[2024-01-24 12:51:05,243] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:51:05,244] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:51:05,245] [INFO] DQC Reference Directory: /var/lib/cwl/stg543d8c63-980a-4766-81d9-f5b9533737d6/dqc_reference
[2024-01-24 12:51:06,451] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:51:06,452] [INFO] Task started: Prodigal
[2024-01-24 12:51:06,452] [INFO] Running command: gunzip -c /var/lib/cwl/stg582ab356-195e-428f-9631-56f645ab5a7e/GCF_023612255.1_ASM2361225v1_genomic.fna.gz | prodigal -d GCF_023612255.1_ASM2361225v1_genomic.fna/cds.fna -a GCF_023612255.1_ASM2361225v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:51:21,140] [INFO] Task succeeded: Prodigal
[2024-01-24 12:51:21,141] [INFO] Task started: HMMsearch
[2024-01-24 12:51:21,141] [INFO] Running command: hmmsearch --tblout GCF_023612255.1_ASM2361225v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg543d8c63-980a-4766-81d9-f5b9533737d6/dqc_reference/reference_markers.hmm GCF_023612255.1_ASM2361225v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:51:21,417] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:51:21,418] [INFO] Found 6/6 markers.
[2024-01-24 12:51:21,457] [INFO] Query marker FASTA was written to GCF_023612255.1_ASM2361225v1_genomic.fna/markers.fasta
[2024-01-24 12:51:21,457] [INFO] Task started: Blastn
[2024-01-24 12:51:21,457] [INFO] Running command: blastn -query GCF_023612255.1_ASM2361225v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg543d8c63-980a-4766-81d9-f5b9533737d6/dqc_reference/reference_markers.fasta -out GCF_023612255.1_ASM2361225v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:51:22,308] [INFO] Task succeeded: Blastn
[2024-01-24 12:51:22,313] [INFO] Selected 13 target genomes.
[2024-01-24 12:51:22,313] [INFO] Target genome list was writen to GCF_023612255.1_ASM2361225v1_genomic.fna/target_genomes.txt
[2024-01-24 12:51:22,315] [INFO] Task started: fastANI
[2024-01-24 12:51:22,315] [INFO] Running command: fastANI --query /var/lib/cwl/stg582ab356-195e-428f-9631-56f645ab5a7e/GCF_023612255.1_ASM2361225v1_genomic.fna.gz --refList GCF_023612255.1_ASM2361225v1_genomic.fna/target_genomes.txt --output GCF_023612255.1_ASM2361225v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:51:33,654] [INFO] Task succeeded: fastANI
[2024-01-24 12:51:33,655] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg543d8c63-980a-4766-81d9-f5b9533737d6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:51:33,655] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg543d8c63-980a-4766-81d9-f5b9533737d6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:51:33,670] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:51:33,670] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:51:33,670] [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
Luteibacter yeojuensis	strain=DSM 17673	GCA_011742875.1	345309	345309	type	True	83.1918	940	1433	95	below_threshold
Luteibacter jiangsuensis	strain=CGMCC 1.10133	GCA_011742555.1	637577	637577	type	True	82.8613	960	1433	95	below_threshold
Luteibacter rhizovicinus	strain=LJ96	GCA_001887595.1	242606	242606	type	True	81.8723	894	1433	95	below_threshold
Luteibacter rhizovicinus	strain=DSM 16549	GCA_001010405.1	242606	242606	type	True	81.7707	778	1433	95	below_threshold
Luteibacter pinisoli	strain=MAH-14	GCA_006385595.1	2589080	2589080	type	True	81.6936	885	1433	95	below_threshold
Luteibacter anthropi	strain=CCUG 25036	GCA_011759365.1	564369	564369	type	True	81.6918	844	1433	95	below_threshold
Frateuria flava	strain=MAH-13	GCA_017837635.1	2821489	2821489	type	True	79.2259	479	1433	95	below_threshold
Dyella japonica	strain=DSM 16301	GCA_001010355.1	231455	231455	type	True	79.1922	422	1433	95	below_threshold
Dyella telluris	strain=G9	GCA_014297575.1	2763498	2763498	type	True	79.1512	537	1433	95	below_threshold
Rhodanobacter fulvus	strain=Jip2	GCA_000264315.1	219571	219571	type	True	78.92	425	1433	95	below_threshold
Dyella acidiphila	strain=7MK23	GCA_014863405.1	2775866	2775866	type	True	78.8123	457	1433	95	below_threshold
Arenimonas caeni	strain=z29	GCA_003024235.1	2058085	2058085	type	True	78.0452	243	1433	95	below_threshold
Hydrocarboniphaga effusa	strain=AP103	GCA_000271305.1	243629	243629	type	True	76.1103	166	1433	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:51:33,672] [INFO] DFAST Taxonomy check result was written to GCF_023612255.1_ASM2361225v1_genomic.fna/tc_result.tsv
[2024-01-24 12:51:33,672] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:51:33,672] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:51:33,672] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg543d8c63-980a-4766-81d9-f5b9533737d6/dqc_reference/checkm_data
