[2024-01-24 13:32:41,212] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:41,213] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:41,214] [INFO] DQC Reference Directory: /var/lib/cwl/stge9cd7f5a-4527-4da4-b670-dfd9f55b02ea/dqc_reference
[2024-01-24 13:32:42,510] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:42,511] [INFO] Task started: Prodigal
[2024-01-24 13:32:42,511] [INFO] Running command: gunzip -c /var/lib/cwl/stg16c8084c-e75c-44ed-b3f1-76aca2d75da5/GCF_003444775.1_ASM344477v1_genomic.fna.gz | prodigal -d GCF_003444775.1_ASM344477v1_genomic.fna/cds.fna -a GCF_003444775.1_ASM344477v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:53,742] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:53,742] [INFO] Task started: HMMsearch
[2024-01-24 13:32:53,742] [INFO] Running command: hmmsearch --tblout GCF_003444775.1_ASM344477v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge9cd7f5a-4527-4da4-b670-dfd9f55b02ea/dqc_reference/reference_markers.hmm GCF_003444775.1_ASM344477v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:54,025] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:54,026] [INFO] Found 6/6 markers.
[2024-01-24 13:32:54,059] [INFO] Query marker FASTA was written to GCF_003444775.1_ASM344477v1_genomic.fna/markers.fasta
[2024-01-24 13:32:54,060] [INFO] Task started: Blastn
[2024-01-24 13:32:54,060] [INFO] Running command: blastn -query GCF_003444775.1_ASM344477v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge9cd7f5a-4527-4da4-b670-dfd9f55b02ea/dqc_reference/reference_markers.fasta -out GCF_003444775.1_ASM344477v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:54,693] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:54,695] [INFO] Selected 14 target genomes.
[2024-01-24 13:32:54,695] [INFO] Target genome list was writen to GCF_003444775.1_ASM344477v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:54,742] [INFO] Task started: fastANI
[2024-01-24 13:32:54,742] [INFO] Running command: fastANI --query /var/lib/cwl/stg16c8084c-e75c-44ed-b3f1-76aca2d75da5/GCF_003444775.1_ASM344477v1_genomic.fna.gz --refList GCF_003444775.1_ASM344477v1_genomic.fna/target_genomes.txt --output GCF_003444775.1_ASM344477v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:33:08,315] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:08,315] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge9cd7f5a-4527-4da4-b670-dfd9f55b02ea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:33:08,315] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge9cd7f5a-4527-4da4-b670-dfd9f55b02ea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:33:08,324] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:33:08,325] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:33:08,325] [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 ficus	strain=CC-FR2-10	GCA_003444775.1	317577	317577	type	True	100.0	1379	1382	95	conclusive
Deinococcus ficus	strain=DSM 19119	GCA_000430865.1	317577	317577	type	True	99.9831	1355	1382	95	conclusive
Deinococcus actinosclerus	strain=BM2	GCA_001507665.1	1768108	1768108	type	True	81.7372	704	1382	95	below_threshold
Deinococcus xianganensis	strain=Y35	GCA_009834985.1	1507289	1507289	type	True	81.6172	691	1382	95	below_threshold
Deinococcus grandis	strain=ATCC 43672	GCA_001485435.1	57498	57498	type	True	81.5668	744	1382	95	below_threshold
Deinococcus soli (ex Cha et al. 2016)	strain=N5	GCA_001007995.1	1309411	1309411	type	True	81.5563	680	1382	95	below_threshold
Deinococcus knuensis	strain=JCM 31406	GCA_014648155.1	1837380	1837380	type	True	81.5428	728	1382	95	below_threshold
Deinococcus seoulensis	strain=JCM 31404	GCA_014648115.1	1837379	1837379	type	True	81.5387	719	1382	95	below_threshold
Deinococcus kurensis	strain=KR-1	GCA_009687825.1	2662757	2662757	type	True	81.4648	743	1382	95	below_threshold
Deinococcus arenae	strain=JCM 31047	GCA_014647995.1	1452751	1452751	type	True	81.4598	742	1382	95	below_threshold
Deinococcus sedimenti	strain=JCM 31405	GCA_014648135.1	1867090	1867090	type	True	81.4036	719	1382	95	below_threshold
Deinococcus saudiensis	strain=CGMCC 1.15089	GCA_014640655.1	1765963	1765963	type	True	81.2909	732	1382	95	below_threshold
