[2024-01-25 19:45:20,938] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:45:20,940] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:45:20,940] [INFO] DQC Reference Directory: /var/lib/cwl/stg374de499-3ca0-4642-82f4-15d13c1338ea/dqc_reference
[2024-01-25 19:45:22,125] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:45:22,126] [INFO] Task started: Prodigal
[2024-01-25 19:45:22,126] [INFO] Running command: gunzip -c /var/lib/cwl/stgb572705a-a1b8-4568-9d85-49a6d917c3c8/GCF_030160375.1_ASM3016037v1_genomic.fna.gz | prodigal -d GCF_030160375.1_ASM3016037v1_genomic.fna/cds.fna -a GCF_030160375.1_ASM3016037v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:45:31,314] [INFO] Task succeeded: Prodigal
[2024-01-25 19:45:31,315] [INFO] Task started: HMMsearch
[2024-01-25 19:45:31,315] [INFO] Running command: hmmsearch --tblout GCF_030160375.1_ASM3016037v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg374de499-3ca0-4642-82f4-15d13c1338ea/dqc_reference/reference_markers.hmm GCF_030160375.1_ASM3016037v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:45:31,563] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:45:31,564] [INFO] Found 6/6 markers.
[2024-01-25 19:45:31,599] [INFO] Query marker FASTA was written to GCF_030160375.1_ASM3016037v1_genomic.fna/markers.fasta
[2024-01-25 19:45:31,599] [INFO] Task started: Blastn
[2024-01-25 19:45:31,599] [INFO] Running command: blastn -query GCF_030160375.1_ASM3016037v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg374de499-3ca0-4642-82f4-15d13c1338ea/dqc_reference/reference_markers.fasta -out GCF_030160375.1_ASM3016037v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:45:32,399] [INFO] Task succeeded: Blastn
[2024-01-25 19:45:32,402] [INFO] Selected 15 target genomes.
[2024-01-25 19:45:32,402] [INFO] Target genome list was writen to GCF_030160375.1_ASM3016037v1_genomic.fna/target_genomes.txt
[2024-01-25 19:45:32,409] [INFO] Task started: fastANI
[2024-01-25 19:45:32,410] [INFO] Running command: fastANI --query /var/lib/cwl/stgb572705a-a1b8-4568-9d85-49a6d917c3c8/GCF_030160375.1_ASM3016037v1_genomic.fna.gz --refList GCF_030160375.1_ASM3016037v1_genomic.fna/target_genomes.txt --output GCF_030160375.1_ASM3016037v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:45:44,993] [INFO] Task succeeded: fastANI
[2024-01-25 19:45:44,994] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg374de499-3ca0-4642-82f4-15d13c1338ea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:45:44,994] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg374de499-3ca0-4642-82f4-15d13c1338ea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:45:45,003] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:45:45,003] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:45:45,003] [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
Mixta calida	strain=DSM 22759	GCA_002953215.1	665913	665913	type	True	84.9419	1063	1413	95	below_threshold
Mixta calida	strain=LMG 25383	GCA_002095355.1	665913	665913	type	True	84.9308	979	1413	95	below_threshold
Mixta gaviniae	strain=DSM 22758	GCA_002953195.1	665914	665914	type	True	84.8553	1058	1413	95	below_threshold
Mixta tenebrionis	strain=BIT-26	GCA_006517625.1	2562439	2562439	type	True	84.1906	1009	1413	95	below_threshold
Pantoea septica	strain=LMG 5345	GCA_002095575.1	472695	472695	type	True	80.1993	740	1413	95	below_threshold
Erwinia iniecta	strain=B120	GCA_001267535.1	1560201	1560201	type	True	80.1448	698	1413	95	below_threshold
Erwinia phyllosphaerae	strain=CMYE1	GCA_019132875.1	2853256	2853256	type	True	79.7406	679	1413	95	below_threshold
Erwinia aphidicola	strain=X001	GCA_024169515.1	68334	68334	type	True	79.7029	682	1413	95	below_threshold
Erwinia aphidicola	strain=JCM 21238	GCA_014773485.1	68334	68334	type	True	79.6994	673	1413	95	below_threshold
Siccibacter turicensis	strain=LMG 23730	GCA_000463155.2	357233	357233	type	True	78.9158	502	1413	95	below_threshold
Cronobacter sakazakii	strain=ATCC 29544	GCA_001971035.1	28141	28141	type	True	78.858	521	1413	95	below_threshold
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	78.73	474	1413	95	below_threshold
Enterobacter roggenkampii	strain=DSM 16690	GCA_024390995.1	1812935	1812935	type	True	78.6561	473	1413	95	below_threshold
