[2024-01-24 12:44:52,321] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:44:52,323] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:44:52,323] [INFO] DQC Reference Directory: /var/lib/cwl/stg29689ade-7853-48e4-a92f-59522cb42ab1/dqc_reference
[2024-01-24 12:44:53,604] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:44:53,605] [INFO] Task started: Prodigal
[2024-01-24 12:44:53,605] [INFO] Running command: gunzip -c /var/lib/cwl/stgc87b19ea-9367-4702-b1b0-a17dd84be329/GCF_003115845.1_ASM311584v1_genomic.fna.gz | prodigal -d GCF_003115845.1_ASM311584v1_genomic.fna/cds.fna -a GCF_003115845.1_ASM311584v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:45:05,453] [INFO] Task succeeded: Prodigal
[2024-01-24 12:45:05,454] [INFO] Task started: HMMsearch
[2024-01-24 12:45:05,454] [INFO] Running command: hmmsearch --tblout GCF_003115845.1_ASM311584v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg29689ade-7853-48e4-a92f-59522cb42ab1/dqc_reference/reference_markers.hmm GCF_003115845.1_ASM311584v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:45:05,724] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:45:05,726] [INFO] Found 6/6 markers.
[2024-01-24 12:45:05,768] [INFO] Query marker FASTA was written to GCF_003115845.1_ASM311584v1_genomic.fna/markers.fasta
[2024-01-24 12:45:05,768] [INFO] Task started: Blastn
[2024-01-24 12:45:05,768] [INFO] Running command: blastn -query GCF_003115845.1_ASM311584v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg29689ade-7853-48e4-a92f-59522cb42ab1/dqc_reference/reference_markers.fasta -out GCF_003115845.1_ASM311584v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:06,658] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:06,662] [INFO] Selected 13 target genomes.
[2024-01-24 12:45:06,662] [INFO] Target genome list was writen to GCF_003115845.1_ASM311584v1_genomic.fna/target_genomes.txt
[2024-01-24 12:45:06,667] [INFO] Task started: fastANI
[2024-01-24 12:45:06,667] [INFO] Running command: fastANI --query /var/lib/cwl/stgc87b19ea-9367-4702-b1b0-a17dd84be329/GCF_003115845.1_ASM311584v1_genomic.fna.gz --refList GCF_003115845.1_ASM311584v1_genomic.fna/target_genomes.txt --output GCF_003115845.1_ASM311584v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:45:18,853] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:18,853] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg29689ade-7853-48e4-a92f-59522cb42ab1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:45:18,854] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg29689ade-7853-48e4-a92f-59522cb42ab1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:45:18,865] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:45:18,865] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:45:18,865] [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 roseae subsp. roseae	strain=LMG 27714	GCA_003115845.1	1508506	1509241	type	True	100.0	1479	1481	95	conclusive
Brenneria roseae subsp. americana	strain=LMG 27715	GCA_003115815.1	1508507	1509241	type	True	96.5707	1335	1481	95	conclusive
Brenneria salicis	strain=DSM 30166	GCA_003315515.1	55214	55214	type	True	85.6169	952	1481	95	below_threshold
Brenneria salicis	strain=DSM 30166	GCA_003666165.1	55214	55214	type	True	85.5897	957	1481	95	below_threshold
Brenneria salicis	strain=ATCC 15712	GCA_012932875.1	55214	55214	type	True	85.562	974	1481	95	below_threshold
Brenneria goodwinii	strain=FRB141	GCA_002291445.1	1109412	1109412	type	True	82.6609	934	1481	95	below_threshold
Brenneria goodwinii	strain=FRB141	GCA_003666235.1	1109412	1109412	type	True	82.6268	909	1481	95	below_threshold
Brenneria alni	strain=NCPPB 3934	GCA_003666245.1	71656	71656	type	True	82.2238	823	1481	95	below_threshold
Pectobacterium quasiaquaticum	strain=A477-S1-J17	GCA_014946775.2	2774015	2774015	type	True	80.9942	775	1481	95	below_threshold
Pectobacterium colocasium	strain=LJ1	GCA_020181655.1	2878098	2878098	type	True	80.9728	788	1481	95	below_threshold
Serratia entomophila	strain=A1	GCA_021462285.1	42906	42906	type	True	78.5793	380	1481	95	below_threshold
Serratia nevei	strain=S15	GCA_008364245.1	2703794	2703794	type	True	78.5553	380	1481	95	below_threshold
