[2024-01-25 19:55:20,670] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:55:20,673] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:55:20,673] [INFO] DQC Reference Directory: /var/lib/cwl/stg349e066a-455f-4cce-8ece-d669f96b0d23/dqc_reference
[2024-01-25 19:55:21,830] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:55:21,830] [INFO] Task started: Prodigal
[2024-01-25 19:55:21,831] [INFO] Running command: gunzip -c /var/lib/cwl/stgad8ed0dd-414e-41fc-80a2-63889a5974de/GCF_000768335.1_ASM76833v1_genomic.fna.gz | prodigal -d GCF_000768335.1_ASM76833v1_genomic.fna/cds.fna -a GCF_000768335.1_ASM76833v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:55:29,615] [INFO] Task succeeded: Prodigal
[2024-01-25 19:55:29,616] [INFO] Task started: HMMsearch
[2024-01-25 19:55:29,616] [INFO] Running command: hmmsearch --tblout GCF_000768335.1_ASM76833v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg349e066a-455f-4cce-8ece-d669f96b0d23/dqc_reference/reference_markers.hmm GCF_000768335.1_ASM76833v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:55:29,809] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:55:29,810] [INFO] Found 6/6 markers.
[2024-01-25 19:55:29,834] [INFO] Query marker FASTA was written to GCF_000768335.1_ASM76833v1_genomic.fna/markers.fasta
[2024-01-25 19:55:29,834] [INFO] Task started: Blastn
[2024-01-25 19:55:29,834] [INFO] Running command: blastn -query GCF_000768335.1_ASM76833v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg349e066a-455f-4cce-8ece-d669f96b0d23/dqc_reference/reference_markers.fasta -out GCF_000768335.1_ASM76833v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:55:30,722] [INFO] Task succeeded: Blastn
[2024-01-25 19:55:30,728] [INFO] Selected 20 target genomes.
[2024-01-25 19:55:30,728] [INFO] Target genome list was writen to GCF_000768335.1_ASM76833v1_genomic.fna/target_genomes.txt
[2024-01-25 19:55:30,742] [INFO] Task started: fastANI
[2024-01-25 19:55:30,742] [INFO] Running command: fastANI --query /var/lib/cwl/stgad8ed0dd-414e-41fc-80a2-63889a5974de/GCF_000768335.1_ASM76833v1_genomic.fna.gz --refList GCF_000768335.1_ASM76833v1_genomic.fna/target_genomes.txt --output GCF_000768335.1_ASM76833v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:55:45,956] [INFO] Task succeeded: fastANI
[2024-01-25 19:55:45,956] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg349e066a-455f-4cce-8ece-d669f96b0d23/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:55:45,956] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg349e066a-455f-4cce-8ece-d669f96b0d23/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:55:45,968] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:55:45,968] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:55:45,968] [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
Lysobacter arseniciresistens	strain=ZS79	GCA_000768335.1	1385522	1385522	type	True	100.0	978	982	95	conclusive
Lysobacter luteus	strain=CECT 30171	GCA_907164845.1	2822368	2822368	type	True	87.8741	764	982	95	below_threshold
Vulcaniibacterium tengchongense	strain=DSM 25623	GCA_003814555.1	1273429	1273429	type	True	84.1871	667	982	95	below_threshold
Vulcaniibacterium tengchongense	strain=YIM 77520	GCA_008033455.1	1273429	1273429	type	True	84.1554	630	982	95	below_threshold
Lysobacter concretionis	strain=Ko07	GCA_000768345.1	262325	262325	type	True	83.9397	662	982	95	below_threshold
Lysobacter defluvii	strain=IMMIB APB-9	GCA_000769985.1	391738	391738	type	True	83.6563	475	982	95	below_threshold
Lysobacter defluvii	strain=DSM 18482	GCA_000423325.1	391738	391738	type	True	83.5794	607	982	95	below_threshold
Lysobacter spongiicola	strain=DSM 21749	GCA_900167055.1	435289	435289	type	True	83.4431	652	982	95	below_threshold
Lysobacter silvisoli	strain=zong2l5	GCA_003382365.1	2293254	2293254	type	True	83.0515	627	982	95	below_threshold
Luteimonas lumbrici	strain=1.1416	GCA_006476065.1	2559601	2559601	type	True	82.9186	557	982	95	below_threshold
Lysobacter enzymogenes	strain=ATCC 29487	GCA_900106525.1	69	69	suspected-type	True	82.7453	668	982	95	below_threshold
Lysobacter alkalisoli	strain=SJ-36	GCA_006547045.1	2591633	2591633	type	True	82.7409	622	982	95	below_threshold
Lysobacter chinensis	strain=TLK-CK17	GCA_021725675.1	2912247	2912247	type	True	82.5713	651	982	95	below_threshold
Luteimonas arsenica	strain=26-35	GCA_004352825.1	1586242	1586242	type	True	82.4235	572	982	95	below_threshold
Lysobacter psychrotolerans	strain=ZS60	GCA_003719825.1	1327343	1327343	type	True	82.4211	591	982	95	below_threshold
Luteimonas marina	strain=FR1330	GCA_007859325.1	488485	488485	type	True	82.4091	613	982	95	below_threshold
Lysobacter spongiae	strain=119BY6-57	GCA_014145325.1	2025720	2025720	type	True	82.4064	619	982	95	below_threshold
Lysobacter capsici	strain=VKM B-2533	GCA_014779555.2	435897	435897	type	True	82.0642	644	982	95	below_threshold
Lysobacter avium	strain=H23M41	GCA_015209745.1	2781023	2781023	type	True	82.0595	577	982	95	below_threshold
Luteibacter rhizovicinus	strain=DSM 16549	GCA_001010405.1	242606	242606	type	True	77.6622	238	982	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:55:45,970] [INFO] DFAST Taxonomy check result was written to GCF_000768335.1_ASM76833v1_genomic.fna/tc_result.tsv
