[2024-01-24 13:13:10,356] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:13:10,359] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:13:10,359] [INFO] DQC Reference Directory: /var/lib/cwl/stga18c9dc8-403c-440e-9ba2-2b58cc1cfd8d/dqc_reference
[2024-01-24 13:13:11,656] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:13:11,659] [INFO] Task started: Prodigal
[2024-01-24 13:13:11,660] [INFO] Running command: gunzip -c /var/lib/cwl/stg00d88620-c1dc-41d6-8c4b-c4ebcc305142/GCF_014647075.1_ASM1464707v1_genomic.fna.gz | prodigal -d GCF_014647075.1_ASM1464707v1_genomic.fna/cds.fna -a GCF_014647075.1_ASM1464707v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:22,529] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:22,529] [INFO] Task started: HMMsearch
[2024-01-24 13:13:22,529] [INFO] Running command: hmmsearch --tblout GCF_014647075.1_ASM1464707v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga18c9dc8-403c-440e-9ba2-2b58cc1cfd8d/dqc_reference/reference_markers.hmm GCF_014647075.1_ASM1464707v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:22,810] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:22,811] [INFO] Found 6/6 markers.
[2024-01-24 13:13:22,845] [INFO] Query marker FASTA was written to GCF_014647075.1_ASM1464707v1_genomic.fna/markers.fasta
[2024-01-24 13:13:22,846] [INFO] Task started: Blastn
[2024-01-24 13:13:22,846] [INFO] Running command: blastn -query GCF_014647075.1_ASM1464707v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga18c9dc8-403c-440e-9ba2-2b58cc1cfd8d/dqc_reference/reference_markers.fasta -out GCF_014647075.1_ASM1464707v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:23,617] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:23,620] [INFO] Selected 14 target genomes.
[2024-01-24 13:13:23,621] [INFO] Target genome list was writen to GCF_014647075.1_ASM1464707v1_genomic.fna/target_genomes.txt
[2024-01-24 13:13:23,700] [INFO] Task started: fastANI
[2024-01-24 13:13:23,700] [INFO] Running command: fastANI --query /var/lib/cwl/stg00d88620-c1dc-41d6-8c4b-c4ebcc305142/GCF_014647075.1_ASM1464707v1_genomic.fna.gz --refList GCF_014647075.1_ASM1464707v1_genomic.fna/target_genomes.txt --output GCF_014647075.1_ASM1464707v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:13:37,223] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:37,224] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga18c9dc8-403c-440e-9ba2-2b58cc1cfd8d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:13:37,224] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga18c9dc8-403c-440e-9ba2-2b58cc1cfd8d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:13:37,236] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:13:37,236] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:13:37,237] [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 aerophilus	strain=JCM 15443	GCA_014647075.1	522488	522488	type	True	100.0	1145	1149	95	conclusive
Deinococcus aerolatus	strain=JCM 15442	GCA_014647055.1	522487	522487	type	True	83.1978	813	1149	95	below_threshold
Deinococcus radiopugnans	strain=DSM 12027	GCA_014201625.1	57497	57497	type	True	83.1374	796	1149	95	below_threshold
Deinococcus radiopugnans	strain=ATCC 19172	GCA_006335125.1	57497	57497	type	True	83.1226	805	1149	95	below_threshold
Deinococcus frigens	strain=DSM 12807	GCA_000701425.1	249403	249403	type	True	82.329	751	1149	95	below_threshold
Deinococcus marmoris	strain=DSM 12784	GCA_000701405.1	249408	249408	type	True	82.0162	777	1149	95	below_threshold
Deinococcus humi	strain=DSM 27939	GCA_014201875.1	662880	662880	type	True	81.5764	749	1149	95	below_threshold
Deinococcus humi	strain=JCM 17915	GCA_014647275.1	662880	662880	type	True	81.575	764	1149	95	below_threshold
Deinococcus metalli	strain=DSM 27521	GCA_014201805.1	1141878	1141878	type	True	80.2461	670	1149	95	below_threshold
Deinococcus kurensis	strain=KR-1	GCA_009687825.1	2662757	2662757	type	True	80.1762	635	1149	95	below_threshold
Deinococcus knuensis	strain=JCM 31406	GCA_014648155.1	1837380	1837380	type	True	80.1627	659	1149	95	below_threshold
Deinococcus actinosclerus	strain=BM2	GCA_001507665.1	1768108	1768108	type	True	80.1149	595	1149	95	below_threshold
Deinococcus malanensis	strain=JCM 30331	GCA_014647655.1	1706855	1706855	type	True	79.5543	511	1149	95	below_threshold
