[2024-01-24 12:53:55,907] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:53:55,909] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:53:55,910] [INFO] DQC Reference Directory: /var/lib/cwl/stga30ca195-4729-40ba-bee7-8ea22aa9e2f0/dqc_reference
[2024-01-24 12:53:57,276] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:53:57,277] [INFO] Task started: Prodigal
[2024-01-24 12:53:57,278] [INFO] Running command: gunzip -c /var/lib/cwl/stg9de87fb2-52c2-4ecc-9998-4332de272141/GCF_006547045.1_ASM654704v1_genomic.fna.gz | prodigal -d GCF_006547045.1_ASM654704v1_genomic.fna/cds.fna -a GCF_006547045.1_ASM654704v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:54:11,775] [INFO] Task succeeded: Prodigal
[2024-01-24 12:54:11,775] [INFO] Task started: HMMsearch
[2024-01-24 12:54:11,775] [INFO] Running command: hmmsearch --tblout GCF_006547045.1_ASM654704v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga30ca195-4729-40ba-bee7-8ea22aa9e2f0/dqc_reference/reference_markers.hmm GCF_006547045.1_ASM654704v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:54:12,026] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:54:12,027] [INFO] Found 6/6 markers.
[2024-01-24 12:54:12,069] [INFO] Query marker FASTA was written to GCF_006547045.1_ASM654704v1_genomic.fna/markers.fasta
[2024-01-24 12:54:12,069] [INFO] Task started: Blastn
[2024-01-24 12:54:12,069] [INFO] Running command: blastn -query GCF_006547045.1_ASM654704v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga30ca195-4729-40ba-bee7-8ea22aa9e2f0/dqc_reference/reference_markers.fasta -out GCF_006547045.1_ASM654704v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:13,014] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:13,017] [INFO] Selected 17 target genomes.
[2024-01-24 12:54:13,018] [INFO] Target genome list was writen to GCF_006547045.1_ASM654704v1_genomic.fna/target_genomes.txt
[2024-01-24 12:54:13,025] [INFO] Task started: fastANI
[2024-01-24 12:54:13,025] [INFO] Running command: fastANI --query /var/lib/cwl/stg9de87fb2-52c2-4ecc-9998-4332de272141/GCF_006547045.1_ASM654704v1_genomic.fna.gz --refList GCF_006547045.1_ASM654704v1_genomic.fna/target_genomes.txt --output GCF_006547045.1_ASM654704v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:54:29,274] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:29,275] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga30ca195-4729-40ba-bee7-8ea22aa9e2f0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:54:29,275] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga30ca195-4729-40ba-bee7-8ea22aa9e2f0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:54:29,289] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:54:29,289] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:54:29,289] [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 alkalisoli	strain=SJ-36	GCA_006547045.1	2591633	2591633	type	True	100.0	1285	1285	95	conclusive
Lysobacter maris	strain=KCTC 42381	GCA_006546735.2	1605891	1605891	type	True	84.7101	755	1285	95	below_threshold
Lysobacter chinensis	strain=TLK-CK17	GCA_021725675.1	2912247	2912247	type	True	84.4698	918	1285	95	below_threshold
Lysobacter aestuarii	strain=JCM 31130	GCA_006546775.1	1706195	1706195	type	True	83.0155	696	1285	95	below_threshold
Vulcaniibacterium tengchongense	strain=DSM 25623	GCA_003814555.1	1273429	1273429	type	True	82.758	706	1285	95	below_threshold
Lysobacter spongiae	strain=119BY6-57	GCA_014145325.1	2025720	2025720	type	True	82.7505	776	1285	95	below_threshold
Vulcaniibacterium tengchongense	strain=YIM 77520	GCA_008033455.1	1273429	1273429	type	True	82.7379	685	1285	95	below_threshold
Lysobacter arseniciresistens	strain=ZS79	GCA_000768335.1	1385522	1385522	type	True	82.7087	618	1285	95	below_threshold
Lysobacter penaei	strain=SG-8	GCA_014145395.1	2759900	2759900	type	True	82.3967	679	1285	95	below_threshold
Lysobacter silvisoli	strain=zong2l5	GCA_003382365.1	2293254	2293254	type	True	81.9912	702	1285	95	below_threshold
Lysobacter arenosi	strain=R7	GCA_016613475.2	2795387	2795387	type	True	81.7908	687	1285	95	below_threshold
Lysobacter luteus	strain=CECT 30171	GCA_907164845.1	2822368	2822368	type	True	81.5923	592	1285	95	below_threshold
Lysobacter prati	strain=SYSU H10001	GCA_009765215.1	2596704	2596704	type	True	81.4056	674	1285	95	below_threshold
Luteimonas padinae	strain=KCTC 52403	GCA_014652935.1	1714359	1714359	type	True	81.2116	560	1285	95	below_threshold
