_markers.hmm GCF_020166415.1_ASM2016641v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:54:49,546] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:54:49,547] [INFO] Found 6/6 markers.
[2024-01-25 19:54:49,586] [INFO] Query marker FASTA was written to GCF_020166415.1_ASM2016641v1_genomic.fna/markers.fasta
[2024-01-25 19:54:49,586] [INFO] Task started: Blastn
[2024-01-25 19:54:49,586] [INFO] Running command: blastn -query GCF_020166415.1_ASM2016641v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg04d21189-fd24-4a07-90df-3dcd9052013c/dqc_reference/reference_markers.fasta -out GCF_020166415.1_ASM2016641v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:54:50,217] [INFO] Task succeeded: Blastn
[2024-01-25 19:54:50,220] [INFO] Selected 15 target genomes.
[2024-01-25 19:54:50,220] [INFO] Target genome list was writen to GCF_020166415.1_ASM2016641v1_genomic.fna/target_genomes.txt
[2024-01-25 19:54:50,258] [INFO] Task started: fastANI
[2024-01-25 19:54:50,258] [INFO] Running command: fastANI --query /var/lib/cwl/stgfd33f5f9-82b5-43e3-8826-90c4a4fead62/GCF_020166415.1_ASM2016641v1_genomic.fna.gz --refList GCF_020166415.1_ASM2016641v1_genomic.fna/target_genomes.txt --output GCF_020166415.1_ASM2016641v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:55:05,149] [INFO] Task succeeded: fastANI
[2024-01-25 19:55:05,150] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg04d21189-fd24-4a07-90df-3dcd9052013c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:55:05,150] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg04d21189-fd24-4a07-90df-3dcd9052013c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:55:05,163] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:55:05,163] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:55:05,164] [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 multiflagellatus	strain=KACC 19287	GCA_020166415.1	1656887	1656887	type	True	100.0	1556	1557	95	conclusive
Deinococcus aquaedulcis	strain=SYSU M42101	GCA_019693445.1	2840455	2840455	type	True	93.3618	1118	1557	95	below_threshold
Deinococcus arcticus	strain=OD32	GCA_003028415.1	2136176	2136176	type	True	88.4203	1066	1557	95	below_threshold
Deinococcus saudiensis	strain=CGMCC 1.15089	GCA_014640655.1	1765963	1765963	type	True	80.8449	792	1557	95	below_threshold
Deinococcus arenae	strain=JCM 31047	GCA_014647995.1	1452751	1452751	type	True	80.8025	775	1557	95	below_threshold
Deinococcus kurensis	strain=KR-1	GCA_009687825.1	2662757	2662757	type	True	80.7507	781	1557	95	below_threshold
Deinococcus grandis	strain=ATCC 43672	GCA_001485435.1	57498	57498	type	True	80.7494	795	1557	95	below_threshold
Deinococcus daejeonensis	strain=JCM 16918	GCA_014647175.1	1007098	1007098	type	True	80.6141	788	1557	95	below_threshold
Deinococcus sedimenti	strain=JCM 31405	GCA_014648135.1	1867090	1867090	type	True	80.6137	776	1557	95	below_threshold
Deinococcus soli (ex Cha et al. 2016)	strain=N5	GCA_001007995.1	1309411	1309411	type	True	80.5226	697	1557	95	below_threshold
Deinococcus xianganensis	strain=Y35	GCA_009834985.1	1507289	1507289	type	True	80.4533	734	1557	95	below_threshold
Deinococcus radiotolerans	strain=JCM 19173	GCA_014647435.1	1309407	1309407	type	True	80.3721	775	1557	95	below_threshold
Deinococcus aerophilus	strain=JCM 15443	GCA_014647075.1	522488	522488	type	True	80.1112	637	1557	95	below_threshold
Deinococcus metalli	strain=DSM 27521	GCA_014201805.1	1141878	1141878	type	True	79.9588	699	1557	95	below_threshold
Deinococcus phoenicis	strain=1P10ME	GCA_000599865.1	1476583	1476583	type	True	79.4857	635	1557	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:55:05,172] [INFO] DFAST Taxonomy check result was written to GCF_020166415.1_ASM2016641v1_genomic.fna/tc_result.tsv
[2024-01-25 19:55:05,173] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:55:05,173] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:55:05,173] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg04d21189-fd24-4a07-90df-3dcd9052013c/dqc_reference/checkm_data
[2024-01-25 19:55:05,174] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:55:05,227] [INFO] Task started: CheckM
[2024-01-25 19:55:05,227] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020166415.1_ASM2016641v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020166415.1_ASM2016641v1_genomic.fna/checkm_input GCF_020166415.1_ASM2016641v1_genomic.fna/checkm_result
[2024-01-25 19:55:47,335] [INFO] Task succeeded: CheckM
[2024-01-25 19:55:47,336] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.39%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:55:47,349] [INFO] ===== Completeness check finished =====
[2024-01-25 19:55:47,349] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:55:47,350] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020166415.1_ASM2016641v1_genomic.fna/markers.fasta)
[2024-01-25 19:55:47,350] [INFO] Task started: Blastn
[2024-01-25 19:55:47,350] [INFO] Running command: blastn -query GCF_020166415.1_ASM2016641v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg04d21189-fd24-4a07-90df-3dcd9052013c/dqc_reference/reference_markers_gtdb.fasta -out GCF_020166415.1_ASM2016641v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:55:48,278] [INFO] Task succeeded: Blastn
[2024-01-25 19:55:48,281] [INFO] Selected 15 target genomes.
[2024-01-25 19:55:48,281] [INFO] Target genome list was writen to GCF_020166415.1_ASM2016641v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:55:48,290] [INFO] Task started: fastANI
[2024-01-25 19:55:48,290] [INFO] Running command: fastANI --query /var/lib/cwl/stgfd33f5f9-82b5-43e3-8826-90c4a4fead62/GCF_020166415.1_ASM2016641v1_genomic.fna.gz --refList GCF_020166415.1_ASM2016641v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020166415.1_ASM2016641v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:56:02,314] [INFO] Task succeeded: fastANI
[2024-01-25 19:56:02,323] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 19:56:02,324] [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_003028415.1	s__Deinococcus sp003028415	88.4034	1067	1557	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009755355.1	s__Deinococcus sp009755355	83.1925	904	1557	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	80.8886	741	1557	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	96.26	96.21	0.94	0.94	4	-
GCF_001485435.1	s__Deinococcus grandis	80.7816	791	1557	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	80.6472	777	1557	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	96.85	96.85	0.84	0.84	2	-
GCF_014648135.1	s__Deinococcus sedimenti	80.5582	784	1557	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	80.5212	697	1557	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	98.09	98.03	0.94	0.93	3	-
GCF_014647435.1	s__Deinococcus radiotolerans	80.4021	771	1557	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	80.2775	734	1557	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	80.1083	639	1557	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013337115.1	s__Deinococcus sp013337115	80.0547	778	1557	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014201805.1	s__Deinococcus metalli	79.9636	700	1557	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000599865.1	s__Deinococcus phoenicis	79.4673	640	1557	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	79.2667	557	1557	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002897375.1	s__Deinococcus aerius	78.9558	609	1557	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:56:02,325] [INFO] GTDB search result was written to GCF_020166415.1_ASM2016641v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:56:02,325] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:56:02,328] [INFO] DFAST_QC result json was written to GCF_020166415.1_ASM2016641v1_genomic.fna/dqc_result.json
[2024-01-25 19:56:02,328] [INFO] DFAST_QC completed!
[2024-01-25 19:56:02,329] [INFO] Total running time: 0h1m27s