Deinococcus radiotolerans	strain=JCM 19173	GCA_014647435.1	1309407	1309407	type	True	79.5301	610	1149	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:13:37,242] [INFO] DFAST Taxonomy check result was written to GCF_014647075.1_ASM1464707v1_genomic.fna/tc_result.tsv
[2024-01-24 13:13:37,243] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:13:37,243] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:13:37,243] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga18c9dc8-403c-440e-9ba2-2b58cc1cfd8d/dqc_reference/checkm_data
[2024-01-24 13:13:37,244] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:13:37,287] [INFO] Task started: CheckM
[2024-01-24 13:13:37,287] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014647075.1_ASM1464707v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014647075.1_ASM1464707v1_genomic.fna/checkm_input GCF_014647075.1_ASM1464707v1_genomic.fna/checkm_result
[2024-01-24 13:14:13,111] [INFO] Task succeeded: CheckM
[2024-01-24 13:14:13,112] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:14:13,136] [INFO] ===== Completeness check finished =====
[2024-01-24 13:14:13,137] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:14:13,137] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014647075.1_ASM1464707v1_genomic.fna/markers.fasta)
[2024-01-24 13:14:13,137] [INFO] Task started: Blastn
[2024-01-24 13:14:13,138] [INFO] Running command: blastn -query GCF_014647075.1_ASM1464707v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga18c9dc8-403c-440e-9ba2-2b58cc1cfd8d/dqc_reference/reference_markers_gtdb.fasta -out GCF_014647075.1_ASM1464707v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:14:14,162] [INFO] Task succeeded: Blastn
[2024-01-24 13:14:14,165] [INFO] Selected 14 target genomes.
[2024-01-24 13:14:14,165] [INFO] Target genome list was writen to GCF_014647075.1_ASM1464707v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:14:14,185] [INFO] Task started: fastANI
[2024-01-24 13:14:14,185] [INFO] Running command: fastANI --query /var/lib/cwl/stg00d88620-c1dc-41d6-8c4b-c4ebcc305142/GCF_014647075.1_ASM1464707v1_genomic.fna.gz --refList GCF_014647075.1_ASM1464707v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014647075.1_ASM1464707v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:14:26,964] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:26,980] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:14:26,980] [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_014647075.1	s__Deinococcus aerophilus	100.0	1145	1149	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014647055.1	s__Deinococcus aerolatus	83.2228	810	1149	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006335125.1	s__Deinococcus radiopugnans	83.117	805	1149	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	98.45	97.61	0.92	0.87	4	-
GCF_000701425.1	s__Deinococcus frigens	82.3491	752	1149	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001949125.1	s__Deinococcus marmoris_A	82.0265	768	1149	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000701405.1	s__Deinococcus marmoris	81.993	780	1149	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014201875.1	s__Deinococcus humi	81.5641	751	1149	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	80.5	650	1149	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	80.2669	667	1149	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001507665.1	s__Deinococcus actinosclerus	80.0999	597	1149	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	96.26	96.21	0.94	0.94	4	-
GCF_000599865.1	s__Deinococcus phoenicis	80.0827	589	1149	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003028415.1	s__Deinococcus sp003028415	80.0415	627	1149	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	79.5301	514	1149	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	79.5206	612	1149	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 13:14:26,982] [INFO] GTDB search result was written to GCF_014647075.1_ASM1464707v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:14:26,983] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:14:26,990] [INFO] DFAST_QC result json was written to GCF_014647075.1_ASM1464707v1_genomic.fna/dqc_result.json
[2024-01-24 13:14:26,990] [INFO] DFAST_QC completed!
[2024-01-24 13:14:26,990] [INFO] Total running time: 0h1m17s