Luteimonas arsenica	strain=26-35	GCA_004352825.1	1586242	1586242	type	True	81.095	597	1285	95	below_threshold
Lysobacter capsici	strain=VKM B-2533	GCA_014779555.2	435897	435897	type	True	81.0501	727	1285	95	below_threshold
Lysobacter psychrotolerans	strain=ZS60	GCA_003719825.1	1327343	1327343	type	True	80.9447	634	1285	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:54:29,291] [INFO] DFAST Taxonomy check result was written to GCF_006547045.1_ASM654704v1_genomic.fna/tc_result.tsv
[2024-01-24 12:54:29,292] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:54:29,292] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:54:29,292] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga30ca195-4729-40ba-bee7-8ea22aa9e2f0/dqc_reference/checkm_data
[2024-01-24 12:54:29,294] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:54:29,333] [INFO] Task started: CheckM
[2024-01-24 12:54:29,333] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006547045.1_ASM654704v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006547045.1_ASM654704v1_genomic.fna/checkm_input GCF_006547045.1_ASM654704v1_genomic.fna/checkm_result
[2024-01-24 12:55:24,192] [INFO] Task succeeded: CheckM
[2024-01-24 12:55:24,193] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:55:24,214] [INFO] ===== Completeness check finished =====
[2024-01-24 12:55:24,214] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:55:24,214] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006547045.1_ASM654704v1_genomic.fna/markers.fasta)
[2024-01-24 12:55:24,215] [INFO] Task started: Blastn
[2024-01-24 12:55:24,215] [INFO] Running command: blastn -query GCF_006547045.1_ASM654704v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga30ca195-4729-40ba-bee7-8ea22aa9e2f0/dqc_reference/reference_markers_gtdb.fasta -out GCF_006547045.1_ASM654704v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:55:25,772] [INFO] Task succeeded: Blastn
[2024-01-24 12:55:25,775] [INFO] Selected 13 target genomes.
[2024-01-24 12:55:25,775] [INFO] Target genome list was writen to GCF_006547045.1_ASM654704v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:55:25,784] [INFO] Task started: fastANI
[2024-01-24 12:55:25,784] [INFO] Running command: fastANI --query /var/lib/cwl/stg9de87fb2-52c2-4ecc-9998-4332de272141/GCF_006547045.1_ASM654704v1_genomic.fna.gz --refList GCF_006547045.1_ASM654704v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006547045.1_ASM654704v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:55:37,317] [INFO] Task succeeded: fastANI
[2024-01-24 12:55:37,328] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:55:37,328] [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_006547045.1	s__Lysobacter alkalisoli	100.0	1285	1285	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_006546735.2	s__Lysobacter maris	84.7166	754	1285	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	98.39	98.39	0.88	0.88	2	-
GCF_006546775.1	s__Lysobacter aestuarii	82.9999	697	1285	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	82.758	706	1285	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	99.99	99.99	0.99	0.99	2	-
GCF_014145325.1	s__Lysobacter spongiae	82.7324	778	1285	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000768335.1	s__Lysobacter arseniciresistens	82.7082	618	1285	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014145395.1	s__Lysobacter penaei	82.4165	677	1285	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	81.9065	655	1285	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	81.8035	770	1285	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	81.7736	568	1285	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	99.71	99.71	0.92	0.92	2	-
GCF_000336385.2	s__Lysobacter antibioticus_A	81.6725	719	1285	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000731095.1	s__Lysobacter antibioticus_B	81.2443	693	1285	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	80.9451	634	1285	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 12:55:37,329] [INFO] GTDB search result was written to GCF_006547045.1_ASM654704v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:55:37,330] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:55:37,333] [INFO] DFAST_QC result json was written to GCF_006547045.1_ASM654704v1_genomic.fna/dqc_result.json
[2024-01-24 12:55:37,333] [INFO] DFAST_QC completed!
[2024-01-24 12:55:37,333] [INFO] Total running time: 0h1m41s