[2024-01-24 13:13:51,525] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:13:51,527] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:13:51,527] [INFO] DQC Reference Directory: /var/lib/cwl/stg624b06a0-32d1-4996-bb9c-8f46dbc192b6/dqc_reference
[2024-01-24 13:13:52,787] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:13:52,788] [INFO] Task started: Prodigal
[2024-01-24 13:13:52,788] [INFO] Running command: gunzip -c /var/lib/cwl/stg7b591bb8-b215-4e22-9953-7bce3be1f5dc/GCF_006546775.1_ASM654677v1_genomic.fna.gz | prodigal -d GCF_006546775.1_ASM654677v1_genomic.fna/cds.fna -a GCF_006546775.1_ASM654677v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:14:02,883] [INFO] Task succeeded: Prodigal
[2024-01-24 13:14:02,884] [INFO] Task started: HMMsearch
[2024-01-24 13:14:02,884] [INFO] Running command: hmmsearch --tblout GCF_006546775.1_ASM654677v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg624b06a0-32d1-4996-bb9c-8f46dbc192b6/dqc_reference/reference_markers.hmm GCF_006546775.1_ASM654677v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:14:03,172] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:14:03,173] [INFO] Found 6/6 markers.
[2024-01-24 13:14:03,215] [INFO] Query marker FASTA was written to GCF_006546775.1_ASM654677v1_genomic.fna/markers.fasta
[2024-01-24 13:14:03,215] [INFO] Task started: Blastn
[2024-01-24 13:14:03,216] [INFO] Running command: blastn -query GCF_006546775.1_ASM654677v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg624b06a0-32d1-4996-bb9c-8f46dbc192b6/dqc_reference/reference_markers.fasta -out GCF_006546775.1_ASM654677v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:14:04,278] [INFO] Task succeeded: Blastn
[2024-01-24 13:14:04,282] [INFO] Selected 12 target genomes.
[2024-01-24 13:14:04,283] [INFO] Target genome list was writen to GCF_006546775.1_ASM654677v1_genomic.fna/target_genomes.txt
[2024-01-24 13:14:04,295] [INFO] Task started: fastANI
[2024-01-24 13:14:04,296] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b591bb8-b215-4e22-9953-7bce3be1f5dc/GCF_006546775.1_ASM654677v1_genomic.fna.gz --refList GCF_006546775.1_ASM654677v1_genomic.fna/target_genomes.txt --output GCF_006546775.1_ASM654677v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:14:15,792] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:15,793] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg624b06a0-32d1-4996-bb9c-8f46dbc192b6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:14:15,793] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg624b06a0-32d1-4996-bb9c-8f46dbc192b6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:14:15,811] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:14:15,811] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:14:15,811] [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 aestuarii	strain=JCM 31130	GCA_006546775.1	1706195	1706195	type	True	100.0	1075	1086	95	conclusive
Lysobacter spongiae	strain=119BY6-57	GCA_014145325.1	2025720	2025720	type	True	92.4106	964	1086	95	below_threshold
Lysobacter maris	strain=KCTC 42381	GCA_006546735.2	1605891	1605891	type	True	83.9433	710	1086	95	below_threshold
Lysobacter chinensis	strain=TLK-CK17	GCA_021725675.1	2912247	2912247	type	True	83.2654	775	1086	95	below_threshold
Lysobacter penaei	strain=SG-8	GCA_014145395.1	2759900	2759900	type	True	83.2201	774	1086	95	below_threshold
Lysobacter alkalisoli	strain=SJ-36	GCA_006547045.1	2591633	2591633	type	True	82.8562	711	1086	95	below_threshold
Lysobacter arseniciresistens	strain=ZS79	GCA_000768335.1	1385522	1385522	type	True	82.1247	576	1086	95	below_threshold
Lysobacter silvisoli	strain=zong2l5	GCA_003382365.1	2293254	2293254	type	True	82.0048	675	1086	95	below_threshold
Lysobacter luteus	strain=CECT 30171	GCA_907164845.1	2822368	2822368	type	True	81.5542	538	1086	95	below_threshold
Lysobacter antibioticus	strain=ATCC 29479	GCA_001442535.1	84531	84531	type	True	81.1614	653	1086	95	below_threshold
Luteimonas arsenica	strain=26-35	GCA_004352825.1	1586242	1586242	type	True	81.0116	552	1086	95	below_threshold
