[2024-01-25 20:14:05,816] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:14:05,820] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:14:05,820] [INFO] DQC Reference Directory: /var/lib/cwl/stg9deeefd4-84e6-42c6-86b4-ce0cd7da27d5/dqc_reference
[2024-01-25 20:14:07,016] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:14:07,023] [INFO] Task started: Prodigal
[2024-01-25 20:14:07,023] [INFO] Running command: gunzip -c /var/lib/cwl/stg2b707524-85eb-4ea0-9767-12a624055f5f/GCF_002953215.1_ASM295321v1_genomic.fna.gz | prodigal -d GCF_002953215.1_ASM295321v1_genomic.fna/cds.fna -a GCF_002953215.1_ASM295321v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:14:17,144] [INFO] Task succeeded: Prodigal
[2024-01-25 20:14:17,144] [INFO] Task started: HMMsearch
[2024-01-25 20:14:17,144] [INFO] Running command: hmmsearch --tblout GCF_002953215.1_ASM295321v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9deeefd4-84e6-42c6-86b4-ce0cd7da27d5/dqc_reference/reference_markers.hmm GCF_002953215.1_ASM295321v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:14:17,403] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:14:17,404] [INFO] Found 6/6 markers.
[2024-01-25 20:14:17,438] [INFO] Query marker FASTA was written to GCF_002953215.1_ASM295321v1_genomic.fna/markers.fasta
[2024-01-25 20:14:17,439] [INFO] Task started: Blastn
[2024-01-25 20:14:17,439] [INFO] Running command: blastn -query GCF_002953215.1_ASM295321v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9deeefd4-84e6-42c6-86b4-ce0cd7da27d5/dqc_reference/reference_markers.fasta -out GCF_002953215.1_ASM295321v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:14:18,273] [INFO] Task succeeded: Blastn
[2024-01-25 20:14:18,276] [INFO] Selected 14 target genomes.
[2024-01-25 20:14:18,276] [INFO] Target genome list was writen to GCF_002953215.1_ASM295321v1_genomic.fna/target_genomes.txt
[2024-01-25 20:14:18,281] [INFO] Task started: fastANI
[2024-01-25 20:14:18,281] [INFO] Running command: fastANI --query /var/lib/cwl/stg2b707524-85eb-4ea0-9767-12a624055f5f/GCF_002953215.1_ASM295321v1_genomic.fna.gz --refList GCF_002953215.1_ASM295321v1_genomic.fna/target_genomes.txt --output GCF_002953215.1_ASM295321v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:14:32,719] [INFO] Task succeeded: fastANI
[2024-01-25 20:14:32,720] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9deeefd4-84e6-42c6-86b4-ce0cd7da27d5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:14:32,720] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9deeefd4-84e6-42c6-86b4-ce0cd7da27d5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:14:32,729] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 20:14:32,729] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:14:32,729] [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	100.0	1435	1436	95	conclusive
Mixta calida	strain=LMG 25383	GCA_002095355.1	665913	665913	type	True	99.8467	1267	1436	95	conclusive
Mixta gaviniae	strain=DSM 22758	GCA_002953195.1	665914	665914	type	True	90.6728	1243	1436	95	below_threshold
Mixta tenebrionis	strain=BIT-26	GCA_006517625.1	2562439	2562439	type	True	85.711	1080	1436	95	below_threshold
Pantoea latae	strain=AS1	GCA_002077695.1	1964541	1964541	type	True	81.8065	902	1436	95	below_threshold
Pantoea septica	strain=LMG 5345	GCA_002095575.1	472695	472695	type	True	81.6495	846	1436	95	below_threshold
Pantoea deleyi	strain=LMG24200	GCA_022647325.1	470932	470932	type	True	80.3348	796	1436	95	below_threshold
Erwinia aphidicola	strain=X001	GCA_024169515.1	68334	68334	type	True	80.2843	774	1436	95	below_threshold
Erwinia iniecta	strain=B120	GCA_001267535.1	1560201	1560201	type	True	80.1437	755	1436	95	below_threshold
Serratia rhizosphaerae	strain=KUDC3025	GCA_009817885.1	2597702	2597702	type	True	80.0391	681	1436	95	below_threshold
Erwinia phyllosphaerae	strain=CMYE1	GCA_019132875.1	2853256	2853256	type	True	79.9532	674	1436	95	below_threshold