Providencia thailandensis	strain=KCTC 23281	GCA_014652175.1	990144	990144	type	True	77.8782	79	1413	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:45:45,004] [INFO] DFAST Taxonomy check result was written to GCF_030160375.1_ASM3016037v1_genomic.fna/tc_result.tsv
[2024-01-25 19:45:45,005] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:45:45,005] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:45:45,005] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg374de499-3ca0-4642-82f4-15d13c1338ea/dqc_reference/checkm_data
[2024-01-25 19:45:45,006] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:45:45,053] [INFO] Task started: CheckM
[2024-01-25 19:45:45,053] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030160375.1_ASM3016037v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030160375.1_ASM3016037v1_genomic.fna/checkm_input GCF_030160375.1_ASM3016037v1_genomic.fna/checkm_result
[2024-01-25 19:46:14,792] [INFO] Task succeeded: CheckM
[2024-01-25 19:46:14,793] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:46:14,810] [INFO] ===== Completeness check finished =====
[2024-01-25 19:46:14,810] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:46:14,811] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030160375.1_ASM3016037v1_genomic.fna/markers.fasta)
[2024-01-25 19:46:14,811] [INFO] Task started: Blastn
[2024-01-25 19:46:14,811] [INFO] Running command: blastn -query GCF_030160375.1_ASM3016037v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg374de499-3ca0-4642-82f4-15d13c1338ea/dqc_reference/reference_markers_gtdb.fasta -out GCF_030160375.1_ASM3016037v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:46:15,998] [INFO] Task succeeded: Blastn
[2024-01-25 19:46:16,005] [INFO] Selected 10 target genomes.
[2024-01-25 19:46:16,005] [INFO] Target genome list was writen to GCF_030160375.1_ASM3016037v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:46:16,016] [INFO] Task started: fastANI
[2024-01-25 19:46:16,017] [INFO] Running command: fastANI --query /var/lib/cwl/stgb572705a-a1b8-4568-9d85-49a6d917c3c8/GCF_030160375.1_ASM3016037v1_genomic.fna.gz --refList GCF_030160375.1_ASM3016037v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030160375.1_ASM3016037v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:46:27,190] [INFO] Task succeeded: fastANI
[2024-01-25 19:46:27,198] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:46:27,198] [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_002895925.1	s__Mixta theicola	99.9843	1395	1413	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Mixta	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002101395.1	s__Mixta alhagi	89.5204	1114	1413	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Mixta	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002953215.1	s__Mixta calida	84.9267	1065	1413	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Mixta	95.0	99.65	99.42	0.96	0.92	22	-
GCF_002953195.1	s__Mixta gaviniae	84.8261	1061	1413	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Mixta	95.0	99.91	99.91	0.99	0.99	2	-
GCF_006517625.1	s__Mixta tenebrionis	84.1892	1009	1413	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Mixta	95.0	99.45	99.45	0.92	0.92	2	-
GCF_009914055.1	s__Mixta intestinalis	83.6296	990	1413	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Mixta	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002920175.1	s__Pantoea sp002920175	80.7763	767	1413	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	99.09	99.09	0.94	0.94	2	-
GCF_002095465.1	s__Pantoea rodasii	79.5932	604	1413	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	99.97	99.97	1.00	1.00	2	-
GCF_018842675.1	s__Pantoea sp018842675	79.4484	584	1413	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002858715.1	s__Chimaeribacter coloradensis	79.002	525	1413	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Chimaeribacter	95.0	98.66	98.66	0.97	0.97	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:46:27,199] [INFO] GTDB search result was written to GCF_030160375.1_ASM3016037v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:46:27,200] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:46:27,206] [INFO] DFAST_QC result json was written to GCF_030160375.1_ASM3016037v1_genomic.fna/dqc_result.json
[2024-01-25 19:46:27,206] [INFO] DFAST_QC completed!
[2024-01-25 19:46:27,206] [INFO] Total running time: 0h1m6s