[2024-01-24 14:55:26,258] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:55:26,261] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:55:26,261] [INFO] DQC Reference Directory: /var/lib/cwl/stg3db611c9-7691-4896-b766-d43bb5d8f566/dqc_reference
[2024-01-24 14:55:27,548] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:55:27,549] [INFO] Task started: Prodigal
[2024-01-24 14:55:27,549] [INFO] Running command: gunzip -c /var/lib/cwl/stg56a07d98-20f5-4ce6-81b5-09f9a4fbf965/GCF_030160075.1_ASM3016007v1_genomic.fna.gz | prodigal -d GCF_030160075.1_ASM3016007v1_genomic.fna/cds.fna -a GCF_030160075.1_ASM3016007v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:55:41,110] [INFO] Task succeeded: Prodigal
[2024-01-24 14:55:41,111] [INFO] Task started: HMMsearch
[2024-01-24 14:55:41,111] [INFO] Running command: hmmsearch --tblout GCF_030160075.1_ASM3016007v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3db611c9-7691-4896-b766-d43bb5d8f566/dqc_reference/reference_markers.hmm GCF_030160075.1_ASM3016007v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:55:41,370] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:55:41,372] [INFO] Found 6/6 markers.
[2024-01-24 14:55:41,421] [INFO] Query marker FASTA was written to GCF_030160075.1_ASM3016007v1_genomic.fna/markers.fasta
[2024-01-24 14:55:41,422] [INFO] Task started: Blastn
[2024-01-24 14:55:41,422] [INFO] Running command: blastn -query GCF_030160075.1_ASM3016007v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3db611c9-7691-4896-b766-d43bb5d8f566/dqc_reference/reference_markers.fasta -out GCF_030160075.1_ASM3016007v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:55:42,397] [INFO] Task succeeded: Blastn
[2024-01-24 14:55:42,403] [INFO] Selected 14 target genomes.
[2024-01-24 14:55:42,404] [INFO] Target genome list was writen to GCF_030160075.1_ASM3016007v1_genomic.fna/target_genomes.txt
[2024-01-24 14:55:42,410] [INFO] Task started: fastANI
[2024-01-24 14:55:42,410] [INFO] Running command: fastANI --query /var/lib/cwl/stg56a07d98-20f5-4ce6-81b5-09f9a4fbf965/GCF_030160075.1_ASM3016007v1_genomic.fna.gz --refList GCF_030160075.1_ASM3016007v1_genomic.fna/target_genomes.txt --output GCF_030160075.1_ASM3016007v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:55:55,049] [INFO] Task succeeded: fastANI
[2024-01-24 14:55:55,049] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3db611c9-7691-4896-b766-d43bb5d8f566/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:55:55,049] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3db611c9-7691-4896-b766-d43bb5d8f566/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:55:55,061] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:55:55,061] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:55:55,061] [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 psychrodurans	strain=4MSK11	GCA_003363265.1	1927960	1927960	type	True	83.0432	948	1345	95	below_threshold
Dyella acidiphila	strain=7MK23	GCA_014863405.1	2775866	2775866	type	True	81.8972	865	1345	95	below_threshold
Dyella flava	strain=DHOC52	GCA_016904955.1	1920170	1920170	type	True	81.7891	855	1345	95	below_threshold
Dyella mobilis	strain=DHON07	GCA_016904945.1	1849582	1849582	type	True	81.5584	810	1345	95	below_threshold
Dyella dinghuensis	strain=DHOA06	GCA_003977615.1	1920169	1920169	type	True	81.4217	809	1345	95	below_threshold
Dyella caseinilytica	strain=CGMCC 1.15434	GCA_014642815.1	1849581	1849581	type	True	81.2888	824	1345	95	below_threshold
Dyella caseinilytica	strain=DHOB09	GCA_016865235.1	1849581	1849581	type	True	81.2773	823	1345	95	below_threshold
Dyella choica	strain=4 M-K27	GCA_003977665.1	1927959	1927959	type	True	80.8325	766	1345	95	below_threshold
Dyella monticola	strain=4 G-K06	GCA_003363155.1	1927958	1927958	type	True	80.6058	747	1345	95	below_threshold
Dyella kyungheensis	strain=THG-B117	GCA_016905005.1	1242174	1242174	type	True	79.8763	593	1345	95	below_threshold
Dyella japonica	strain=DSM 16301	GCA_001010355.1	231455	231455	type	True	79.8715	480	1345	95	below_threshold
Dyella telluris	strain=G9	GCA_014297575.1	2763498	2763498	type	True	79.6786	558	1345	95	below_threshold
Frateuria flava	strain=MAH-13	GCA_017837635.1	2821489	2821489	type	True	79.3941	462	1345	95	below_threshold
