[2024-01-25 18:45:50,626] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:45:50,627] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:45:50,628] [INFO] DQC Reference Directory: /var/lib/cwl/stg0122e002-4ecc-4c55-9509-267e22023e8d/dqc_reference
[2024-01-25 18:45:51,760] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:45:51,761] [INFO] Task started: Prodigal
[2024-01-25 18:45:51,761] [INFO] Running command: gunzip -c /var/lib/cwl/stgdcda19c2-84e4-487e-94f9-1156bc8a64f2/GCF_000768345.1_ASM76834v1_genomic.fna.gz | prodigal -d GCF_000768345.1_ASM76834v1_genomic.fna/cds.fna -a GCF_000768345.1_ASM76834v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:46:00,318] [INFO] Task succeeded: Prodigal
[2024-01-25 18:46:00,319] [INFO] Task started: HMMsearch
[2024-01-25 18:46:00,319] [INFO] Running command: hmmsearch --tblout GCF_000768345.1_ASM76834v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0122e002-4ecc-4c55-9509-267e22023e8d/dqc_reference/reference_markers.hmm GCF_000768345.1_ASM76834v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:46:00,516] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:46:00,517] [INFO] Found 6/6 markers.
[2024-01-25 18:46:00,544] [INFO] Query marker FASTA was written to GCF_000768345.1_ASM76834v1_genomic.fna/markers.fasta
[2024-01-25 18:46:00,544] [INFO] Task started: Blastn
[2024-01-25 18:46:00,544] [INFO] Running command: blastn -query GCF_000768345.1_ASM76834v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0122e002-4ecc-4c55-9509-267e22023e8d/dqc_reference/reference_markers.fasta -out GCF_000768345.1_ASM76834v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:46:01,416] [INFO] Task succeeded: Blastn
[2024-01-25 18:46:01,419] [INFO] Selected 15 target genomes.
[2024-01-25 18:46:01,419] [INFO] Target genome list was writen to GCF_000768345.1_ASM76834v1_genomic.fna/target_genomes.txt
[2024-01-25 18:46:01,431] [INFO] Task started: fastANI
[2024-01-25 18:46:01,431] [INFO] Running command: fastANI --query /var/lib/cwl/stgdcda19c2-84e4-487e-94f9-1156bc8a64f2/GCF_000768345.1_ASM76834v1_genomic.fna.gz --refList GCF_000768345.1_ASM76834v1_genomic.fna/target_genomes.txt --output GCF_000768345.1_ASM76834v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:46:12,962] [INFO] Task succeeded: fastANI
[2024-01-25 18:46:12,963] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0122e002-4ecc-4c55-9509-267e22023e8d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:46:12,963] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0122e002-4ecc-4c55-9509-267e22023e8d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:46:12,973] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:46:12,973] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:46:12,973] [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 concretionis	strain=Ko07	GCA_000768345.1	262325	262325	type	True	100.0	998	999	95	conclusive
Lysobacter ciconiae	strain=H21R20	GCA_015209725.1	2781022	2781022	type	True	84.1011	702	999	95	below_threshold
Lysobacter arseniciresistens	strain=ZS79	GCA_000768335.1	1385522	1385522	type	True	84.0983	636	999	95	below_threshold
Lysobacter avium	strain=H23M41	GCA_015209745.1	2781023	2781023	type	True	83.2411	653	999	95	below_threshold
Lysobacter antarcticus	strain=GW1-59	GCA_019802285.1	2862543	2862543	type	True	82.8262	624	999	95	below_threshold
Lysobacter luteus	strain=CECT 30171	GCA_907164845.1	2822368	2822368	type	True	82.8124	631	999	95	below_threshold
Vulcaniibacterium tengchongense	strain=DSM 25623	GCA_003814555.1	1273429	1273429	type	True	82.3774	608	999	95	below_threshold
Lysobacter spongiicola	strain=DSM 21749	GCA_900167055.1	435289	435289	type	True	82.0851	596	999	95	below_threshold
Lysobacter silvisoli	strain=zong2l5	GCA_003382365.1	2293254	2293254	type	True	81.6593	610	999	95	below_threshold
Lysobacter psychrotolerans	strain=ZS60	GCA_003719825.1	1327343	1327343	type	True	81.451	571	999	95	below_threshold
Lysobacter arenosi	strain=R7	GCA_016613475.2	2795387	2795387	type	True	81.4216	593	999	95	below_threshold
Luteimonas mephitis	strain=DSM 12574	GCA_000422305.1	83615	83615	type	True	81.2431	601	999	95	below_threshold
Lysobacter daejeonensis	strain=GH1-9	GCA_000768355.1	346181	346181	type	True	81.2091	547	999	95	below_threshold
Lysobacter capsici	strain=VKM B-2533	GCA_014779555.2	435897	435897	type	True	81.1161	610	999	95	below_threshold
Lysobacter bugurensis	strain=KCTC 23077	GCA_014652095.1	543356	543356	type	True	79.9756	489	999	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:46:12,975] [INFO] DFAST Taxonomy check result was written to GCF_000768345.1_ASM76834v1_genomic.fna/tc_result.tsv
