[2024-01-25 19:52:35,459] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:52:35,460] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:52:35,460] [INFO] DQC Reference Directory: /var/lib/cwl/stg5ded83fd-4b28-4365-b87a-58fd18c68ce2/dqc_reference
[2024-01-25 19:52:36,630] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:52:36,633] [INFO] Task started: Prodigal
[2024-01-25 19:52:36,634] [INFO] Running command: gunzip -c /var/lib/cwl/stg298d773a-80d6-4d01-84c4-68528745b21b/GCF_014651995.1_ASM1465199v1_genomic.fna.gz | prodigal -d GCF_014651995.1_ASM1465199v1_genomic.fna/cds.fna -a GCF_014651995.1_ASM1465199v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:52:44,588] [INFO] Task succeeded: Prodigal
[2024-01-25 19:52:44,588] [INFO] Task started: HMMsearch
[2024-01-25 19:52:44,588] [INFO] Running command: hmmsearch --tblout GCF_014651995.1_ASM1465199v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5ded83fd-4b28-4365-b87a-58fd18c68ce2/dqc_reference/reference_markers.hmm GCF_014651995.1_ASM1465199v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:52:44,798] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:52:44,799] [INFO] Found 6/6 markers.
[2024-01-25 19:52:44,824] [INFO] Query marker FASTA was written to GCF_014651995.1_ASM1465199v1_genomic.fna/markers.fasta
[2024-01-25 19:52:44,824] [INFO] Task started: Blastn
[2024-01-25 19:52:44,824] [INFO] Running command: blastn -query GCF_014651995.1_ASM1465199v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5ded83fd-4b28-4365-b87a-58fd18c68ce2/dqc_reference/reference_markers.fasta -out GCF_014651995.1_ASM1465199v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:52:45,685] [INFO] Task succeeded: Blastn
[2024-01-25 19:52:45,688] [INFO] Selected 18 target genomes.
[2024-01-25 19:52:45,688] [INFO] Target genome list was writen to GCF_014651995.1_ASM1465199v1_genomic.fna/target_genomes.txt
[2024-01-25 19:52:45,699] [INFO] Task started: fastANI
[2024-01-25 19:52:45,699] [INFO] Running command: fastANI --query /var/lib/cwl/stg298d773a-80d6-4d01-84c4-68528745b21b/GCF_014651995.1_ASM1465199v1_genomic.fna.gz --refList GCF_014651995.1_ASM1465199v1_genomic.fna/target_genomes.txt --output GCF_014651995.1_ASM1465199v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:52:58,954] [INFO] Task succeeded: fastANI
[2024-01-25 19:52:58,955] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5ded83fd-4b28-4365-b87a-58fd18c68ce2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:52:58,955] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5ded83fd-4b28-4365-b87a-58fd18c68ce2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:52:58,966] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:52:58,966] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:52:58,966] [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 xinjiangensis	strain=KCTC 22558	GCA_014651995.1	546892	546892	type	True	100.0	1009	1010	95	conclusive
Lysobacter segetis	strain=17J68-2	GCA_004359965.1	2492394	2492394	type	True	85.9652	749	1010	95	below_threshold
Lysobacter terrigena	strain=17J7-1	GCA_004361065.1	2488749	2488749	type	True	85.0046	770	1010	95	below_threshold
Lysobacter lacus	strain=UKS-15	GCA_008274655.1	1643323	1643323	type	True	83.6772	610	1010	95	below_threshold
Vulcaniibacterium tengchongense	strain=DSM 25623	GCA_003814555.1	1273429	1273429	type	True	82.1877	638	1010	95	below_threshold
Vulcaniibacterium gelatinicum	strain=R-5-52-3	GCA_008033445.1	2598725	2598725	type	True	81.4622	542	1010	95	below_threshold
Lysobacter niastensis	strain=DSM 18481	GCA_015453285.1	380629	380629	type	True	81.4412	596	1010	95	below_threshold
Lysobacter soli	strain=KCTC 22011	GCA_003382285.1	453783	453783	type	True	81.425	626	1010	95	below_threshold
Luteimonas lumbrici	strain=1.1416	GCA_006476065.1	2559601	2559601	type	True	81.12	531	1010	95	below_threshold
Lysobacter luteus	strain=CECT 30171	GCA_907164845.1	2822368	2822368	type	True	81.0842	573	1010	95	below_threshold
Luteimonas aquatica	strain=RIB1-20	GCA_022662575.1	450364	450364	type	True	81.0806	587	1010	95	below_threshold
Lysobacter ruishenii	strain=CGMCC 1.10136	GCA_007830115.1	686800	686800	type	True	80.9206	553	1010	95	below_threshold
