[2024-01-24 14:46:55,073] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:46:55,075] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:46:55,076] [INFO] DQC Reference Directory: /var/lib/cwl/stgc2580b58-dff3-443a-b183-bfaaf24a5791/dqc_reference
[2024-01-24 14:46:58,017] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:46:58,018] [INFO] Task started: Prodigal
[2024-01-24 14:46:58,018] [INFO] Running command: gunzip -c /var/lib/cwl/stgfffe55c7-aaf8-41ba-8aa1-a101c9f2be5f/GCF_003363265.1_ASM336326v1_genomic.fna.gz | prodigal -d GCF_003363265.1_ASM336326v1_genomic.fna/cds.fna -a GCF_003363265.1_ASM336326v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:47:14,398] [INFO] Task succeeded: Prodigal
[2024-01-24 14:47:14,399] [INFO] Task started: HMMsearch
[2024-01-24 14:47:14,399] [INFO] Running command: hmmsearch --tblout GCF_003363265.1_ASM336326v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc2580b58-dff3-443a-b183-bfaaf24a5791/dqc_reference/reference_markers.hmm GCF_003363265.1_ASM336326v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:47:14,698] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:47:14,699] [INFO] Found 6/6 markers.
[2024-01-24 14:47:14,741] [INFO] Query marker FASTA was written to GCF_003363265.1_ASM336326v1_genomic.fna/markers.fasta
[2024-01-24 14:47:14,741] [INFO] Task started: Blastn
[2024-01-24 14:47:14,742] [INFO] Running command: blastn -query GCF_003363265.1_ASM336326v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc2580b58-dff3-443a-b183-bfaaf24a5791/dqc_reference/reference_markers.fasta -out GCF_003363265.1_ASM336326v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:47:15,958] [INFO] Task succeeded: Blastn
[2024-01-24 14:47:15,963] [INFO] Selected 15 target genomes.
[2024-01-24 14:47:15,964] [INFO] Target genome list was writen to GCF_003363265.1_ASM336326v1_genomic.fna/target_genomes.txt
[2024-01-24 14:47:15,973] [INFO] Task started: fastANI
[2024-01-24 14:47:15,973] [INFO] Running command: fastANI --query /var/lib/cwl/stgfffe55c7-aaf8-41ba-8aa1-a101c9f2be5f/GCF_003363265.1_ASM336326v1_genomic.fna.gz --refList GCF_003363265.1_ASM336326v1_genomic.fna/target_genomes.txt --output GCF_003363265.1_ASM336326v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:47:30,631] [INFO] Task succeeded: fastANI
[2024-01-24 14:47:30,632] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc2580b58-dff3-443a-b183-bfaaf24a5791/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:47:30,632] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc2580b58-dff3-443a-b183-bfaaf24a5791/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:47:30,645] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:47:30,645] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:47:30,646] [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	100.0	1503	1504	95	conclusive
Dyella acidiphila	strain=7MK23	GCA_014863405.1	2775866	2775866	type	True	82.3338	900	1504	95	below_threshold
Dyella mobilis	strain=DHON07	GCA_016904945.1	1849582	1849582	type	True	82.2087	841	1504	95	below_threshold
Dyella dinghuensis	strain=DHOA06	GCA_003977615.1	1920169	1920169	type	True	81.6024	837	1504	95	below_threshold
Dyella caseinilytica	strain=DHOB09	GCA_016865235.1	1849581	1849581	type	True	81.5987	842	1504	95	below_threshold
Dyella caseinilytica	strain=CGMCC 1.15434	GCA_014642815.1	1849581	1849581	type	True	81.5603	849	1504	95	below_threshold
Dyella choica	strain=4 M-K27	GCA_003977665.1	1927959	1927959	type	True	81.3057	818	1504	95	below_threshold
Dyella monticola	strain=4 G-K06	GCA_003363155.1	1927958	1927958	type	True	81.0629	824	1504	95	below_threshold
Dyella japonica	strain=DSM 16301	GCA_001010355.1	231455	231455	type	True	80.3123	515	1504	95	below_threshold
Dyella solisilvae	strain=DHG54	GCA_003351225.1	1920168	1920168	type	True	80.2571	615	1504	95	below_threshold
Dyella kyungheensis	strain=THG-B117	GCA_016905005.1	1242174	1242174	type	True	80.2508	654	1504	95	below_threshold
Dyella telluris	strain=G9	GCA_014297575.1	2763498	2763498	type	True	80.0939	611	1504	95	below_threshold
Fulvimonas soli	strain=LMG 19981	GCA_006352285.1	155197	155197	type	True	80.0441	549	1504	95	below_threshold
Frateuria flava	strain=MAH-13	GCA_017837635.1	2821489	2821489	type	True	79.7374	508	1504	95	below_threshold
