[2024-01-25 19:04:35,749] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:04:35,750] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:04:35,750] [INFO] DQC Reference Directory: /var/lib/cwl/stge0763f4f-7dcc-46f0-9068-6637faad4746/dqc_reference
[2024-01-25 19:04:36,875] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:04:36,876] [INFO] Task started: Prodigal
[2024-01-25 19:04:36,876] [INFO] Running command: gunzip -c /var/lib/cwl/stgf30b9d7a-8898-4837-8cb0-30e3908acf11/GCF_025840185.1_ASM2584018v1_genomic.fna.gz | prodigal -d GCF_025840185.1_ASM2584018v1_genomic.fna/cds.fna -a GCF_025840185.1_ASM2584018v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:04:46,236] [INFO] Task succeeded: Prodigal
[2024-01-25 19:04:46,236] [INFO] Task started: HMMsearch
[2024-01-25 19:04:46,236] [INFO] Running command: hmmsearch --tblout GCF_025840185.1_ASM2584018v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge0763f4f-7dcc-46f0-9068-6637faad4746/dqc_reference/reference_markers.hmm GCF_025840185.1_ASM2584018v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:04:46,469] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:04:46,470] [INFO] Found 6/6 markers.
[2024-01-25 19:04:46,498] [INFO] Query marker FASTA was written to GCF_025840185.1_ASM2584018v1_genomic.fna/markers.fasta
[2024-01-25 19:04:46,498] [INFO] Task started: Blastn
[2024-01-25 19:04:46,498] [INFO] Running command: blastn -query GCF_025840185.1_ASM2584018v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge0763f4f-7dcc-46f0-9068-6637faad4746/dqc_reference/reference_markers.fasta -out GCF_025840185.1_ASM2584018v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:04:47,254] [INFO] Task succeeded: Blastn
[2024-01-25 19:04:47,257] [INFO] Selected 10 target genomes.
[2024-01-25 19:04:47,257] [INFO] Target genome list was writen to GCF_025840185.1_ASM2584018v1_genomic.fna/target_genomes.txt
[2024-01-25 19:04:47,262] [INFO] Task started: fastANI
[2024-01-25 19:04:47,262] [INFO] Running command: fastANI --query /var/lib/cwl/stgf30b9d7a-8898-4837-8cb0-30e3908acf11/GCF_025840185.1_ASM2584018v1_genomic.fna.gz --refList GCF_025840185.1_ASM2584018v1_genomic.fna/target_genomes.txt --output GCF_025840185.1_ASM2584018v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:04:56,969] [INFO] Task succeeded: fastANI
[2024-01-25 19:04:56,969] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge0763f4f-7dcc-46f0-9068-6637faad4746/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:04:56,970] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge0763f4f-7dcc-46f0-9068-6637faad4746/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:04:56,977] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:04:56,977] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:04:56,977] [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
Brenneria salicis	strain=DSM 30166	GCA_003315515.1	55214	55214	type	True	94.4431	1085	1275	95	below_threshold
Brenneria salicis	strain=DSM 30166	GCA_003666165.1	55214	55214	type	True	94.4213	1081	1275	95	below_threshold
Brenneria salicis	strain=ATCC 15712	GCA_012932875.1	55214	55214	type	True	94.3148	1113	1275	95	below_threshold
Brenneria roseae subsp. americana	strain=LMG 27715	GCA_003115815.1	1508507	1509241	type	True	85.7482	977	1275	95	below_threshold
Brenneria roseae subsp. roseae	strain=LMG 27714	GCA_003115845.1	1508506	1509241	type	True	85.5801	992	1275	95	below_threshold
Pectobacterium colocasium	strain=LJ1	GCA_020181655.1	2878098	2878098	type	True	80.6595	711	1275	95	below_threshold
Pectobacterium quasiaquaticum	strain=A477-S1-J17	GCA_014946775.2	2774015	2774015	type	True	80.4728	715	1275	95	below_threshold
Serratia nevei	strain=S15	GCA_008364245.1	2703794	2703794	type	True	78.4674	373	1275	95	below_threshold
Serratia bockelmannii	strain=S3	GCA_008011855.1	2703793	2703793	type	True	78.4011	372	1275	95	below_threshold
Rahnella perminowiae	strain=SL6	GCA_019049755.1	2816244	2816244	type	True	78.3846	284	1275	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:04:56,979] [INFO] DFAST Taxonomy check result was written to GCF_025840185.1_ASM2584018v1_genomic.fna/tc_result.tsv