[2024-01-25 18:46:12,976] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:46:12,976] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:46:12,976] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0122e002-4ecc-4c55-9509-267e22023e8d/dqc_reference/checkm_data
[2024-01-25 18:46:12,977] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:46:13,006] [INFO] Task started: CheckM
[2024-01-25 18:46:13,007] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000768345.1_ASM76834v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000768345.1_ASM76834v1_genomic.fna/checkm_input GCF_000768345.1_ASM76834v1_genomic.fna/checkm_result
[2024-01-25 18:46:50,599] [INFO] Task succeeded: CheckM
[2024-01-25 18:46:50,601] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:46:50,624] [INFO] ===== Completeness check finished =====
[2024-01-25 18:46:50,624] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:46:50,624] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000768345.1_ASM76834v1_genomic.fna/markers.fasta)
[2024-01-25 18:46:50,625] [INFO] Task started: Blastn
[2024-01-25 18:46:50,625] [INFO] Running command: blastn -query GCF_000768345.1_ASM76834v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0122e002-4ecc-4c55-9509-267e22023e8d/dqc_reference/reference_markers_gtdb.fasta -out GCF_000768345.1_ASM76834v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:46:52,427] [INFO] Task succeeded: Blastn
[2024-01-25 18:46:52,430] [INFO] Selected 17 target genomes.
[2024-01-25 18:46:52,430] [INFO] Target genome list was writen to GCF_000768345.1_ASM76834v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:46:52,463] [INFO] Task started: fastANI
[2024-01-25 18:46:52,463] [INFO] Running command: fastANI --query /var/lib/cwl/stgdcda19c2-84e4-487e-94f9-1156bc8a64f2/GCF_000768345.1_ASM76834v1_genomic.fna.gz --refList GCF_000768345.1_ASM76834v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000768345.1_ASM76834v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:47:05,627] [INFO] Task succeeded: fastANI
[2024-01-25 18:47:05,638] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:47:05,638] [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_000768345.1	s__Lysobacter concretionis	100.0	998	999	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_015209725.1	s__Lysobacter sp015209725	84.1014	702	999	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	96.91	96.91	0.94	0.94	2	-
GCF_000768335.1	s__Lysobacter arseniciresistens	84.0925	637	999	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015209765.1	s__Lysobacter sp015209765	83.4161	643	999	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	98.00	98.00	0.93	0.93	2	-
GCF_000855665.1	s__Lysobacter sp000855665	82.8574	616	999	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_907164845.1	s__Lysobacter sp907164845	82.808	631	999	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	82.3721	607	999	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	99.99	99.99	0.99	0.99	2	-
GCA_001830245.1	s__Lysobacter sp001830245	82.1218	548	999	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	99.71	99.71	0.92	0.92	2	-
GCF_900167055.1	s__Lysobacter spongiicola	82.1105	594	999	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	81.7718	643	999	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	81.6548	572	999	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428685.1	s__Lysobacter sp001428685	81.5941	620	999	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	99.42	98.61	0.98	0.96	4	-
GCF_003719825.1	s__Lysobacter psychrotolerans	81.4991	567	999	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	81.3986	595	999	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000422305.1	s__Luteimonas mephitis	81.2155	602	999	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000768355.1	s__Lysobacter daejeonensis	81.2087	547	999	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014652095.1	s__Lysobacter bugurensis	79.9982	487	999	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 18:47:05,642] [INFO] GTDB search result was written to GCF_000768345.1_ASM76834v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:47:05,643] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:47:05,646] [INFO] DFAST_QC result json was written to GCF_000768345.1_ASM76834v1_genomic.fna/dqc_result.json
[2024-01-25 18:47:05,646] [INFO] DFAST_QC completed!
[2024-01-25 18:47:05,646] [INFO] Total running time: 0h1m15s