[2024-01-24 13:49:44,995] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:45,003] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:45,003] [INFO] DQC Reference Directory: /var/lib/cwl/stg872b32a2-53ad-4fc5-a02e-7641b6f5ffb1/dqc_reference
[2024-01-24 13:49:46,443] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:46,444] [INFO] Task started: Prodigal
[2024-01-24 13:49:46,444] [INFO] Running command: gunzip -c /var/lib/cwl/stg6c016304-af90-4b6e-be81-d43af470e06b/GCF_014489475.1_ASM1448947v1_genomic.fna.gz | prodigal -d GCF_014489475.1_ASM1448947v1_genomic.fna/cds.fna -a GCF_014489475.1_ASM1448947v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:57,076] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:57,077] [INFO] Task started: HMMsearch
[2024-01-24 13:49:57,077] [INFO] Running command: hmmsearch --tblout GCF_014489475.1_ASM1448947v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg872b32a2-53ad-4fc5-a02e-7641b6f5ffb1/dqc_reference/reference_markers.hmm GCF_014489475.1_ASM1448947v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:57,347] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:57,349] [INFO] Found 6/6 markers.
[2024-01-24 13:49:57,376] [INFO] Query marker FASTA was written to GCF_014489475.1_ASM1448947v1_genomic.fna/markers.fasta
[2024-01-24 13:49:57,376] [INFO] Task started: Blastn
[2024-01-24 13:49:57,377] [INFO] Running command: blastn -query GCF_014489475.1_ASM1448947v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg872b32a2-53ad-4fc5-a02e-7641b6f5ffb1/dqc_reference/reference_markers.fasta -out GCF_014489475.1_ASM1448947v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:58,419] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:58,422] [INFO] Selected 20 target genomes.
[2024-01-24 13:49:58,423] [INFO] Target genome list was writen to GCF_014489475.1_ASM1448947v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:58,455] [INFO] Task started: fastANI
[2024-01-24 13:49:58,455] [INFO] Running command: fastANI --query /var/lib/cwl/stg6c016304-af90-4b6e-be81-d43af470e06b/GCF_014489475.1_ASM1448947v1_genomic.fna.gz --refList GCF_014489475.1_ASM1448947v1_genomic.fna/target_genomes.txt --output GCF_014489475.1_ASM1448947v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:15,030] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:15,031] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg872b32a2-53ad-4fc5-a02e-7641b6f5ffb1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:15,032] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg872b32a2-53ad-4fc5-a02e-7641b6f5ffb1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:15,053] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:50:15,053] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:50:15,054] [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 terrestris	strain=II4	GCA_014489475.1	2865112	2865112	type	True	100.0	1047	1049	95	conclusive
Vulcaniibacterium tengchongense	strain=YIM 77520	GCA_008033455.1	1273429	1273429	type	True	83.6651	654	1049	95	below_threshold
Vulcaniibacterium tengchongense	strain=DSM 25623	GCA_003814555.1	1273429	1273429	type	True	83.5814	692	1049	95	below_threshold
Lysobacter solisilvae	strain=R19	GCA_016613535.2	2763317	2763317	type	True	83.5623	779	1049	95	below_threshold
Lysobacter panacisoli	strain=JCM 19212	GCA_009765165.1	1255263	1255263	type	True	83.3646	726	1049	95	below_threshold
Lysobacter arenosi	strain=R7	GCA_016613475.2	2795387	2795387	type	True	83.0732	713	1049	95	below_threshold
Lysobacter silvisoli	strain=zong2l5	GCA_003382365.1	2293254	2293254	type	True	83.0161	742	1049	95	below_threshold
Lysobacter prati	strain=SYSU H10001	GCA_009765215.1	2596704	2596704	type	True	82.9608	690	1049	95	below_threshold
Lysobacter niastensis	strain=DSM 18481	GCA_015453285.1	380629	380629	type	True	82.9446	714	1049	95	below_threshold
Lysobacter soli	strain=KCTC 22011	GCA_003382285.1	453783	453783	type	True	82.8798	701	1049	95	below_threshold
Lysobacter arseniciresistens	strain=ZS79	GCA_000768335.1	1385522	1385522	type	True	82.5704	594	1049	95	below_threshold
Lysobacter ruishenii	strain=CGMCC 1.10136	GCA_007830115.1	686800	686800	type	True	82.4677	611	1049	95	below_threshold
Lysobacter capsici	strain=VKM B-2533	GCA_014779555.2	435897	435897	type	True	82.2839	730	1049	95	below_threshold
Lysobacter daejeonensis	strain=GH1-9	GCA_000768355.1	346181	346181	type	True	82.2092	630	1049	95	below_threshold
Vulcaniibacterium gelatinicum	strain=R-5-52-3	GCA_008033445.1	2598725	2598725	type	True	82.2076	606	1049	95	below_threshold
Lysobacter antibioticus	strain=ATCC 29479	GCA_001442535.1	84531	84531	type	True	82.1487	719	1049	95	below_threshold
Lysobacter chinensis	strain=TLK-CK17	GCA_021725675.1	2912247	2912247	type	True	81.7144	676	1049	95	below_threshold
