[2024-01-24 11:59:11,209] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:59:11,212] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:59:11,212] [INFO] DQC Reference Directory: /var/lib/cwl/stg9f7d9977-3f6d-4ac4-8972-bfb7eb64bc3d/dqc_reference
[2024-01-24 11:59:12,467] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:59:12,469] [INFO] Task started: Prodigal
[2024-01-24 11:59:12,469] [INFO] Running command: gunzip -c /var/lib/cwl/stg9bc70d1f-64a6-48cc-b992-943eb1040d81/GCF_019132875.1_ASM1913287v1_genomic.fna.gz | prodigal -d GCF_019132875.1_ASM1913287v1_genomic.fna/cds.fna -a GCF_019132875.1_ASM1913287v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:59:24,371] [INFO] Task succeeded: Prodigal
[2024-01-24 11:59:24,371] [INFO] Task started: HMMsearch
[2024-01-24 11:59:24,371] [INFO] Running command: hmmsearch --tblout GCF_019132875.1_ASM1913287v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9f7d9977-3f6d-4ac4-8972-bfb7eb64bc3d/dqc_reference/reference_markers.hmm GCF_019132875.1_ASM1913287v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:59:24,739] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:59:24,741] [INFO] Found 6/6 markers.
[2024-01-24 11:59:24,784] [INFO] Query marker FASTA was written to GCF_019132875.1_ASM1913287v1_genomic.fna/markers.fasta
[2024-01-24 11:59:24,784] [INFO] Task started: Blastn
[2024-01-24 11:59:24,784] [INFO] Running command: blastn -query GCF_019132875.1_ASM1913287v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9f7d9977-3f6d-4ac4-8972-bfb7eb64bc3d/dqc_reference/reference_markers.fasta -out GCF_019132875.1_ASM1913287v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:25,672] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:25,676] [INFO] Selected 19 target genomes.
[2024-01-24 11:59:25,676] [INFO] Target genome list was writen to GCF_019132875.1_ASM1913287v1_genomic.fna/target_genomes.txt
[2024-01-24 11:59:25,683] [INFO] Task started: fastANI
[2024-01-24 11:59:25,683] [INFO] Running command: fastANI --query /var/lib/cwl/stg9bc70d1f-64a6-48cc-b992-943eb1040d81/GCF_019132875.1_ASM1913287v1_genomic.fna.gz --refList GCF_019132875.1_ASM1913287v1_genomic.fna/target_genomes.txt --output GCF_019132875.1_ASM1913287v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:59:43,329] [INFO] Task succeeded: fastANI
[2024-01-24 11:59:43,330] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9f7d9977-3f6d-4ac4-8972-bfb7eb64bc3d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:59:43,330] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9f7d9977-3f6d-4ac4-8972-bfb7eb64bc3d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:59:43,345] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:59:43,345] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:59:43,345] [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
Erwinia phyllosphaerae	strain=CMYE1	GCA_019132875.1	2853256	2853256	type	True	100.0	1559	1561	95	conclusive
Erwinia aphidicola	strain=X001	GCA_024169515.1	68334	68334	type	True	80.6276	789	1561	95	below_threshold
Erwinia aphidicola	strain=JCM 21238	GCA_014773485.1	68334	68334	type	True	80.5203	789	1561	95	below_threshold
Erwinia iniecta	strain=B120	GCA_001267535.1	1560201	1560201	type	True	80.0882	666	1561	95	below_threshold
Mixta gaviniae	strain=DSM 22758	GCA_002953195.1	665914	665914	type	True	80.0468	714	1561	95	below_threshold
Erwinia piriflorinigrans	strain=CFBP 5888	GCA_001050515.1	665097	665097	type	True	80.0029	567	1561	95	below_threshold
Mixta calida	strain=LMG 25383	GCA_002095355.1	665913	665913	type	True	80.0004	652	1561	95	below_threshold
Erwinia persicina	strain=NBRC 102418	GCA_001571305.1	55211	55211	type	True	79.8242	655	1561	95	below_threshold
Erwinia tasmaniensis	strain=Et1/99	GCA_000026185.1	338565	338565	type	True	79.7847	607	1561	95	below_threshold
Erwinia pyrifoliae	strain=DSM 12163	GCA_000026985.1	79967	79967	type	True	79.7472	588	1561	95	below_threshold
Erwinia amylovora	strain=NBRC 12687	GCA_000696075.1	552	552	type	True	79.7341	559	1561	95	below_threshold
Erwinia amylovora	strain=ATCC 15580	GCA_017161565.1	552	552	type	True	79.7031	571	1561	95	below_threshold
Mixta tenebrionis	strain=BIT-26	GCA_006517625.1	2562439	2562439	type	True	79.496	683	1561	95	below_threshold
Pantoea deleyi	strain=LMG24200	GCA_022647325.1	470932	470932	type	True	79.1258	655	1561	95	below_threshold
Pantoea endophytica	strain=596	GCA_002858935.1	92488	92488	type	True	78.9646	647	1561	95	below_threshold
Enterobacter roggenkampii	strain=DSM 16690	GCA_024390995.1	1812935	1812935	type	True	78.8749	449	1561	95	below_threshold
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	78.8194	471	1561	95	below_threshold
Serratia ureilytica	strain=CCUG:50595	GCA_013375155.1	300181	300181	type	True	78.6176	474	1561	95	below_threshold