Serratia nevei	strain=S15	GCA_008364245.1	2703794	2703794	type	True	79.6563	683	1436	95	below_threshold
Cronobacter sakazakii	strain=ATCC 29544	GCA_001971035.1	28141	28141	type	True	79.375	621	1436	95	below_threshold
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	78.9273	581	1436	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:14:32,731] [INFO] DFAST Taxonomy check result was written to GCF_002953215.1_ASM295321v1_genomic.fna/tc_result.tsv
[2024-01-25 20:14:32,732] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:14:32,732] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:14:32,732] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9deeefd4-84e6-42c6-86b4-ce0cd7da27d5/dqc_reference/checkm_data
[2024-01-25 20:14:32,733] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:14:32,776] [INFO] Task started: CheckM
[2024-01-25 20:14:32,776] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002953215.1_ASM295321v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002953215.1_ASM295321v1_genomic.fna/checkm_input GCF_002953215.1_ASM295321v1_genomic.fna/checkm_result
[2024-01-25 20:15:05,318] [INFO] Task succeeded: CheckM
[2024-01-25 20:15:05,319] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:15:05,337] [INFO] ===== Completeness check finished =====
[2024-01-25 20:15:05,337] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:15:05,337] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002953215.1_ASM295321v1_genomic.fna/markers.fasta)
[2024-01-25 20:15:05,337] [INFO] Task started: Blastn
[2024-01-25 20:15:05,337] [INFO] Running command: blastn -query GCF_002953215.1_ASM295321v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9deeefd4-84e6-42c6-86b4-ce0cd7da27d5/dqc_reference/reference_markers_gtdb.fasta -out GCF_002953215.1_ASM295321v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:15:06,525] [INFO] Task succeeded: Blastn
[2024-01-25 20:15:06,528] [INFO] Selected 6 target genomes.
[2024-01-25 20:15:06,528] [INFO] Target genome list was writen to GCF_002953215.1_ASM295321v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:15:06,531] [INFO] Task started: fastANI
[2024-01-25 20:15:06,532] [INFO] Running command: fastANI --query /var/lib/cwl/stg2b707524-85eb-4ea0-9767-12a624055f5f/GCF_002953215.1_ASM295321v1_genomic.fna.gz --refList GCF_002953215.1_ASM295321v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002953215.1_ASM295321v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:15:13,697] [INFO] Task succeeded: fastANI
[2024-01-25 20:15:13,703] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:15:13,703] [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_002953215.1	s__Mixta calida	100.0	1435	1436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Mixta	95.0	99.65	99.42	0.96	0.92	22	conclusive
GCF_002953195.1	s__Mixta gaviniae	90.6659	1239	1436	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	85.711	1080	1436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Mixta	95.0	99.45	99.45	0.92	0.92	2	-
GCF_002895925.1	s__Mixta theicola	84.8259	1090	1436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Mixta	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009914055.1	s__Mixta intestinalis	84.6856	1063	1436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Mixta	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002101395.1	s__Mixta alhagi	84.4352	1112	1436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Mixta	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:15:13,704] [INFO] GTDB search result was written to GCF_002953215.1_ASM295321v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:15:13,705] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:15:13,707] [INFO] DFAST_QC result json was written to GCF_002953215.1_ASM295321v1_genomic.fna/dqc_result.json
[2024-01-25 20:15:13,708] [INFO] DFAST_QC completed!
[2024-01-25 20:15:13,708] [INFO] Total running time: 0h1m8s