[2024-01-24 12:53:37,271] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:53:37,272] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:53:37,272] [INFO] DQC Reference Directory: /var/lib/cwl/stgf9349d4c-7ddd-4175-a33c-66c4e26cc530/dqc_reference
[2024-01-24 12:53:38,479] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:53:38,479] [INFO] Task started: Prodigal
[2024-01-24 12:53:38,480] [INFO] Running command: gunzip -c /var/lib/cwl/stgee5e22fa-1ada-40a4-a385-124f4482f03b/GCF_901472495.1_32868_C01_genomic.fna.gz | prodigal -d GCF_901472495.1_32868_C01_genomic.fna/cds.fna -a GCF_901472495.1_32868_C01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:53:50,502] [INFO] Task succeeded: Prodigal
[2024-01-24 12:53:50,502] [INFO] Task started: HMMsearch
[2024-01-24 12:53:50,502] [INFO] Running command: hmmsearch --tblout GCF_901472495.1_32868_C01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf9349d4c-7ddd-4175-a33c-66c4e26cc530/dqc_reference/reference_markers.hmm GCF_901472495.1_32868_C01_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:53:50,781] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:53:50,782] [INFO] Found 6/6 markers.
[2024-01-24 12:53:50,820] [INFO] Query marker FASTA was written to GCF_901472495.1_32868_C01_genomic.fna/markers.fasta
[2024-01-24 12:53:50,820] [INFO] Task started: Blastn
[2024-01-24 12:53:50,820] [INFO] Running command: blastn -query GCF_901472495.1_32868_C01_genomic.fna/markers.fasta -db /var/lib/cwl/stgf9349d4c-7ddd-4175-a33c-66c4e26cc530/dqc_reference/reference_markers.fasta -out GCF_901472495.1_32868_C01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:53:51,685] [INFO] Task succeeded: Blastn
[2024-01-24 12:53:51,689] [INFO] Selected 12 target genomes.
[2024-01-24 12:53:51,689] [INFO] Target genome list was writen to GCF_901472495.1_32868_C01_genomic.fna/target_genomes.txt
[2024-01-24 12:53:51,696] [INFO] Task started: fastANI
[2024-01-24 12:53:51,696] [INFO] Running command: fastANI --query /var/lib/cwl/stgee5e22fa-1ada-40a4-a385-124f4482f03b/GCF_901472495.1_32868_C01_genomic.fna.gz --refList GCF_901472495.1_32868_C01_genomic.fna/target_genomes.txt --output GCF_901472495.1_32868_C01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:54:06,337] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:06,337] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf9349d4c-7ddd-4175-a33c-66c4e26cc530/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:54:06,338] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf9349d4c-7ddd-4175-a33c-66c4e26cc530/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:54:06,354] [INFO] Found 12 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 12:54:06,354] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:54:06,354] [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
Yersinia enterocolitica subsp. enterocolitica	strain=NCTC12982	GCA_901472495.1	150052	630	type	True	100.0	1519	1519	95	conclusive
Yersinia enterocolitica	strain=ATCC 9610	GCA_000755055.1	630	630	type	True	99.9788	1505	1519	95	conclusive
Yersinia enterocolitica subsp. enterocolitica	strain=NBRC 105693	GCA_001598735.1	150052	630	type	True	99.9577	1461	1519	95	conclusive
Yersinia enterocolitica subsp. palearctica	strain=NCTC13769	GCA_900637005.1	150053	630	type	True	96.9106	1310	1519	95	conclusive
Yersinia enterocolitica subsp. palearctica	strain=Y11	GCA_000253175.1	150053	630	type	True	96.8725	1317	1519	95	conclusive
Yersinia proxima	strain=IP37424	GCA_902170785.1	2890316	2890316	type	True	93.8588	1304	1519	95	below_threshold
Yersinia hibernica	strain=CFS1934	GCA_004124235.1	2339259	2339259	type	True	86.4154	1214	1519	95	below_threshold
Yersinia aldovae	strain=IP06005	GCA_001091225.1	29483	29483	type	True	85.7152	1088	1519	95	below_threshold
Serratia entomophila	strain=A1	GCA_021462285.1	42906	42906	type	True	79.4716	422	1519	95	below_threshold
Serratia nevei	strain=S15	GCA_008364245.1	2703794	2703794	type	True	78.8449	415	1519	95	below_threshold
Serratia bockelmannii	strain=S3	GCA_008011855.1	2703793	2703793	type	True	78.8235	400	1519	95	below_threshold
Photorhabdus temperata	strain=DSM 14550	GCA_025384845.1	574560	574560	type	True	77.8427	203	1519	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:54:06,356] [INFO] DFAST Taxonomy check result was written to GCF_901472495.1_32868_C01_genomic.fna/tc_result.tsv
