[2024-01-24 13:31:26,280] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:26,282] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:26,283] [INFO] DQC Reference Directory: /var/lib/cwl/stg0e8e754e-ec84-4604-bb59-f017e43a358f/dqc_reference
[2024-01-24 13:31:27,491] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:27,492] [INFO] Task started: Prodigal
[2024-01-24 13:31:27,492] [INFO] Running command: gunzip -c /var/lib/cwl/stg476798d4-8264-496d-bd06-c3b219615ea9/GCF_004342425.1_ASM434242v1_genomic.fna.gz | prodigal -d GCF_004342425.1_ASM434242v1_genomic.fna/cds.fna -a GCF_004342425.1_ASM434242v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:31:41,341] [INFO] Task succeeded: Prodigal
[2024-01-24 13:31:41,341] [INFO] Task started: HMMsearch
[2024-01-24 13:31:41,341] [INFO] Running command: hmmsearch --tblout GCF_004342425.1_ASM434242v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0e8e754e-ec84-4604-bb59-f017e43a358f/dqc_reference/reference_markers.hmm GCF_004342425.1_ASM434242v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:31:41,600] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:31:41,603] [INFO] Found 6/6 markers.
[2024-01-24 13:31:41,646] [INFO] Query marker FASTA was written to GCF_004342425.1_ASM434242v1_genomic.fna/markers.fasta
[2024-01-24 13:31:41,647] [INFO] Task started: Blastn
[2024-01-24 13:31:41,647] [INFO] Running command: blastn -query GCF_004342425.1_ASM434242v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0e8e754e-ec84-4604-bb59-f017e43a358f/dqc_reference/reference_markers.fasta -out GCF_004342425.1_ASM434242v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:31:42,662] [INFO] Task succeeded: Blastn
[2024-01-24 13:31:42,666] [INFO] Selected 17 target genomes.
[2024-01-24 13:31:42,666] [INFO] Target genome list was writen to GCF_004342425.1_ASM434242v1_genomic.fna/target_genomes.txt
[2024-01-24 13:31:42,807] [INFO] Task started: fastANI
[2024-01-24 13:31:42,807] [INFO] Running command: fastANI --query /var/lib/cwl/stg476798d4-8264-496d-bd06-c3b219615ea9/GCF_004342425.1_ASM434242v1_genomic.fna.gz --refList GCF_004342425.1_ASM434242v1_genomic.fna/target_genomes.txt --output GCF_004342425.1_ASM434242v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:31:57,765] [INFO] Task succeeded: fastANI
[2024-01-24 13:31:57,765] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0e8e754e-ec84-4604-bb59-f017e43a358f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:31:57,766] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0e8e754e-ec84-4604-bb59-f017e43a358f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:31:57,796] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:31:57,797] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:31:57,797] [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
Dokdonella fugitiva	strain=A3	GCA_004342425.1	328517	328517	type	True	100.0	1407	1408	95	conclusive
Dokdonella koreensis	strain=DS-123	GCA_001632775.1	323415	323415	type	True	79.6716	654	1408	95	below_threshold
Tahibacter caeni	strain=BUT-6	GCA_024609805.1	1453545	1453545	type	True	79.5826	640	1408	95	below_threshold
Rudaea cellulosilytica	strain=DSM 22992	GCA_000378125.1	540746	540746	type	True	79.0767	552	1408	95	below_threshold
Fulvimonas soli	strain=DSM 14263	GCA_003148905.1	155197	155197	type	True	79.0108	561	1408	95	below_threshold
Fulvimonas soli	strain=LMG 19981	GCA_006352285.1	155197	155197	type	True	78.9639	537	1408	95	below_threshold
Dokdonella immobilis	strain=CGMCC 1.7659	GCA_900115085.1	578942	578942	type	True	78.7586	519	1408	95	below_threshold
Rhodanobacter thiooxydans	strain=LCS2	GCA_000264375.1	416169	416169	type	True	78.7512	449	1408	95	below_threshold
Vulcaniibacterium thermophilum	strain=KCTC 32020	GCA_014656335.1	1169913	1169913	type	True	78.5727	490	1408	95	below_threshold
Frateuria flava	strain=MAH-13	GCA_017837635.1	2821489	2821489	type	True	78.5038	455	1408	95	below_threshold
Dyella solisilvae	strain=DHG54	GCA_003351225.1	1920168	1920168	type	True	78.2714	414	1408	95	below_threshold
Luteibacter yeojuensis	strain=DSM 17673	GCA_011742875.1	345309	345309	type	True	78.1689	389	1408	95	below_threshold
Pseudoxanthomonas taiwanensis	strain=DSM 22914	GCA_010093135.1	176598	176598	type	True	78.0566	369	1408	95	below_threshold
Dyella telluris	strain=G9	GCA_014297575.1	2763498	2763498	type	True	77.9841	367	1408	95	below_threshold
