[2024-01-24 13:31:44,450] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:44,453] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:44,453] [INFO] DQC Reference Directory: /var/lib/cwl/stgcf871f1d-24c0-4279-a9fc-32c049a6af8a/dqc_reference
[2024-01-24 13:31:45,714] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:45,715] [INFO] Task started: Prodigal
[2024-01-24 13:31:45,715] [INFO] Running command: gunzip -c /var/lib/cwl/stgd50f9225-2156-470f-80b0-3ef71b39cc67/GCF_004959795.1_ASM495979v1_genomic.fna.gz | prodigal -d GCF_004959795.1_ASM495979v1_genomic.fna/cds.fna -a GCF_004959795.1_ASM495979v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:31:54,568] [INFO] Task succeeded: Prodigal
[2024-01-24 13:31:54,568] [INFO] Task started: HMMsearch
[2024-01-24 13:31:54,569] [INFO] Running command: hmmsearch --tblout GCF_004959795.1_ASM495979v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcf871f1d-24c0-4279-a9fc-32c049a6af8a/dqc_reference/reference_markers.hmm GCF_004959795.1_ASM495979v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:31:54,909] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:31:54,910] [INFO] Found 6/6 markers.
[2024-01-24 13:31:54,946] [INFO] Query marker FASTA was written to GCF_004959795.1_ASM495979v1_genomic.fna/markers.fasta
[2024-01-24 13:31:54,947] [INFO] Task started: Blastn
[2024-01-24 13:31:54,947] [INFO] Running command: blastn -query GCF_004959795.1_ASM495979v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcf871f1d-24c0-4279-a9fc-32c049a6af8a/dqc_reference/reference_markers.fasta -out GCF_004959795.1_ASM495979v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:31:55,802] [INFO] Task succeeded: Blastn
[2024-01-24 13:31:55,807] [INFO] Selected 12 target genomes.
[2024-01-24 13:31:55,807] [INFO] Target genome list was writen to GCF_004959795.1_ASM495979v1_genomic.fna/target_genomes.txt
[2024-01-24 13:31:55,812] [INFO] Task started: fastANI
[2024-01-24 13:31:55,813] [INFO] Running command: fastANI --query /var/lib/cwl/stgd50f9225-2156-470f-80b0-3ef71b39cc67/GCF_004959795.1_ASM495979v1_genomic.fna.gz --refList GCF_004959795.1_ASM495979v1_genomic.fna/target_genomes.txt --output GCF_004959795.1_ASM495979v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:06,618] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:06,619] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcf871f1d-24c0-4279-a9fc-32c049a6af8a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:06,619] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcf871f1d-24c0-4279-a9fc-32c049a6af8a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:06,633] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:32:06,633] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:32:06,633] [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
Pragia fontium	strain=DSM 5563	GCA_004959795.1	82985	82985	type	True	100.0	1308	1310	95	conclusive
Pragia fontium	strain=DSM 5563	GCA_900112475.1	82985	82985	type	True	99.9702	1296	1310	95	conclusive
Jinshanibacter allomyrinae	strain=BWR-B9	GCA_016649425.1	2791986	2791986	type	True	80.5984	608	1310	95	below_threshold
Jinshanibacter zhutongyuii	strain=CF-458	GCA_004295645.1	2498113	2498113	type	True	80.4786	624	1310	95	below_threshold
Budvicia aquatica	strain=DSM 5075	GCA_000427805.1	82979	82979	type	True	79.5368	543	1310	95	below_threshold
Budvicia aquatica	strain=NCTC12282	GCA_900706715.1	82979	82979	type	True	79.4669	551	1310	95	below_threshold
Budvicia diplopodorum	strain=D9	GCA_009800925.1	1119056	1119056	type	True	79.34	464	1310	95	below_threshold
Leminorella grimontii	strain=JCM 5902	GCA_024343555.1	82981	82981	type	True	78.314	331	1310	95	below_threshold
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	77.8176	115	1310	95	below_threshold
Citrobacter rodentium	strain=DSM 16636	GCA_021278985.1	67825	67825	type	True	77.6613	147	1310	95	below_threshold
Salmonella enterica subsp. enterica	strain=PartC-Senterica-RM8376	GCA_022869965.1	59201	28901	suspected-type	True	77.5445	154	1310	95	below_threshold
Enterobacter sichuanensis	strain=WCHECL1597	GCA_025002605.1	2071710	2071710	type	True	77.5195	126	1310	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:06,635] [INFO] DFAST Taxonomy check result was written to GCF_004959795.1_ASM495979v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:06,635] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:06,636] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:06,636] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcf871f1d-24c0-4279-a9fc-32c049a6af8a/dqc_reference/checkm_data
[2024-01-24 13:32:06,637] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:06,677] [INFO] Task started: CheckM
[2024-01-24 13:32:06,677] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004959795.1_ASM495979v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004959795.1_ASM495979v1_genomic.fna/checkm_input GCF_004959795.1_ASM495979v1_genomic.fna/checkm_result
[2024-01-24 13:32:38,979] [INFO] Task succeeded: CheckM
[2024-01-24 13:32:38,980] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:32:39,002] [INFO] ===== Completeness check finished =====
[2024-01-24 13:32:39,002] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:32:39,003] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004959795.1_ASM495979v1_genomic.fna/markers.fasta)
[2024-01-24 13:32:39,003] [INFO] Task started: Blastn
[2024-01-24 13:32:39,003] [INFO] Running command: blastn -query GCF_004959795.1_ASM495979v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcf871f1d-24c0-4279-a9fc-32c049a6af8a/dqc_reference/reference_markers_gtdb.fasta -out GCF_004959795.1_ASM495979v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:40,377] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:40,381] [INFO] Selected 7 target genomes.
[2024-01-24 13:32:40,381] [INFO] Target genome list was writen to GCF_004959795.1_ASM495979v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:32:40,389] [INFO] Task started: fastANI
[2024-01-24 13:32:40,389] [INFO] Running command: fastANI --query /var/lib/cwl/stgd50f9225-2156-470f-80b0-3ef71b39cc67/GCF_004959795.1_ASM495979v1_genomic.fna.gz --refList GCF_004959795.1_ASM495979v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004959795.1_ASM495979v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:32:46,637] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:46,649] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:32:46,650] [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_900112475.1	s__Pragia fontium	99.9702	1296	1310	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pragia	95.0	99.20	98.63	0.97	0.95	5	conclusive
GCA_016649425.1	s__Limnobaculum allomyrinae	80.5925	609	1310	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Limnobaculum	95.0	99.99	99.99	0.99	0.99	2	-
GCF_013394855.1	s__Limnobaculum xujianqingii	80.5821	617	1310	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Limnobaculum	95.0	98.42	97.65	0.92	0.89	4	-
GCF_003096015.2	s__Limnobaculum parvum	80.5548	525	1310	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Limnobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004295645.1	s__Limnobaculum zhutongyuii	80.489	622	1310	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Limnobaculum	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000427805.1	s__Budvicia aquatica	79.5368	543	1310	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Budvicia	95.0	99.94	99.91	1.00	1.00	3	-
GCF_009800925.1	s__Budvicia diplopodorum	79.3297	466	1310	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Budvicia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:32:46,652] [INFO] GTDB search result was written to GCF_004959795.1_ASM495979v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:32:46,652] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:32:46,655] [INFO] DFAST_QC result json was written to GCF_004959795.1_ASM495979v1_genomic.fna/dqc_result.json
[2024-01-24 13:32:46,656] [INFO] DFAST_QC completed!
[2024-01-24 13:32:46,656] [INFO] Total running time: 0h1m2s