[2024-01-25 18:40:35,779] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:40:35,780] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:40:35,780] [INFO] DQC Reference Directory: /var/lib/cwl/stgf5b0655b-4ef1-410b-aa2b-2b8fb6b1acf4/dqc_reference
[2024-01-25 18:40:36,876] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:40:36,877] [INFO] Task started: Prodigal
[2024-01-25 18:40:36,877] [INFO] Running command: gunzip -c /var/lib/cwl/stgfb5f8628-d708-4d90-bbb0-7dbea7558b66/GCF_030160055.1_ASM3016005v1_genomic.fna.gz | prodigal -d GCF_030160055.1_ASM3016005v1_genomic.fna/cds.fna -a GCF_030160055.1_ASM3016005v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:40:56,036] [INFO] Task succeeded: Prodigal
[2024-01-25 18:40:56,036] [INFO] Task started: HMMsearch
[2024-01-25 18:40:56,036] [INFO] Running command: hmmsearch --tblout GCF_030160055.1_ASM3016005v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf5b0655b-4ef1-410b-aa2b-2b8fb6b1acf4/dqc_reference/reference_markers.hmm GCF_030160055.1_ASM3016005v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:40:56,313] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:40:56,314] [INFO] Found 6/6 markers.
[2024-01-25 18:40:56,357] [INFO] Query marker FASTA was written to GCF_030160055.1_ASM3016005v1_genomic.fna/markers.fasta
[2024-01-25 18:40:56,357] [INFO] Task started: Blastn
[2024-01-25 18:40:56,357] [INFO] Running command: blastn -query GCF_030160055.1_ASM3016005v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf5b0655b-4ef1-410b-aa2b-2b8fb6b1acf4/dqc_reference/reference_markers.fasta -out GCF_030160055.1_ASM3016005v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:40:57,209] [INFO] Task succeeded: Blastn
[2024-01-25 18:40:57,212] [INFO] Selected 12 target genomes.
[2024-01-25 18:40:57,213] [INFO] Target genome list was writen to GCF_030160055.1_ASM3016005v1_genomic.fna/target_genomes.txt
[2024-01-25 18:40:57,216] [INFO] Task started: fastANI
[2024-01-25 18:40:57,216] [INFO] Running command: fastANI --query /var/lib/cwl/stgfb5f8628-d708-4d90-bbb0-7dbea7558b66/GCF_030160055.1_ASM3016005v1_genomic.fna.gz --refList GCF_030160055.1_ASM3016005v1_genomic.fna/target_genomes.txt --output GCF_030160055.1_ASM3016005v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:41:09,827] [INFO] Task succeeded: fastANI
[2024-01-25 18:41:09,828] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf5b0655b-4ef1-410b-aa2b-2b8fb6b1acf4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:41:09,828] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf5b0655b-4ef1-410b-aa2b-2b8fb6b1acf4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:41:09,837] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:41:09,837] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:41:09,838] [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
Dyella nitratireducens	strain=CGMCC 1.15439	GCA_014642835.1	1849580	1849580	type	True	99.9972	1886	1889	95	conclusive
Dyella choica	strain=4 M-K27	GCA_003977665.1	1927959	1927959	type	True	83.0361	1118	1889	95	below_threshold
Dyella monticola	strain=4 G-K06	GCA_003363155.1	1927958	1927958	type	True	81.6424	965	1889	95	below_threshold
Dyella acidiphila	strain=7MK23	GCA_014863405.1	2775866	2775866	type	True	81.6189	1010	1889	95	below_threshold
Dyella psychrodurans	strain=4MSK11	GCA_003363265.1	1927960	1927960	type	True	81.3363	872	1889	95	below_threshold
Dyella flava	strain=DHOC52	GCA_016904955.1	1920170	1920170	type	True	81.1672	842	1889	95	below_threshold
Dyella mobilis	strain=DHON07	GCA_016904945.1	1849582	1849582	type	True	81.1096	896	1889	95	below_threshold
Dyella caseinilytica	strain=DHOB09	GCA_016865235.1	1849581	1849581	type	True	80.7421	880	1889	95	below_threshold
Dyella japonica	strain=DSM 16301	GCA_001010355.1	231455	231455	type	True	79.701	514	1889	95	below_threshold
Dyella telluris	strain=G9	GCA_014297575.1	2763498	2763498	type	True	79.5964	637	1889	95	below_threshold
Frateuria flava	strain=MAH-13	GCA_017837635.1	2821489	2821489	type	True	79.1153	489	1889	95	below_threshold