Arenimonas caeni	strain=z29	GCA_003024235.1	2058085	2058085	type	True	77.6859	195	1345	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:55:55,063] [INFO] DFAST Taxonomy check result was written to GCF_030160075.1_ASM3016007v1_genomic.fna/tc_result.tsv
[2024-01-24 14:55:55,064] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:55:55,064] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:55:55,064] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3db611c9-7691-4896-b766-d43bb5d8f566/dqc_reference/checkm_data
[2024-01-24 14:55:55,065] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:55:55,106] [INFO] Task started: CheckM
[2024-01-24 14:55:55,106] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030160075.1_ASM3016007v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030160075.1_ASM3016007v1_genomic.fna/checkm_input GCF_030160075.1_ASM3016007v1_genomic.fna/checkm_result
[2024-01-24 14:56:36,670] [INFO] Task succeeded: CheckM
[2024-01-24 14:56:36,671] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:56:36,688] [INFO] ===== Completeness check finished =====
[2024-01-24 14:56:36,689] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:56:36,689] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030160075.1_ASM3016007v1_genomic.fna/markers.fasta)
[2024-01-24 14:56:36,689] [INFO] Task started: Blastn
[2024-01-24 14:56:36,689] [INFO] Running command: blastn -query GCF_030160075.1_ASM3016007v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3db611c9-7691-4896-b766-d43bb5d8f566/dqc_reference/reference_markers_gtdb.fasta -out GCF_030160075.1_ASM3016007v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:56:38,649] [INFO] Task succeeded: Blastn
[2024-01-24 14:56:38,655] [INFO] Selected 14 target genomes.
[2024-01-24 14:56:38,655] [INFO] Target genome list was writen to GCF_030160075.1_ASM3016007v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:56:38,666] [INFO] Task started: fastANI
[2024-01-24 14:56:38,666] [INFO] Running command: fastANI --query /var/lib/cwl/stg56a07d98-20f5-4ce6-81b5-09f9a4fbf965/GCF_030160075.1_ASM3016007v1_genomic.fna.gz --refList GCF_030160075.1_ASM3016007v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030160075.1_ASM3016007v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:56:53,363] [INFO] Task succeeded: fastANI
[2024-01-24 14:56:53,377] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 14:56:53,377] [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
GCA_903970555.1	s__Dyella_B sp903970555	83.1112	827	1345	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_003363265.1	s__Dyella_B psychrodurans	83.0585	946	1345	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_015655335.1	s__Dyella_B sp015655335	82.9222	731	1345	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	81.9053	864	1345	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	81.7937	854	1345	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	81.5672	809	1345	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_003977615.1	s__Dyella_B dinghuensis	81.4318	807	1345	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_016865235.1	s__Dyella_B caseinilytica	81.2776	823	1345	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella_B	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014873315.1	s__Dyella_B sp014873315	81.0469	790	1345	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_003977665.1	s__Dyella_B choica	80.8339	767	1345	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_016586165.1	s__Dyella sp016586165	79.9117	564	1345	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001010355.1	s__Dyella japonica	79.8774	479	1345	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114325.1	s__Rhodanobacter glycinis	79.7832	525	1345	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	97.24	96.89	0.85	0.82	5	-
GCF_003688835.1	s__Dyella sp003688835	79.741	558	1345	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:56:53,385] [INFO] GTDB search result was written to GCF_030160075.1_ASM3016007v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:56:53,386] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:56:53,389] [INFO] DFAST_QC result json was written to GCF_030160075.1_ASM3016007v1_genomic.fna/dqc_result.json
[2024-01-24 14:56:53,390] [INFO] DFAST_QC completed!
[2024-01-24 14:56:53,390] [INFO] Total running time: 0h1m27s