Deinococcus radiotolerans	strain=JCM 19173	GCA_014647435.1	1309407	1309407	type	True	81.2121	740	1382	95	below_threshold
Deinococcus metalli	strain=DSM 27521	GCA_014201805.1	1141878	1141878	type	True	80.628	709	1382	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:33:08,326] [INFO] DFAST Taxonomy check result was written to GCF_003444775.1_ASM344477v1_genomic.fna/tc_result.tsv
[2024-01-24 13:33:08,327] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:33:08,327] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:33:08,327] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge9cd7f5a-4527-4da4-b670-dfd9f55b02ea/dqc_reference/checkm_data
[2024-01-24 13:33:08,328] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:33:08,368] [INFO] Task started: CheckM
[2024-01-24 13:33:08,368] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003444775.1_ASM344477v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003444775.1_ASM344477v1_genomic.fna/checkm_input GCF_003444775.1_ASM344477v1_genomic.fna/checkm_result
[2024-01-24 13:33:54,463] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:54,464] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:54,482] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:54,482] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:54,482] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003444775.1_ASM344477v1_genomic.fna/markers.fasta)
[2024-01-24 13:33:54,482] [INFO] Task started: Blastn
[2024-01-24 13:33:54,482] [INFO] Running command: blastn -query GCF_003444775.1_ASM344477v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge9cd7f5a-4527-4da4-b670-dfd9f55b02ea/dqc_reference/reference_markers_gtdb.fasta -out GCF_003444775.1_ASM344477v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:55,462] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:55,472] [INFO] Selected 11 target genomes.
[2024-01-24 13:33:55,472] [INFO] Target genome list was writen to GCF_003444775.1_ASM344477v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:55,479] [INFO] Task started: fastANI
[2024-01-24 13:33:55,479] [INFO] Running command: fastANI --query /var/lib/cwl/stg16c8084c-e75c-44ed-b3f1-76aca2d75da5/GCF_003444775.1_ASM344477v1_genomic.fna.gz --refList GCF_003444775.1_ASM344477v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003444775.1_ASM344477v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:34:06,062] [INFO] Task succeeded: fastANI
[2024-01-24 13:34:06,070] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:34:06,070] [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_003444775.1	s__Deinococcus ficus	100.0	1380	1382	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	98.33	97.44	0.95	0.88	4	conclusive
GCF_001507665.1	s__Deinococcus actinosclerus	81.7401	704	1382	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	81.715	718	1382	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	99.28	99.28	0.90	0.90	2	-
GCF_001485435.1	s__Deinococcus grandis	81.5726	743	1382	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	81.5212	714	1382	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	81.5132	720	1382	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	97.69	97.69	0.87	0.87	2	-
GCF_001007995.1	s__Deinococcus soli	81.499	683	1382	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	98.09	98.03	0.94	0.93	3	-
GCF_014648135.1	s__Deinococcus sedimenti	81.3886	721	1382	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	81.2189	738	1382	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	80.5963	715	1382	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014647655.1	s__Deinococcus malanensis	79.3777	531	1382	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 13:34:06,071] [INFO] GTDB search result was written to GCF_003444775.1_ASM344477v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:34:06,072] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:34:06,074] [INFO] DFAST_QC result json was written to GCF_003444775.1_ASM344477v1_genomic.fna/dqc_result.json
[2024-01-24 13:34:06,075] [INFO] DFAST_QC completed!
[2024-01-24 13:34:06,075] [INFO] Total running time: 0h1m25s