Lysobacter solisilvae	strain=R19	GCA_016613535.2	2763317	2763317	type	True	80.9097	600	1010	95	below_threshold
Lysobacter enzymogenes	strain=ATCC 29487	GCA_900106525.1	69	69	suspected-type	True	80.8585	658	1010	95	below_threshold
Lysobacter chinensis	strain=TLK-CK17	GCA_021725675.1	2912247	2912247	type	True	80.8163	582	1010	95	below_threshold
Xanthomonas translucens	strain=ATCC 19319	GCA_020880735.1	343	343	type	True	79.7864	466	1010	95	below_threshold
Arenimonas oryziterrae	strain=DSM 21050	GCA_000420545.1	498055	498055	type	True	78.9955	369	1010	95	below_threshold
Arenimonas oryziterrae	strain=YC6267	GCA_000747135.1	498055	498055	type	True	78.8435	370	1010	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:52:58,970] [INFO] DFAST Taxonomy check result was written to GCF_014651995.1_ASM1465199v1_genomic.fna/tc_result.tsv
[2024-01-25 19:52:58,971] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:52:58,971] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:52:58,971] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5ded83fd-4b28-4365-b87a-58fd18c68ce2/dqc_reference/checkm_data
[2024-01-25 19:52:58,972] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:52:59,004] [INFO] Task started: CheckM
[2024-01-25 19:52:59,005] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014651995.1_ASM1465199v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014651995.1_ASM1465199v1_genomic.fna/checkm_input GCF_014651995.1_ASM1465199v1_genomic.fna/checkm_result
[2024-01-25 19:53:27,448] [INFO] Task succeeded: CheckM
[2024-01-25 19:53:27,449] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:53:27,470] [INFO] ===== Completeness check finished =====
[2024-01-25 19:53:27,470] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:53:27,471] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014651995.1_ASM1465199v1_genomic.fna/markers.fasta)
[2024-01-25 19:53:27,471] [INFO] Task started: Blastn
[2024-01-25 19:53:27,471] [INFO] Running command: blastn -query GCF_014651995.1_ASM1465199v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5ded83fd-4b28-4365-b87a-58fd18c68ce2/dqc_reference/reference_markers_gtdb.fasta -out GCF_014651995.1_ASM1465199v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:53:29,085] [INFO] Task succeeded: Blastn
[2024-01-25 19:53:29,088] [INFO] Selected 7 target genomes.
[2024-01-25 19:53:29,089] [INFO] Target genome list was writen to GCF_014651995.1_ASM1465199v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:53:29,095] [INFO] Task started: fastANI
[2024-01-25 19:53:29,095] [INFO] Running command: fastANI --query /var/lib/cwl/stg298d773a-80d6-4d01-84c4-68528745b21b/GCF_014651995.1_ASM1465199v1_genomic.fna.gz --refList GCF_014651995.1_ASM1465199v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014651995.1_ASM1465199v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:53:34,769] [INFO] Task succeeded: fastANI
[2024-01-25 19:53:34,775] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:53:34,775] [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_014651995.1	s__Lysobacter xinjiangensis	100.0	1009	1010	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_004359965.1	s__Lysobacter segetis	85.9716	748	1010	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004361065.1	s__Lysobacter terrigena	84.9927	771	1010	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003367355.1	s__Lysobacter sp003367355	84.7546	776	1010	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000426005.1	s__Lysobacter sp000426005	84.6404	768	1010	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008274655.1	s__Lysobacter lacus	83.6915	609	1010	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	80.902	555	1010	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:53:34,776] [INFO] GTDB search result was written to GCF_014651995.1_ASM1465199v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:53:34,777] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:53:34,780] [INFO] DFAST_QC result json was written to GCF_014651995.1_ASM1465199v1_genomic.fna/dqc_result.json
[2024-01-25 19:53:34,780] [INFO] DFAST_QC completed!
[2024-01-25 19:53:34,780] [INFO] Total running time: 0h0m59s