[2024-01-24 12:54:06,357] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:54:06,357] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:54:06,357] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf9349d4c-7ddd-4175-a33c-66c4e26cc530/dqc_reference/checkm_data
[2024-01-24 12:54:06,359] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:54:06,404] [INFO] Task started: CheckM
[2024-01-24 12:54:06,404] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_901472495.1_32868_C01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_901472495.1_32868_C01_genomic.fna/checkm_input GCF_901472495.1_32868_C01_genomic.fna/checkm_result
[2024-01-24 12:54:45,074] [INFO] Task succeeded: CheckM
[2024-01-24 12:54:45,076] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:54:45,093] [INFO] ===== Completeness check finished =====
[2024-01-24 12:54:45,093] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:54:45,094] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_901472495.1_32868_C01_genomic.fna/markers.fasta)
[2024-01-24 12:54:45,094] [INFO] Task started: Blastn
[2024-01-24 12:54:45,094] [INFO] Running command: blastn -query GCF_901472495.1_32868_C01_genomic.fna/markers.fasta -db /var/lib/cwl/stgf9349d4c-7ddd-4175-a33c-66c4e26cc530/dqc_reference/reference_markers_gtdb.fasta -out GCF_901472495.1_32868_C01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:46,329] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:46,333] [INFO] Selected 11 target genomes.
[2024-01-24 12:54:46,334] [INFO] Target genome list was writen to GCF_901472495.1_32868_C01_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:54:46,349] [INFO] Task started: fastANI
[2024-01-24 12:54:46,349] [INFO] Running command: fastANI --query /var/lib/cwl/stgee5e22fa-1ada-40a4-a385-124f4482f03b/GCF_901472495.1_32868_C01_genomic.fna.gz --refList GCF_901472495.1_32868_C01_genomic.fna/target_genomes_gtdb.txt --output GCF_901472495.1_32868_C01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:54:59,769] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:59,789] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:54:59,790] [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_901472495.1	s__Yersinia enterocolitica	100.0	1519	1519	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	97.11	96.22	0.89	0.83	185	conclusive
GCF_001995075.1	s__Yersinia enterocolitica_F	93.823	1312	1519	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.25	99.14	0.94	0.92	3	-
GCF_902726525.1	s__Yersinia enterocolitica_H	93.7242	1287	1519	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.97	99.97	0.99	0.99	3	-
GCF_001123825.1	s__Yersinia kristensenii_C	88.2557	1168	1519	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.60	99.58	0.95	0.93	4	-
GCF_003600645.1	s__Yersinia rochesterensis	88.2053	1199	1519	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.46	98.81	0.94	0.91	13	-
GCF_900460525.1	s__Yersinia kristensenii	88.19	1229	1519	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	98.20	97.89	0.92	0.89	22	-
GCF_009831415.1	s__Yersinia canariae	87.7532	1256	1519	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	98.93	98.81	0.93	0.92	3	-
GCF_004124235.1	s__Yersinia hibernica	86.4087	1216	1519	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	98.98	98.46	0.91	0.87	4	-
GCF_000173735.1	s__Yersinia aldovae	85.7947	1043	1519	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.00	96.65	0.94	0.91	11	-
GCF_001098625.1	s__Yersinia frederiksenii_C	85.6937	1191	1519	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	98.63	97.69	0.93	0.89	21	-
GCF_001152565.1	s__Yersinia pekkanenii	84.7158	1056	1519	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.90	99.90	0.98	0.98	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:54:59,791] [INFO] GTDB search result was written to GCF_901472495.1_32868_C01_genomic.fna/result_gtdb.tsv
[2024-01-24 12:54:59,793] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:54:59,798] [INFO] DFAST_QC result json was written to GCF_901472495.1_32868_C01_genomic.fna/dqc_result.json
[2024-01-24 12:54:59,799] [INFO] DFAST_QC completed!
[2024-01-24 12:54:59,799] [INFO] Total running time: 0h1m23s