[2024-01-25 19:55:45,970] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:55:45,970] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:55:45,970] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg349e066a-455f-4cce-8ece-d669f96b0d23/dqc_reference/checkm_data
[2024-01-25 19:55:45,971] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:55:46,004] [INFO] Task started: CheckM
[2024-01-25 19:55:46,004] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000768335.1_ASM76833v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000768335.1_ASM76833v1_genomic.fna/checkm_input GCF_000768335.1_ASM76833v1_genomic.fna/checkm_result
[2024-01-25 19:56:25,206] [INFO] Task succeeded: CheckM
[2024-01-25 19:56:25,207] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:56:25,228] [INFO] ===== Completeness check finished =====
[2024-01-25 19:56:25,229] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:56:25,230] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000768335.1_ASM76833v1_genomic.fna/markers.fasta)
[2024-01-25 19:56:25,230] [INFO] Task started: Blastn
[2024-01-25 19:56:25,230] [INFO] Running command: blastn -query GCF_000768335.1_ASM76833v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg349e066a-455f-4cce-8ece-d669f96b0d23/dqc_reference/reference_markers_gtdb.fasta -out GCF_000768335.1_ASM76833v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:56:26,906] [INFO] Task succeeded: Blastn
[2024-01-25 19:56:26,909] [INFO] Selected 20 target genomes.
[2024-01-25 19:56:26,909] [INFO] Target genome list was writen to GCF_000768335.1_ASM76833v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:56:26,924] [INFO] Task started: fastANI
[2024-01-25 19:56:26,924] [INFO] Running command: fastANI --query /var/lib/cwl/stgad8ed0dd-414e-41fc-80a2-63889a5974de/GCF_000768335.1_ASM76833v1_genomic.fna.gz --refList GCF_000768335.1_ASM76833v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000768335.1_ASM76833v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:56:42,420] [INFO] Task succeeded: fastANI
[2024-01-25 19:56:42,432] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:56:42,433] [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_000768335.1	s__Lysobacter arseniciresistens	100.0	978	982	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_907164845.1	s__Lysobacter sp907164845	87.8741	764	982	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003586305.1	s__Lysobacter tabacisoli	83.9646	650	982	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000768345.1	s__Lysobacter concretionis	83.933	662	982	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_001830245.1	s__Lysobacter sp001830245	83.5639	610	982	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	99.71	99.71	0.92	0.92	2	-
GCF_000423325.1	s__Lysobacter defluvii	83.5592	608	982	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900167055.1	s__Lysobacter spongiicola	83.4431	652	982	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001442515.1	s__Lysobacter enzymogenes_B	82.9526	678	982	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	97.93	95.70	0.94	0.91	4	-
GCF_006476065.1	s__Luteimonas_B lumbrici	82.8893	559	982	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013361435.1	s__Lysobacter sp013361435	82.7721	567	982	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114355.1	s__Lysobacter sp900114355	82.7061	650	982	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000336385.2	s__Lysobacter antibioticus_A	82.7024	631	982	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014489475.1	s__Lysobacter solisilvae	82.5431	612	982	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003719825.1	s__Lysobacter psychrotolerans	82.4434	589	982	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004352825.1	s__Luteimonas arsenica	82.4378	570	982	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007859325.1	s__Luteimonas marina	82.4175	612	982	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004118975.1	s__Luteimonas sp004118975	81.4701	570	982	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009912395.1	s__Luteibacter sp009912395	78.0104	306	982	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Luteibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001887595.1	s__Luteibacter rhizovicinus	77.8353	260	982	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Luteibacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_011759605.1	s__Luteibacter sp011759605	77.5841	260	982	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Luteibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:56:42,434] [INFO] GTDB search result was written to GCF_000768335.1_ASM76833v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:56:42,435] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:56:42,439] [INFO] DFAST_QC result json was written to GCF_000768335.1_ASM76833v1_genomic.fna/dqc_result.json
[2024-01-25 19:56:42,439] [INFO] DFAST_QC completed!
[2024-01-25 19:56:42,439] [INFO] Total running time: 0h1m22s