Tahibacter caeni	strain=BUT-6	GCA_024609805.1	1453545	1453545	type	True	77.7733	259	1504	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:47:30,647] [INFO] DFAST Taxonomy check result was written to GCF_003363265.1_ASM336326v1_genomic.fna/tc_result.tsv
[2024-01-24 14:47:30,648] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:47:30,648] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:47:30,648] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc2580b58-dff3-443a-b183-bfaaf24a5791/dqc_reference/checkm_data
[2024-01-24 14:47:30,649] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:47:30,693] [INFO] Task started: CheckM
[2024-01-24 14:47:30,694] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003363265.1_ASM336326v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003363265.1_ASM336326v1_genomic.fna/checkm_input GCF_003363265.1_ASM336326v1_genomic.fna/checkm_result
[2024-01-24 14:48:19,001] [INFO] Task succeeded: CheckM
[2024-01-24 14:48:19,003] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:48:19,024] [INFO] ===== Completeness check finished =====
[2024-01-24 14:48:19,025] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:48:19,025] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003363265.1_ASM336326v1_genomic.fna/markers.fasta)
[2024-01-24 14:48:19,026] [INFO] Task started: Blastn
[2024-01-24 14:48:19,026] [INFO] Running command: blastn -query GCF_003363265.1_ASM336326v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc2580b58-dff3-443a-b183-bfaaf24a5791/dqc_reference/reference_markers_gtdb.fasta -out GCF_003363265.1_ASM336326v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:48:20,924] [INFO] Task succeeded: Blastn
[2024-01-24 14:48:20,929] [INFO] Selected 16 target genomes.
[2024-01-24 14:48:20,929] [INFO] Target genome list was writen to GCF_003363265.1_ASM336326v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:48:20,941] [INFO] Task started: fastANI
[2024-01-24 14:48:20,942] [INFO] Running command: fastANI --query /var/lib/cwl/stgfffe55c7-aaf8-41ba-8aa1-a101c9f2be5f/GCF_003363265.1_ASM336326v1_genomic.fna.gz --refList GCF_003363265.1_ASM336326v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003363265.1_ASM336326v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:48:37,125] [INFO] Task succeeded: fastANI
[2024-01-24 14:48:37,149] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:48:37,150] [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_003363265.1	s__Dyella_B psychrodurans	100.0	1503	1504	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
GCA_903970555.1	s__Dyella_B sp903970555	82.4033	783	1504	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	82.3253	901	1504	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	82.1994	842	1504	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	82.184	918	1504	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	81.9709	700	1504	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	81.611	835	1504	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	81.5887	842	1504	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	81.4465	823	1504	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	81.2937	819	1504	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	81.0462	826	1504	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	80.425	665	1504	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	96.64	95.58	0.92	0.90	4	-
GCF_001010355.1	s__Dyella japonica	80.3456	512	1504	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016586165.1	s__Dyella sp016586165	80.2304	607	1504	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	80.0318	570	1504	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	97.24	96.89	0.85	0.82	5	-
GCF_014842975.1	s__Rhodanobacter sp014842975	79.9778	623	1504	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:48:37,152] [INFO] GTDB search result was written to GCF_003363265.1_ASM336326v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:48:37,152] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:48:37,156] [INFO] DFAST_QC result json was written to GCF_003363265.1_ASM336326v1_genomic.fna/dqc_result.json
[2024-01-24 14:48:37,156] [INFO] DFAST_QC completed!
[2024-01-24 14:48:37,156] [INFO] Total running time: 0h1m42s