Cronobacter sakazakii	strain=ATCC 29544	GCA_001971035.1	28141	28141	type	True	78.604	457	1561	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:59:43,347] [INFO] DFAST Taxonomy check result was written to GCF_019132875.1_ASM1913287v1_genomic.fna/tc_result.tsv
[2024-01-24 11:59:43,348] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:59:43,348] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:59:43,348] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9f7d9977-3f6d-4ac4-8972-bfb7eb64bc3d/dqc_reference/checkm_data
[2024-01-24 11:59:43,349] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:59:43,409] [INFO] Task started: CheckM
[2024-01-24 11:59:43,409] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019132875.1_ASM1913287v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019132875.1_ASM1913287v1_genomic.fna/checkm_input GCF_019132875.1_ASM1913287v1_genomic.fna/checkm_result
[2024-01-24 12:00:22,640] [INFO] Task succeeded: CheckM
[2024-01-24 12:00:22,641] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:00:22,665] [INFO] ===== Completeness check finished =====
[2024-01-24 12:00:22,666] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:00:22,666] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019132875.1_ASM1913287v1_genomic.fna/markers.fasta)
[2024-01-24 12:00:22,666] [INFO] Task started: Blastn
[2024-01-24 12:00:22,667] [INFO] Running command: blastn -query GCF_019132875.1_ASM1913287v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9f7d9977-3f6d-4ac4-8972-bfb7eb64bc3d/dqc_reference/reference_markers_gtdb.fasta -out GCF_019132875.1_ASM1913287v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:00:23,910] [INFO] Task succeeded: Blastn
[2024-01-24 12:00:23,919] [INFO] Selected 14 target genomes.
[2024-01-24 12:00:23,920] [INFO] Target genome list was writen to GCF_019132875.1_ASM1913287v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:00:23,953] [INFO] Task started: fastANI
[2024-01-24 12:00:23,953] [INFO] Running command: fastANI --query /var/lib/cwl/stg9bc70d1f-64a6-48cc-b992-943eb1040d81/GCF_019132875.1_ASM1913287v1_genomic.fna.gz --refList GCF_019132875.1_ASM1913287v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019132875.1_ASM1913287v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:00:36,622] [INFO] Task succeeded: fastANI
[2024-01-24 12:00:36,636] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:00:36,636] [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
GCA_019132875.1	s__Erwinia sp019132875	100.0	1559	1561	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003937915.1	s__Erwinia sp003937915	84.1664	1124	1561	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003512805.1	s__Erwinia sp003512805	83.5364	578	1561	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007981265.1	s__Erwinia sp007981265	82.0004	1000	1561	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009765445.1	s__Erwinia sp009765445	81.4988	870	1561	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001756855.1	s__Erwinia dacicola	81.2374	278	1561	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	98.47	98.24	0.66	0.61	4	-
GCF_000196615.1	s__Erwinia billingiae	81.1017	847	1561	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	97.77	97.43	0.91	0.82	7	-
GCF_000599885.1	s__Erwinia sp000599885	80.7938	767	1561	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014773485.1	s__Erwinia aphidicola	80.5109	792	1561	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	99.08	98.09	0.88	0.85	7	-
GCF_018141005.1	s__Erwinia sp001422605	80.4414	714	1561	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	98.39	98.36	0.92	0.92	3	-
GCF_900068835.1	s__Pantoea ludwigii_B	79.1385	625	1561	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	97.17	96.60	0.91	0.89	10	-
GCF_001187905.1	s__Pantoea sp001187905	78.9915	591	1561	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	98.42	98.35	0.91	0.90	3	-
GCF_001896205.1	s__Edwardsiella piscicida	77.7139	290	1561	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Edwardsiella	95.0	99.37	99.20	0.95	0.93	23	-
GCF_000264785.1	s__Edwardsiella ictaluri	77.607	242	1561	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Edwardsiella	95.0	99.74	99.41	0.96	0.93	11	-
--------------------------------------------------------------------------------
[2024-01-24 12:00:36,638] [INFO] GTDB search result was written to GCF_019132875.1_ASM1913287v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:00:36,638] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:00:36,642] [INFO] DFAST_QC result json was written to GCF_019132875.1_ASM1913287v1_genomic.fna/dqc_result.json
[2024-01-24 12:00:36,642] [INFO] DFAST_QC completed!
[2024-01-24 12:00:36,642] [INFO] Total running time: 0h1m25s