Lysobacter luteus	strain=CECT 30171	GCA_907164845.1	2822368	2822368	type	True	81.5359	581	1049	95	below_threshold
Lysobacter penaei	strain=SG-8	GCA_014145395.1	2759900	2759900	type	True	81.313	567	1049	95	below_threshold
Arenimonas malthae	strain=CC-JY-1	GCA_000747075.1	354197	354197	type	True	80.5969	497	1049	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:15,056] [INFO] DFAST Taxonomy check result was written to GCF_014489475.1_ASM1448947v1_genomic.fna/tc_result.tsv
[2024-01-24 13:50:15,057] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:15,057] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:15,057] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg872b32a2-53ad-4fc5-a02e-7641b6f5ffb1/dqc_reference/checkm_data
[2024-01-24 13:50:15,058] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:15,089] [INFO] Task started: CheckM
[2024-01-24 13:50:15,090] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014489475.1_ASM1448947v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014489475.1_ASM1448947v1_genomic.fna/checkm_input GCF_014489475.1_ASM1448947v1_genomic.fna/checkm_result
[2024-01-24 13:50:51,385] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:51,386] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:51,408] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:51,409] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:51,409] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014489475.1_ASM1448947v1_genomic.fna/markers.fasta)
[2024-01-24 13:50:51,410] [INFO] Task started: Blastn
[2024-01-24 13:50:51,410] [INFO] Running command: blastn -query GCF_014489475.1_ASM1448947v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg872b32a2-53ad-4fc5-a02e-7641b6f5ffb1/dqc_reference/reference_markers_gtdb.fasta -out GCF_014489475.1_ASM1448947v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:53,400] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:53,405] [INFO] Selected 17 target genomes.
[2024-01-24 13:50:53,405] [INFO] Target genome list was writen to GCF_014489475.1_ASM1448947v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:53,421] [INFO] Task started: fastANI
[2024-01-24 13:50:53,422] [INFO] Running command: fastANI --query /var/lib/cwl/stg6c016304-af90-4b6e-be81-d43af470e06b/GCF_014489475.1_ASM1448947v1_genomic.fna.gz --refList GCF_014489475.1_ASM1448947v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014489475.1_ASM1448947v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:51:08,516] [INFO] Task succeeded: fastANI
[2024-01-24 13:51:08,535] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:51:08,535] [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_014489475.1	s__Lysobacter solisilvae	100.0	1047	1049	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_001427225.1	s__Lysobacter sp001427225	84.9639	797	1049	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	83.5844	692	1049	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	99.99	99.99	0.99	0.99	2	-
GCF_016613535.2	s__Lysobacter solisilvae_A	83.5591	780	1049	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	83.3772	725	1049	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016735495.2	s__Lysobacter sp016735495	83.1793	715	1049	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	83.1557	721	1049	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	83.0417	716	1049	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	83.0319	740	1049	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107375.1	s__Lysobacter sp900107375	82.9895	752	1049	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015453285.1	s__Lysobacter niastensis	82.9328	715	1049	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	82.8944	700	1049	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	96.84	96.81	0.94	0.93	3	-
GCA_013361435.1	s__Lysobacter sp013361435	82.8738	657	1049	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	82.774	687	1049	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007830115.1	s__Lysobacter ruishenii	82.481	610	1049	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008033445.1	s__Vulcaniibacterium_B gelatinicum	82.2168	605	1049	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Vulcaniibacterium_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000768355.1	s__Lysobacter daejeonensis	82.1971	631	1049	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 13:51:08,537] [INFO] GTDB search result was written to GCF_014489475.1_ASM1448947v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:51:08,538] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:51:08,542] [INFO] DFAST_QC result json was written to GCF_014489475.1_ASM1448947v1_genomic.fna/dqc_result.json
[2024-01-24 13:51:08,542] [INFO] DFAST_QC completed!
[2024-01-24 13:51:08,543] [INFO] Total running time: 0h1m24s