Luteimonas lumbrici	strain=1.1416	GCA_006476065.1	2559601	2559601	type	True	77.5181	187	1889	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:41:09,840] [INFO] DFAST Taxonomy check result was written to GCF_030160055.1_ASM3016005v1_genomic.fna/tc_result.tsv
[2024-01-25 18:41:09,841] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:41:09,841] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:41:09,841] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf5b0655b-4ef1-410b-aa2b-2b8fb6b1acf4/dqc_reference/checkm_data
[2024-01-25 18:41:09,842] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:41:09,895] [INFO] Task started: CheckM
[2024-01-25 18:41:09,896] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030160055.1_ASM3016005v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030160055.1_ASM3016005v1_genomic.fna/checkm_input GCF_030160055.1_ASM3016005v1_genomic.fna/checkm_result
[2024-01-25 18:42:05,431] [INFO] Task succeeded: CheckM
[2024-01-25 18:42:05,432] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:42:05,457] [INFO] ===== Completeness check finished =====
[2024-01-25 18:42:05,457] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:42:05,459] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030160055.1_ASM3016005v1_genomic.fna/markers.fasta)
[2024-01-25 18:42:05,459] [INFO] Task started: Blastn
[2024-01-25 18:42:05,459] [INFO] Running command: blastn -query GCF_030160055.1_ASM3016005v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf5b0655b-4ef1-410b-aa2b-2b8fb6b1acf4/dqc_reference/reference_markers_gtdb.fasta -out GCF_030160055.1_ASM3016005v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:42:07,156] [INFO] Task succeeded: Blastn
[2024-01-25 18:42:07,158] [INFO] Selected 10 target genomes.
[2024-01-25 18:42:07,158] [INFO] Target genome list was writen to GCF_030160055.1_ASM3016005v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:42:07,165] [INFO] Task started: fastANI
[2024-01-25 18:42:07,165] [INFO] Running command: fastANI --query /var/lib/cwl/stgfb5f8628-d708-4d90-bbb0-7dbea7558b66/GCF_030160055.1_ASM3016005v1_genomic.fna.gz --refList GCF_030160055.1_ASM3016005v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030160055.1_ASM3016005v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:42:18,958] [INFO] Task succeeded: fastANI
[2024-01-25 18:42:18,964] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:42:18,965] [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_014642835.1	s__Dyella_B nitratireducens	99.9972	1886	1889	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella_B	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003977665.1	s__Dyella_B choica	83.0291	1120	1889	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014873315.1	s__Dyella_B sp014873315	82.6707	1118	1889	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003363155.1	s__Dyella_B monticola	81.6499	964	1889	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014863405.1	s__Dyella_B sp014863405	81.6035	1012	1889	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016904955.1	s__Dyella_B flava	81.1543	844	1889	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016904945.1	s__Dyella_B mobilis	81.0829	900	1889	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004114615.1	s__Dyella_B sp004114615	80.6078	587	1889	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903970555.1	s__Dyella_B sp903970555	80.3754	717	1889	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012275375.1	s__Dyella sp012275375	79.7627	710	1889	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	96.64	95.58	0.92	0.90	4	-
--------------------------------------------------------------------------------
[2024-01-25 18:42:18,967] [INFO] GTDB search result was written to GCF_030160055.1_ASM3016005v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:42:18,968] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:42:18,971] [INFO] DFAST_QC result json was written to GCF_030160055.1_ASM3016005v1_genomic.fna/dqc_result.json
[2024-01-25 18:42:18,971] [INFO] DFAST_QC completed!
[2024-01-25 18:42:18,971] [INFO] Total running time: 0h1m43s