[2024-01-24 14:13:01,599] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:13:01,601] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:13:01,601] [INFO] DQC Reference Directory: /var/lib/cwl/stg15299977-4127-44fe-b1da-2779c201c61c/dqc_reference
[2024-01-24 14:13:02,803] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:13:02,804] [INFO] Task started: Prodigal
[2024-01-24 14:13:02,804] [INFO] Running command: gunzip -c /var/lib/cwl/stgc8f38481-9d09-4f96-ab04-0085feb2375c/GCF_007830115.1_ASM783011v1_genomic.fna.gz | prodigal -d GCF_007830115.1_ASM783011v1_genomic.fna/cds.fna -a GCF_007830115.1_ASM783011v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:13:14,175] [INFO] Task succeeded: Prodigal
[2024-01-24 14:13:14,175] [INFO] Task started: HMMsearch
[2024-01-24 14:13:14,175] [INFO] Running command: hmmsearch --tblout GCF_007830115.1_ASM783011v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg15299977-4127-44fe-b1da-2779c201c61c/dqc_reference/reference_markers.hmm GCF_007830115.1_ASM783011v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:13:14,413] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:13:14,414] [INFO] Found 6/6 markers.
[2024-01-24 14:13:14,450] [INFO] Query marker FASTA was written to GCF_007830115.1_ASM783011v1_genomic.fna/markers.fasta
[2024-01-24 14:13:14,451] [INFO] Task started: Blastn
[2024-01-24 14:13:14,451] [INFO] Running command: blastn -query GCF_007830115.1_ASM783011v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg15299977-4127-44fe-b1da-2779c201c61c/dqc_reference/reference_markers.fasta -out GCF_007830115.1_ASM783011v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:13:15,415] [INFO] Task succeeded: Blastn
[2024-01-24 14:13:15,420] [INFO] Selected 18 target genomes.
[2024-01-24 14:13:15,421] [INFO] Target genome list was writen to GCF_007830115.1_ASM783011v1_genomic.fna/target_genomes.txt
[2024-01-24 14:13:15,475] [INFO] Task started: fastANI
[2024-01-24 14:13:15,475] [INFO] Running command: fastANI --query /var/lib/cwl/stgc8f38481-9d09-4f96-ab04-0085feb2375c/GCF_007830115.1_ASM783011v1_genomic.fna.gz --refList GCF_007830115.1_ASM783011v1_genomic.fna/target_genomes.txt --output GCF_007830115.1_ASM783011v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:13:29,650] [INFO] Task succeeded: fastANI
[2024-01-24 14:13:29,650] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg15299977-4127-44fe-b1da-2779c201c61c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:13:29,651] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg15299977-4127-44fe-b1da-2779c201c61c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:13:29,665] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:13:29,665] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:13:29,665] [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 ruishenii	strain=CGMCC 1.10136	GCA_007830115.1	686800	686800	type	True	100.0	1105	1107	95	conclusive
Lysobacter daejeonensis	strain=GH1-9	GCA_000768355.1	346181	346181	type	True	87.2739	773	1107	95	below_threshold
Vulcaniibacterium tengchongense	strain=YIM 77520	GCA_008033455.1	1273429	1273429	type	True	82.8556	613	1107	95	below_threshold
Vulcaniibacterium tengchongense	strain=DSM 25623	GCA_003814555.1	1273429	1273429	type	True	82.7092	651	1107	95	below_threshold
Lysobacter silvisoli	strain=zong2l5	GCA_003382365.1	2293254	2293254	type	True	82.6964	666	1107	95	below_threshold
Lysobacter arseniciresistens	strain=ZS79	GCA_000768335.1	1385522	1385522	type	True	82.532	602	1107	95	below_threshold
Lysobacter terrestris	strain=II4	GCA_014489475.1	2865112	2865112	type	True	82.3943	631	1107	95	below_threshold
Lysobacter panacisoli	strain=JCM 19212	GCA_009765165.1	1255263	1255263	type	True	82.2363	641	1107	95	below_threshold
Lysobacter arenosi	strain=R7	GCA_016613475.2	2795387	2795387	type	True	82.204	624	1107	95	below_threshold
Lysobacter psychrotolerans	strain=ZS60	GCA_003719825.1	1327343	1327343	type	True	81.9102	604	1107	95	below_threshold
Lysobacter enzymogenes	strain=ATCC 29487	GCA_900106525.1	69	69	suspected-type	True	81.8631	642	1107	95	below_threshold
Lysobacter soli	strain=KCTC 22011	GCA_003382285.1	453783	453783	type	True	81.8166	610	1107	95	below_threshold
Lysobacter solisilvae	strain=R19	GCA_016613535.2	2763317	2763317	type	True	81.6298	610	1107	95	below_threshold
Lysobacter chinensis	strain=TLK-CK17	GCA_021725675.1	2912247	2912247	type	True	81.4419	592	1107	95	below_threshold
Lysobacter capsici	strain=VKM B-2533	GCA_014779555.2	435897	435897	type	True	81.3896	619	1107	95	below_threshold
Luteimonas aquatica	strain=RIB1-20	GCA_022662575.1	450364	450364	type	True	81.375	580	1107	95	below_threshold
Thermomonas fusca	strain=DSM 15424	GCA_000423885.1	215690	215690	type	True	81.2732	565	1107	95	below_threshold
