[2023-06-27 10:50:11,422] [INFO] DFAST_QC pipeline started.
[2023-06-27 10:50:11,424] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 10:50:11,424] [INFO] DQC Reference Directory: /var/lib/cwl/stgc1ff8122-9a62-43a2-a6d4-665c8330a876/dqc_reference
[2023-06-27 10:50:12,656] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 10:50:12,656] [INFO] Task started: Prodigal
[2023-06-27 10:50:12,657] [INFO] Running command: gunzip -c /var/lib/cwl/stg1b981f16-3fc7-4369-b145-2b3c476aec6e/GCA_027352655.1_ASM2735265v1_genomic.fna.gz | prodigal -d GCA_027352655.1_ASM2735265v1_genomic.fna/cds.fna -a GCA_027352655.1_ASM2735265v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 10:50:18,369] [INFO] Task succeeded: Prodigal
[2023-06-27 10:50:18,369] [INFO] Task started: HMMsearch
[2023-06-27 10:50:18,369] [INFO] Running command: hmmsearch --tblout GCA_027352655.1_ASM2735265v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc1ff8122-9a62-43a2-a6d4-665c8330a876/dqc_reference/reference_markers.hmm GCA_027352655.1_ASM2735265v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 10:50:18,527] [INFO] Task succeeded: HMMsearch
[2023-06-27 10:50:18,528] [INFO] Found 6/6 markers.
[2023-06-27 10:50:18,547] [INFO] Query marker FASTA was written to GCA_027352655.1_ASM2735265v1_genomic.fna/markers.fasta
[2023-06-27 10:50:18,547] [INFO] Task started: Blastn
[2023-06-27 10:50:18,548] [INFO] Running command: blastn -query GCA_027352655.1_ASM2735265v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc1ff8122-9a62-43a2-a6d4-665c8330a876/dqc_reference/reference_markers.fasta -out GCA_027352655.1_ASM2735265v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 10:50:19,434] [INFO] Task succeeded: Blastn
[2023-06-27 10:50:19,455] [INFO] Selected 23 target genomes.
[2023-06-27 10:50:19,455] [INFO] Target genome list was writen to GCA_027352655.1_ASM2735265v1_genomic.fna/target_genomes.txt
[2023-06-27 10:50:19,460] [INFO] Task started: fastANI
[2023-06-27 10:50:19,461] [INFO] Running command: fastANI --query /var/lib/cwl/stg1b981f16-3fc7-4369-b145-2b3c476aec6e/GCA_027352655.1_ASM2735265v1_genomic.fna.gz --refList GCA_027352655.1_ASM2735265v1_genomic.fna/target_genomes.txt --output GCA_027352655.1_ASM2735265v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 10:50:33,937] [INFO] Task succeeded: fastANI
[2023-06-27 10:50:33,937] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc1ff8122-9a62-43a2-a6d4-665c8330a876/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 10:50:33,938] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc1ff8122-9a62-43a2-a6d4-665c8330a876/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 10:50:33,955] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 10:50:33,955] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 10:50:33,955] [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
Fulvimonas soli	strain=DSM 14263	GCA_003148905.1	155197	155197	type	True	78.7192	265	577	95	below_threshold
Oleiagrimonas citrea	strain=MEBiC09124	GCA_012395255.1	1665687	1665687	type	True	78.6633	177	577	95	below_threshold
Fulvimonas soli	strain=LMG 19981	GCA_006352285.1	155197	155197	type	True	78.6391	246	577	95	below_threshold
Rhodanobacter thiooxydans	strain=LCS2	GCA_000264375.1	416169	416169	type	True	78.4729	248	577	95	below_threshold
Frateuria flava	strain=MAH-13	GCA_017837635.1	2821489	2821489	type	True	78.4129	210	577	95	below_threshold
Frateuria terrea	strain=CGMCC 1.7053	GCA_900115705.1	529704	529704	type	True	78.4105	219	577	95	below_threshold
Frateuria terrea	strain=DSM 26515	GCA_900109025.1	529704	529704	type	True	78.3961	216	577	95	below_threshold
Rhodanobacter spathiphylli	strain=B39	GCA_000264295.1	347483	347483	type	True	78.3827	227	577	95	below_threshold
Oleiagrimonas soli	strain=3.5X	GCA_000761445.1	1543381	1543381	type	True	78.3597	222	577	95	below_threshold
Rhodanobacter denitrificans	strain=2APBS1	GCA_000230695.3	666685	666685	type	True	78.3018	263	577	95	below_threshold
Oleiagrimonas soli	strain=DSM 107085	GCA_014201555.1	1543381	1543381	type	True	78.2784	224	577	95	below_threshold
Dyella solisilvae	strain=DHG54	GCA_003351225.1	1920168	1920168	type	True	78.192	182	577	95	below_threshold
Rhodanobacter fulvus	strain=Jip2	GCA_000264315.1	219571	219571	type	True	78.0284	202	577	95	below_threshold
Dokdonella fugitiva	strain=A3	GCA_004342425.1	328517	328517	type	True	77.8919	213	577	95	below_threshold
Dyella acidiphila	strain=7MK23	GCA_014863405.1	2775866	2775866	type	True	77.7325	192	577	95	below_threshold
Dyella kyungheensis	strain=THG-B117	GCA_016905005.1	1242174	1242174	type	True	77.7283	197	577	95	below_threshold
Dokdonella koreensis	strain=DS-123	GCA_001632775.1	323415	323415	type	True	77.7262	199	577	95	below_threshold
Dyella japonica	strain=DSM 16301	GCA_001010355.1	231455	231455	type	True	77.6952	164	577	95	below_threshold
Luteimonas aquatica	strain=RIB1-20	GCA_022662575.1	450364	450364	type	True	77.6854	201	577	95	below_threshold
Xanthomonas translucens	strain=ATCC 19319	GCA_020880735.1	343	343	type	True	77.6254	155	577	95	below_threshold
Luteibacter jiangsuensis	strain=CGMCC 1.10133	GCA_011742555.1	637577	637577	type	True	77.497	163	577	95	below_threshold