Serratia bockelmannii	strain=S3	GCA_008011855.1	2703793	2703793	type	True	78.4854	381	1481	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:45:18,867] [INFO] DFAST Taxonomy check result was written to GCF_003115845.1_ASM311584v1_genomic.fna/tc_result.tsv
[2024-01-24 12:45:18,868] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:45:18,868] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:45:18,869] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg29689ade-7853-48e4-a92f-59522cb42ab1/dqc_reference/checkm_data
[2024-01-24 12:45:18,870] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:45:18,914] [INFO] Task started: CheckM
[2024-01-24 12:45:18,915] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003115845.1_ASM311584v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003115845.1_ASM311584v1_genomic.fna/checkm_input GCF_003115845.1_ASM311584v1_genomic.fna/checkm_result
[2024-01-24 12:45:58,112] [INFO] Task succeeded: CheckM
[2024-01-24 12:45:58,114] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:45:58,152] [INFO] ===== Completeness check finished =====
[2024-01-24 12:45:58,153] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:45:58,153] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003115845.1_ASM311584v1_genomic.fna/markers.fasta)
[2024-01-24 12:45:58,154] [INFO] Task started: Blastn
[2024-01-24 12:45:58,154] [INFO] Running command: blastn -query GCF_003115845.1_ASM311584v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg29689ade-7853-48e4-a92f-59522cb42ab1/dqc_reference/reference_markers_gtdb.fasta -out GCF_003115845.1_ASM311584v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:59,513] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:59,517] [INFO] Selected 8 target genomes.
[2024-01-24 12:45:59,517] [INFO] Target genome list was writen to GCF_003115845.1_ASM311584v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:45:59,532] [INFO] Task started: fastANI
[2024-01-24 12:45:59,532] [INFO] Running command: fastANI --query /var/lib/cwl/stgc87b19ea-9367-4702-b1b0-a17dd84be329/GCF_003115845.1_ASM311584v1_genomic.fna.gz --refList GCF_003115845.1_ASM311584v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003115845.1_ASM311584v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:46:08,270] [INFO] Task succeeded: fastANI
[2024-01-24 12:46:08,283] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:46:08,283] [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_003115845.1	s__Brenneria roseae	100.0	1479	1481	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Brenneria	95.0	96.57	96.57	0.91	0.91	2	conclusive
GCF_005484945.1	s__Brenneria rubrifaciens	85.9008	952	1481	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Brenneria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003315515.1	s__Brenneria salicis	85.6287	951	1481	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Brenneria	95.0	99.99	99.99	1.00	0.99	3	-
GCF_013155275.1	s__Brenneria sp013155275	82.9481	933	1481	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Brenneria	95.0	99.39	99.39	0.93	0.93	2	-
GCF_002291445.1	s__Brenneria goodwinii	82.6592	933	1481	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Brenneria	95.0	99.30	98.94	0.94	0.91	4	-
GCF_003666245.1	s__Brenneria alni	82.2173	824	1481	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Brenneria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005484965.1	s__Brenneria nigrifluens	81.8505	910	1481	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Brenneria	95.0	98.35	95.07	0.92	0.76	4	-
GCF_017569925.1	s__Brenneria izadpanahii	81.8169	919	1481	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Brenneria	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:46:08,285] [INFO] GTDB search result was written to GCF_003115845.1_ASM311584v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:46:08,285] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:46:08,288] [INFO] DFAST_QC result json was written to GCF_003115845.1_ASM311584v1_genomic.fna/dqc_result.json
[2024-01-24 12:46:08,289] [INFO] DFAST_QC completed!
[2024-01-24 12:46:08,289] [INFO] Total running time: 0h1m16s