Dyella japonica	strain=DSM 16301	GCA_001010355.1	231455	231455	type	True	77.9181	310	1408	95	below_threshold
Dyella acidiphila	strain=7MK23	GCA_014863405.1	2775866	2775866	type	True	77.7344	337	1408	95	below_threshold
Tahibacter aquaticus	strain=DSM 21667	GCA_004363655.1	520092	520092	type	True	77.6408	535	1408	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:31:57,801] [INFO] DFAST Taxonomy check result was written to GCF_004342425.1_ASM434242v1_genomic.fna/tc_result.tsv
[2024-01-24 13:31:57,802] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:31:57,803] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:31:57,803] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0e8e754e-ec84-4604-bb59-f017e43a358f/dqc_reference/checkm_data
[2024-01-24 13:31:57,806] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:31:57,854] [INFO] Task started: CheckM
[2024-01-24 13:31:57,854] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004342425.1_ASM434242v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004342425.1_ASM434242v1_genomic.fna/checkm_input GCF_004342425.1_ASM434242v1_genomic.fna/checkm_result
[2024-01-24 13:32:45,205] [INFO] Task succeeded: CheckM
[2024-01-24 13:32:45,206] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:32:45,227] [INFO] ===== Completeness check finished =====
[2024-01-24 13:32:45,227] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:32:45,227] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004342425.1_ASM434242v1_genomic.fna/markers.fasta)
[2024-01-24 13:32:45,228] [INFO] Task started: Blastn
[2024-01-24 13:32:45,228] [INFO] Running command: blastn -query GCF_004342425.1_ASM434242v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0e8e754e-ec84-4604-bb59-f017e43a358f/dqc_reference/reference_markers_gtdb.fasta -out GCF_004342425.1_ASM434242v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:47,239] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:47,244] [INFO] Selected 10 target genomes.
[2024-01-24 13:32:47,244] [INFO] Target genome list was writen to GCF_004342425.1_ASM434242v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:32:47,286] [INFO] Task started: fastANI
[2024-01-24 13:32:47,287] [INFO] Running command: fastANI --query /var/lib/cwl/stg476798d4-8264-496d-bd06-c3b219615ea9/GCF_004342425.1_ASM434242v1_genomic.fna.gz --refList GCF_004342425.1_ASM434242v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004342425.1_ASM434242v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:32:58,627] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:58,643] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:32:58,643] [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_004342425.1	s__Dokdonella_A fugitiva	100.0	1407	1408	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella_A	95.0	99.45	99.45	0.96	0.96	2	conclusive
GCF_014138265.1	s__Dokdonella_A fugitiva_A	88.9309	1177	1408	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009996615.1	s__Dokdonella_A sp009996615	83.1583	828	1408	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017744955.1	s__Dokdonella_A sp017744955	82.4084	900	1408	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002297645.1	s__Dokdonella_A sp002297645	82.239	683	1408	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella_A	95.0	99.81	99.81	0.89	0.89	2	-
GCA_004143945.1	s__Dokdonella_A sp004143945	82.2365	832	1408	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014338185.1	s__Dokdonella_A sp014338185	81.0246	636	1408	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella_A	95.0	96.24	96.24	0.88	0.88	2	-
GCA_003241385.1	s__Dokdonella denitrificans_A	80.0261	688	1408	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003148905.1	s__Fulvimonas soli	78.9936	563	1408	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Fulvimonas	95.0	99.99	99.99	0.99	0.99	2	-
GCF_900112865.1	s__Dyella marensis	78.4794	523	1408	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:32:58,645] [INFO] GTDB search result was written to GCF_004342425.1_ASM434242v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:32:58,645] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:32:58,668] [INFO] DFAST_QC result json was written to GCF_004342425.1_ASM434242v1_genomic.fna/dqc_result.json
[2024-01-24 13:32:58,668] [INFO] DFAST_QC completed!
[2024-01-24 13:32:58,668] [INFO] Total running time: 0h1m32s