Lysobacter capsici	strain=VKM B-2533	GCA_014779555.2	435897	435897	type	True	80.8909	650	1086	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:14:15,815] [INFO] DFAST Taxonomy check result was written to GCF_006546775.1_ASM654677v1_genomic.fna/tc_result.tsv
[2024-01-24 13:14:15,816] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:14:15,817] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:14:15,817] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg624b06a0-32d1-4996-bb9c-8f46dbc192b6/dqc_reference/checkm_data
[2024-01-24 13:14:15,821] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:14:15,862] [INFO] Task started: CheckM
[2024-01-24 13:14:15,862] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006546775.1_ASM654677v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006546775.1_ASM654677v1_genomic.fna/checkm_input GCF_006546775.1_ASM654677v1_genomic.fna/checkm_result
[2024-01-24 13:15:08,514] [INFO] Task succeeded: CheckM
[2024-01-24 13:15:08,515] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:15:08,535] [INFO] ===== Completeness check finished =====
[2024-01-24 13:15:08,535] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:15:08,536] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006546775.1_ASM654677v1_genomic.fna/markers.fasta)
[2024-01-24 13:15:08,536] [INFO] Task started: Blastn
[2024-01-24 13:15:08,536] [INFO] Running command: blastn -query GCF_006546775.1_ASM654677v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg624b06a0-32d1-4996-bb9c-8f46dbc192b6/dqc_reference/reference_markers_gtdb.fasta -out GCF_006546775.1_ASM654677v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:15:10,470] [INFO] Task succeeded: Blastn
[2024-01-24 13:15:10,473] [INFO] Selected 11 target genomes.
[2024-01-24 13:15:10,473] [INFO] Target genome list was writen to GCF_006546775.1_ASM654677v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:15:10,549] [INFO] Task started: fastANI
[2024-01-24 13:15:10,550] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b591bb8-b215-4e22-9953-7bce3be1f5dc/GCF_006546775.1_ASM654677v1_genomic.fna.gz --refList GCF_006546775.1_ASM654677v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006546775.1_ASM654677v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:15:20,297] [INFO] Task succeeded: fastANI
[2024-01-24 13:15:20,307] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:15:20,307] [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_006546775.1	s__Lysobacter aestuarii	100.0	1075	1086	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_014145325.1	s__Lysobacter spongiae	92.4106	964	1086	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006546735.2	s__Lysobacter maris	83.9642	709	1086	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	98.39	98.39	0.88	0.88	2	-
GCF_014145395.1	s__Lysobacter penaei	83.2145	775	1086	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006547045.1	s__Lysobacter alkalisoli	82.8666	710	1086	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	82.2147	669	1086	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	99.99	99.99	0.99	0.99	2	-
GCF_000768335.1	s__Lysobacter arseniciresistens	82.1288	576	1086	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	81.7346	684	1086	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013361435.1	s__Lysobacter sp013361435	81.6981	599	1086	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	81.5186	654	1086	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002798175.1	s__Luteimonas sp002798175	80.4162	500	1086	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:15:20,309] [INFO] GTDB search result was written to GCF_006546775.1_ASM654677v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:15:20,310] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:15:20,313] [INFO] DFAST_QC result json was written to GCF_006546775.1_ASM654677v1_genomic.fna/dqc_result.json
[2024-01-24 13:15:20,314] [INFO] DFAST_QC completed!
[2024-01-24 13:15:20,314] [INFO] Total running time: 0h1m29s