Xanthomonas massiliensis	strain=SN8	GCA_900018785.1	1720302	1720302	type	True	77.4469	172	577	95	below_threshold
Dyella telluris	strain=G9	GCA_014297575.1	2763498	2763498	type	True	77.3554	191	577	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 10:50:33,957] [INFO] DFAST Taxonomy check result was written to GCA_027352655.1_ASM2735265v1_genomic.fna/tc_result.tsv
[2023-06-27 10:50:33,958] [INFO] ===== Taxonomy check completed =====
[2023-06-27 10:50:33,958] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 10:50:33,958] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc1ff8122-9a62-43a2-a6d4-665c8330a876/dqc_reference/checkm_data
[2023-06-27 10:50:33,959] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 10:50:33,981] [INFO] Task started: CheckM
[2023-06-27 10:50:33,982] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_027352655.1_ASM2735265v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_027352655.1_ASM2735265v1_genomic.fna/checkm_input GCA_027352655.1_ASM2735265v1_genomic.fna/checkm_result
[2023-06-27 10:50:56,897] [INFO] Task succeeded: CheckM
[2023-06-27 10:50:56,898] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 54.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 10:50:56,919] [INFO] ===== Completeness check finished =====
[2023-06-27 10:50:56,919] [INFO] ===== Start GTDB Search =====
[2023-06-27 10:50:56,919] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_027352655.1_ASM2735265v1_genomic.fna/markers.fasta)
[2023-06-27 10:50:56,919] [INFO] Task started: Blastn
[2023-06-27 10:50:56,919] [INFO] Running command: blastn -query GCA_027352655.1_ASM2735265v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc1ff8122-9a62-43a2-a6d4-665c8330a876/dqc_reference/reference_markers_gtdb.fasta -out GCA_027352655.1_ASM2735265v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 10:50:58,692] [INFO] Task succeeded: Blastn
[2023-06-27 10:50:58,696] [INFO] Selected 14 target genomes.
[2023-06-27 10:50:58,696] [INFO] Target genome list was writen to GCA_027352655.1_ASM2735265v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 10:50:58,703] [INFO] Task started: fastANI
[2023-06-27 10:50:58,703] [INFO] Running command: fastANI --query /var/lib/cwl/stg1b981f16-3fc7-4369-b145-2b3c476aec6e/GCA_027352655.1_ASM2735265v1_genomic.fna.gz --refList GCA_027352655.1_ASM2735265v1_genomic.fna/target_genomes_gtdb.txt --output GCA_027352655.1_ASM2735265v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 10:51:07,040] [INFO] Task succeeded: fastANI
[2023-06-27 10:51:07,052] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-27 10:51:07,052] [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_004299705.1	s__66-474 sp004299705	82.1072	425	577	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__66-474	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001899805.1	s__66-474 sp001899805	82.0246	429	577	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__66-474	95.0	100.00	100.00	0.98	0.97	3	-
GCA_018971925.1	s__66-474 sp018971925	81.9612	290	577	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__66-474	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018241365.1	s__66-474 sp018241365	81.2538	380	577	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__66-474	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004299555.1	s__66-474 sp004299555	79.6347	311	577	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__66-474	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018241145.1	s__66-474 sp018241145	79.5174	273	577	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__66-474	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000953855.2	s__Mizugakiibacter sediminis	78.9066	269	577	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Mizugakiibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000761445.1	s__Oleiagrimonas soli	78.3264	224	577	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Oleiagrimonas	95.0	99.99	99.99	1.00	1.00	2	-
GCF_003201105.1	s__Dyella jiangningensis_B	77.9312	223	577	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	99.99	99.99	0.99	0.99	2	-
GCF_003332825.1	s__Dyella sp003332825	77.7769	201	577	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011759385.1	s__Oleiagrimonas sp011759385	77.7205	170	577	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Oleiagrimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014205795.1	s__Rhodanobacter sp014205795	77.4957	157	577	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011742555.1	s__Luteibacter jiangsuensis	77.4948	163	577	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Luteibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011759605.1	s__Luteibacter sp011759605	77.4013	146	577	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Luteibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 10:51:07,068] [INFO] GTDB search result was written to GCA_027352655.1_ASM2735265v1_genomic.fna/result_gtdb.tsv
[2023-06-27 10:51:07,068] [INFO] ===== GTDB Search completed =====
[2023-06-27 10:51:07,073] [INFO] DFAST_QC result json was written to GCA_027352655.1_ASM2735265v1_genomic.fna/dqc_result.json
[2023-06-27 10:51:07,073] [INFO] DFAST_QC completed!
[2023-06-27 10:51:07,073] [INFO] Total running time: 0h0m56s