[2024-01-25 19:04:56,979] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:04:56,979] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:04:56,979] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge0763f4f-7dcc-46f0-9068-6637faad4746/dqc_reference/checkm_data
[2024-01-25 19:04:56,980] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:04:57,020] [INFO] Task started: CheckM
[2024-01-25 19:04:57,020] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025840185.1_ASM2584018v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025840185.1_ASM2584018v1_genomic.fna/checkm_input GCF_025840185.1_ASM2584018v1_genomic.fna/checkm_result
[2024-01-25 19:05:27,654] [INFO] Task succeeded: CheckM
[2024-01-25 19:05:27,655] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:05:27,671] [INFO] ===== Completeness check finished =====
[2024-01-25 19:05:27,671] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:05:27,671] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025840185.1_ASM2584018v1_genomic.fna/markers.fasta)
[2024-01-25 19:05:27,671] [INFO] Task started: Blastn
[2024-01-25 19:05:27,671] [INFO] Running command: blastn -query GCF_025840185.1_ASM2584018v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge0763f4f-7dcc-46f0-9068-6637faad4746/dqc_reference/reference_markers_gtdb.fasta -out GCF_025840185.1_ASM2584018v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:05:28,746] [INFO] Task succeeded: Blastn
[2024-01-25 19:05:28,749] [INFO] Selected 10 target genomes.
[2024-01-25 19:05:28,749] [INFO] Target genome list was writen to GCF_025840185.1_ASM2584018v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:05:28,762] [INFO] Task started: fastANI
[2024-01-25 19:05:28,762] [INFO] Running command: fastANI --query /var/lib/cwl/stgf30b9d7a-8898-4837-8cb0-30e3908acf11/GCF_025840185.1_ASM2584018v1_genomic.fna.gz --refList GCF_025840185.1_ASM2584018v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025840185.1_ASM2584018v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:05:38,603] [INFO] Task succeeded: fastANI
[2024-01-25 19:05:38,609] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 19:05:38,609] [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_003315515.1	s__Brenneria salicis	94.443	1085	1275	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Brenneria	95.0	99.99	99.99	1.00	0.99	3	-
GCF_003115845.1	s__Brenneria roseae	85.5889	991	1275	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Brenneria	95.0	96.57	96.57	0.91	0.91	2	-
GCF_005484945.1	s__Brenneria rubrifaciens	84.3068	931	1275	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Brenneria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013155275.1	s__Brenneria sp013155275	82.2372	878	1275	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Brenneria	95.0	99.39	99.39	0.93	0.93	2	-
GCF_005484965.1	s__Brenneria nigrifluens	81.5867	859	1275	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Brenneria	95.0	98.35	95.07	0.92	0.76	4	-
GCF_003666245.1	s__Brenneria alni	81.5432	792	1275	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Brenneria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002291445.1	s__Brenneria goodwinii	81.3202	784	1275	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Brenneria	95.0	99.30	98.94	0.94	0.91	4	-
GCF_017569925.1	s__Brenneria izadpanahii	81.3193	773	1275	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Brenneria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012427845.1	s__Pectobacterium punjabense	80.7861	701	1275	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	99.35	98.67	0.97	0.93	5	-
--------------------------------------------------------------------------------
[2024-01-25 19:05:38,610] [INFO] GTDB search result was written to GCF_025840185.1_ASM2584018v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:05:38,611] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:05:38,613] [INFO] DFAST_QC result json was written to GCF_025840185.1_ASM2584018v1_genomic.fna/dqc_result.json
[2024-01-25 19:05:38,613] [INFO] DFAST_QC completed!
[2024-01-25 19:05:38,613] [INFO] Total running time: 0h1m3s