[2024-01-24 13:46:01,514] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:01,516] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:01,516] [INFO] DQC Reference Directory: /var/lib/cwl/stg288ebe56-adc2-4de5-82b4-5d0793a584f9/dqc_reference
[2024-01-24 13:46:02,951] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:02,953] [INFO] Task started: Prodigal
[2024-01-24 13:46:02,953] [INFO] Running command: gunzip -c /var/lib/cwl/stg493a07ed-58eb-4496-a289-d447b053151b/GCF_014875735.1_ASM1487573v1_genomic.fna.gz | prodigal -d GCF_014875735.1_ASM1487573v1_genomic.fna/cds.fna -a GCF_014875735.1_ASM1487573v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:13,956] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:13,957] [INFO] Task started: HMMsearch
[2024-01-24 13:46:13,957] [INFO] Running command: hmmsearch --tblout GCF_014875735.1_ASM1487573v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg288ebe56-adc2-4de5-82b4-5d0793a584f9/dqc_reference/reference_markers.hmm GCF_014875735.1_ASM1487573v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:14,247] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:14,248] [INFO] Found 6/6 markers.
[2024-01-24 13:46:14,285] [INFO] Query marker FASTA was written to GCF_014875735.1_ASM1487573v1_genomic.fna/markers.fasta
[2024-01-24 13:46:14,285] [INFO] Task started: Blastn
[2024-01-24 13:46:14,285] [INFO] Running command: blastn -query GCF_014875735.1_ASM1487573v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg288ebe56-adc2-4de5-82b4-5d0793a584f9/dqc_reference/reference_markers.fasta -out GCF_014875735.1_ASM1487573v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:14,948] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:14,956] [INFO] Selected 6 target genomes.
[2024-01-24 13:46:14,956] [INFO] Target genome list was writen to GCF_014875735.1_ASM1487573v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:14,967] [INFO] Task started: fastANI
[2024-01-24 13:46:14,968] [INFO] Running command: fastANI --query /var/lib/cwl/stg493a07ed-58eb-4496-a289-d447b053151b/GCF_014875735.1_ASM1487573v1_genomic.fna.gz --refList GCF_014875735.1_ASM1487573v1_genomic.fna/target_genomes.txt --output GCF_014875735.1_ASM1487573v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:48:20,801] [INFO] Task succeeded: fastANI
[2024-01-24 13:48:20,802] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg288ebe56-adc2-4de5-82b4-5d0793a584f9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:48:20,803] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg288ebe56-adc2-4de5-82b4-5d0793a584f9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:48:20,814] [INFO] Found 6 fastANI hits (6 hits with ANI > threshold)
[2024-01-24 13:48:20,814] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:48:20,814] [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 wulumuqiensis	strain=R12	GCA_014875845.1	980427	980427	type	True	99.8789	1092	1313	95	conclusive
Deinococcus wulumuqiensis	strain=R12	GCA_014875835.1	980427	980427	type	True	99.8446	983	1313	95	conclusive
Deinococcus wulumuqiensis	strain=R12	GCA_014875745.1	980427	980427	type	True	99.8437	1052	1313	95	conclusive
Deinococcus wulumuqiensis	strain=R12	GCA_000348665.1	980427	980427	type	True	99.8303	980	1313	95	conclusive
Deinococcus wulumuqiensis	strain=R12	GCA_014875975.1	980427	980427	type	True	99.8239	1025	1313	95	conclusive
Deinococcus wulumuqiensis	strain=R12	GCA_014875875.1	980427	980427	type	True	99.7919	991	1313	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 13:48:20,816] [INFO] DFAST Taxonomy check result was written to GCF_014875735.1_ASM1487573v1_genomic.fna/tc_result.tsv
[2024-01-24 13:48:20,817] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:48:20,817] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:48:20,818] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg288ebe56-adc2-4de5-82b4-5d0793a584f9/dqc_reference/checkm_data
[2024-01-24 13:48:20,819] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:48:20,861] [INFO] Task started: CheckM
[2024-01-24 13:48:20,862] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014875735.1_ASM1487573v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014875735.1_ASM1487573v1_genomic.fna/checkm_input GCF_014875735.1_ASM1487573v1_genomic.fna/checkm_result
[2024-01-24 13:48:54,402] [INFO] Task succeeded: CheckM
[2024-01-24 13:48:54,403] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 13:48:54,426] [INFO] ===== Completeness check finished =====
[2024-01-24 13:48:54,427] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:48:54,427] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014875735.1_ASM1487573v1_genomic.fna/markers.fasta)
[2024-01-24 13:48:54,427] [INFO] Task started: Blastn
[2024-01-24 13:48:54,428] [INFO] Running command: blastn -query GCF_014875735.1_ASM1487573v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg288ebe56-adc2-4de5-82b4-5d0793a584f9/dqc_reference/reference_markers_gtdb.fasta -out GCF_014875735.1_ASM1487573v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:48:55,329] [INFO] Task succeeded: Blastn
[2024-01-24 13:48:55,332] [INFO] Selected 18 target genomes.
[2024-01-24 13:48:55,332] [INFO] Target genome list was writen to GCF_014875735.1_ASM1487573v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:48:55,355] [INFO] Task started: fastANI
[2024-01-24 13:48:55,356] [INFO] Running command: fastANI --query /var/lib/cwl/stg493a07ed-58eb-4496-a289-d447b053151b/GCF_014875735.1_ASM1487573v1_genomic.fna.gz --refList GCF_014875735.1_ASM1487573v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014875735.1_ASM1487573v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:49:12,780] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:12,794] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:49:12,795] [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_011067105.1	s__Deinococcus wulumuqiensis	99.8789	1092	1313	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	99.82	97.50	0.97	0.83	19	conclusive
GCF_000008565.1	s__Deinococcus radiodurans	87.2662	857	1313	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	99.94	99.91	0.99	0.99	8	-
GCF_900109185.1	s__Deinococcus reticulitermitis	80.8204	679	1313	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	80.6043	622	1313	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002953415.1	s__Deinococcus sp002953415	79.9141	554	1313	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014201885.1	s__Deinococcus budaensis	79.8999	576	1313	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	79.8376	547	1313	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018260275.1	s__Deinococcus sp018260275	79.6929	370	1313	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018260405.1	s__Deinococcus sp018260405	79.5513	433	1313	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004758605.1	s__Deinococcus metallilatus	79.4576	565	1313	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	100.00	100.00	0.98	0.98	4	-
GCF_014647075.1	s__Deinococcus aerophilus	79.3178	510	1313	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	79.2043	500	1313	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	98.33	97.44	0.95	0.88	4	-
GCF_000190555.1	s__Deinococcus proteolyticus	79.0617	386	1313	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	79.0002	497	1313	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	98.09	98.03	0.94	0.93	3	-
GCF_001485435.1	s__Deinococcus grandis	78.9579	529	1313	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	78.9148	518	1313	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000701425.1	s__Deinococcus frigens	78.8519	504	1313	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	78.4928	482	1313	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 13:49:12,796] [INFO] GTDB search result was written to GCF_014875735.1_ASM1487573v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:49:12,797] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:49:12,800] [INFO] DFAST_QC result json was written to GCF_014875735.1_ASM1487573v1_genomic.fna/dqc_result.json
[2024-01-24 13:49:12,800] [INFO] DFAST_QC completed!
[2024-01-24 13:49:12,800] [INFO] Total running time: 0h3m11s