Luteimonas arsenica	strain=26-35	GCA_004352825.1	1586242	1586242	type	True	81.0971	546	1107	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:13:29,667] [INFO] DFAST Taxonomy check result was written to GCF_007830115.1_ASM783011v1_genomic.fna/tc_result.tsv
[2024-01-24 14:13:29,668] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:13:29,668] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:13:29,668] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg15299977-4127-44fe-b1da-2779c201c61c/dqc_reference/checkm_data
[2024-01-24 14:13:29,669] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:13:29,703] [INFO] Task started: CheckM
[2024-01-24 14:13:29,703] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007830115.1_ASM783011v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007830115.1_ASM783011v1_genomic.fna/checkm_input GCF_007830115.1_ASM783011v1_genomic.fna/checkm_result
[2024-01-24 14:14:16,045] [INFO] Task succeeded: CheckM
[2024-01-24 14:14:16,047] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:14:16,068] [INFO] ===== Completeness check finished =====
[2024-01-24 14:14:16,068] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:14:16,069] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007830115.1_ASM783011v1_genomic.fna/markers.fasta)
[2024-01-24 14:14:16,069] [INFO] Task started: Blastn
[2024-01-24 14:14:16,070] [INFO] Running command: blastn -query GCF_007830115.1_ASM783011v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg15299977-4127-44fe-b1da-2779c201c61c/dqc_reference/reference_markers_gtdb.fasta -out GCF_007830115.1_ASM783011v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:17,702] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:17,705] [INFO] Selected 17 target genomes.
[2024-01-24 14:14:17,705] [INFO] Target genome list was writen to GCF_007830115.1_ASM783011v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:14:17,722] [INFO] Task started: fastANI
[2024-01-24 14:14:17,722] [INFO] Running command: fastANI --query /var/lib/cwl/stgc8f38481-9d09-4f96-ab04-0085feb2375c/GCF_007830115.1_ASM783011v1_genomic.fna.gz --refList GCF_007830115.1_ASM783011v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007830115.1_ASM783011v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:14:31,440] [INFO] Task succeeded: fastANI
[2024-01-24 14:14:31,455] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:14:31,455] [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_007830115.1	s__Lysobacter ruishenii	100.0	1105	1107	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_000768355.1	s__Lysobacter daejeonensis	87.2903	772	1107	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003382365.1	s__Lysobacter silvisoli	82.721	664	1107	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003814555.1	s__Lysobacter tengchongensis	82.6967	652	1107	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	99.99	99.99	0.99	0.99	2	-
GCF_003586305.1	s__Lysobacter tabacisoli	82.6793	621	1107	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	82.4278	628	1107	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009765165.1	s__Lysobacter panacisoli	82.2334	641	1107	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016613475.2	s__Lysobacter arenosi	82.2165	623	1107	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001830245.1	s__Lysobacter sp001830245	82.1351	564	1107	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	99.71	99.71	0.92	0.92	2	-
GCA_013361435.1	s__Lysobacter sp013361435	82.1205	581	1107	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017308985.1	s__Lysobacter sp017308985	82.0728	651	1107	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	82.0468	685	1107	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	97.93	95.70	0.94	0.91	4	-
GCF_009765215.1	s__Lysobacter prati	82.0452	622	1107	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	81.9226	603	1107	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	81.8879	619	1107	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003382285.1	s__Lysobacter soli	81.813	610	1107	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	96.84	96.81	0.94	0.93	3	-
GCF_016613535.2	s__Lysobacter solisilvae_A	81.6298	610	1107	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:14:31,456] [INFO] GTDB search result was written to GCF_007830115.1_ASM783011v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:14:31,457] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:14:31,461] [INFO] DFAST_QC result json was written to GCF_007830115.1_ASM783011v1_genomic.fna/dqc_result.json
[2024-01-24 14:14:31,461] [INFO] DFAST_QC completed!
[2024-01-24 14:14:31,461] [INFO] Total running time: 0h1m30s