[2024-01-24 12:51:33,673] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:51:33,714] [INFO] Task started: CheckM
[2024-01-24 12:51:33,714] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_023612255.1_ASM2361225v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_023612255.1_ASM2361225v1_genomic.fna/checkm_input GCF_023612255.1_ASM2361225v1_genomic.fna/checkm_result
[2024-01-24 12:52:21,340] [INFO] Task succeeded: CheckM
[2024-01-24 12:52:21,342] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:52:21,372] [INFO] ===== Completeness check finished =====
[2024-01-24 12:52:21,373] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:52:21,373] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_023612255.1_ASM2361225v1_genomic.fna/markers.fasta)
[2024-01-24 12:52:21,373] [INFO] Task started: Blastn
[2024-01-24 12:52:21,374] [INFO] Running command: blastn -query GCF_023612255.1_ASM2361225v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg543d8c63-980a-4766-81d9-f5b9533737d6/dqc_reference/reference_markers_gtdb.fasta -out GCF_023612255.1_ASM2361225v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:52:22,809] [INFO] Task succeeded: Blastn
[2024-01-24 12:52:22,813] [INFO] Selected 14 target genomes.
[2024-01-24 12:52:22,813] [INFO] Target genome list was writen to GCF_023612255.1_ASM2361225v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:52:22,869] [INFO] Task started: fastANI
[2024-01-24 12:52:22,869] [INFO] Running command: fastANI --query /var/lib/cwl/stg582ab356-195e-428f-9631-56f645ab5a7e/GCF_023612255.1_ASM2361225v1_genomic.fna.gz --refList GCF_023612255.1_ASM2361225v1_genomic.fna/target_genomes_gtdb.txt --output GCF_023612255.1_ASM2361225v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:52:35,258] [INFO] Task succeeded: fastANI
[2024-01-24 12:52:35,272] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:52:35,272] [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_900119235.1	s__Luteibacter sp900119235	96.4656	1305	1433	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Luteibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900110505.1	s__Luteibacter sp900110505	83.2054	907	1433	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Luteibacter	95.0	97.58	97.58	0.93	0.93	2	-
GCF_011742875.1	s__Luteibacter yeojuensis	83.1781	942	1433	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Luteibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109915.1	s__Luteibacter sp900109915	82.9661	905	1433	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Luteibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011742555.1	s__Luteibacter jiangsuensis	82.8593	960	1433	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Luteibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011759605.1	s__Luteibacter sp011759605	82.8021	972	1433	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Luteibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007829075.1	s__Luteibacter yeojuensis_B	82.1158	885	1433	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Luteibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_018889975.1	s__Luteibacter sp018889975	82.0128	857	1433	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Luteibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000964085.1	s__Luteibacter yeojuensis_A	81.8319	809	1433	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Luteibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011759365.1	s__Luteibacter anthropi	81.6969	845	1433	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Luteibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002429615.1	s__Stenotrophomonas_A sp002429615	77.882	251	1433	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017302215.1	s__Dokdonella sp017302215	77.8482	258	1433	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001899855.1	s__Dokdonella sp001899855	77.2859	235	1433	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000271305.1	s__Hydrocarboniphaga effusa	76.1191	165	1433	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Hydrocarboniphaga	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:52:35,276] [INFO] GTDB search result was written to GCF_023612255.1_ASM2361225v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:52:35,277] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:52:35,283] [INFO] DFAST_QC result json was written to GCF_023612255.1_ASM2361225v1_genomic.fna/dqc_result.json
[2024-01-24 12:52:35,283] [INFO] DFAST_QC completed!
[2024-01-24 12:52:35,283] [INFO] Total running time: 0h1m30s