[2024-01-24 13:13:34,118] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:13:34,119] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:13:34,119] [INFO] DQC Reference Directory: /var/lib/cwl/stg3094fae6-af24-4cb2-a605-adb157fcec77/dqc_reference
[2024-01-24 13:13:35,332] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:13:35,333] [INFO] Task started: Prodigal
[2024-01-24 13:13:35,333] [INFO] Running command: gunzip -c /var/lib/cwl/stg1899a99c-9667-4892-81a0-81f88fb64875/GCF_902170565.1_IP34646_genomic.fna.gz | prodigal -d GCF_902170565.1_IP34646_genomic.fna/cds.fna -a GCF_902170565.1_IP34646_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:46,486] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:46,487] [INFO] Task started: HMMsearch
[2024-01-24 13:13:46,487] [INFO] Running command: hmmsearch --tblout GCF_902170565.1_IP34646_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3094fae6-af24-4cb2-a605-adb157fcec77/dqc_reference/reference_markers.hmm GCF_902170565.1_IP34646_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:46,752] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:46,754] [INFO] Found 6/6 markers.
[2024-01-24 13:13:46,796] [INFO] Query marker FASTA was written to GCF_902170565.1_IP34646_genomic.fna/markers.fasta
[2024-01-24 13:13:46,796] [INFO] Task started: Blastn
[2024-01-24 13:13:46,796] [INFO] Running command: blastn -query GCF_902170565.1_IP34646_genomic.fna/markers.fasta -db /var/lib/cwl/stg3094fae6-af24-4cb2-a605-adb157fcec77/dqc_reference/reference_markers.fasta -out GCF_902170565.1_IP34646_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:47,662] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:47,665] [INFO] Selected 16 target genomes.
[2024-01-24 13:13:47,665] [INFO] Target genome list was writen to GCF_902170565.1_IP34646_genomic.fna/target_genomes.txt
[2024-01-24 13:13:47,677] [INFO] Task started: fastANI
[2024-01-24 13:13:47,677] [INFO] Running command: fastANI --query /var/lib/cwl/stg1899a99c-9667-4892-81a0-81f88fb64875/GCF_902170565.1_IP34646_genomic.fna.gz --refList GCF_902170565.1_IP34646_genomic.fna/target_genomes.txt --output GCF_902170565.1_IP34646_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:14:04,340] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:04,340] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3094fae6-af24-4cb2-a605-adb157fcec77/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:14:04,340] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3094fae6-af24-4cb2-a605-adb157fcec77/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:14:04,354] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:14:04,355] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:14:04,355] [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 thracica	strain=IP34646	GCA_902170565.1	2890319	2890319	type	True	100.0	1374	1377	95	conclusive
Yersinia rochesterensis	strain=ATCC BAA-2637	GCA_003600645.1	1604335	1604335	type	True	94.9926	1212	1377	95	below_threshold
Yersinia kristensenii	strain=NCTC11471	GCA_900460525.1	28152	28152	type	True	93.2109	1222	1377	95	below_threshold
Yersinia kristensenii	strain=ATCC 33638	GCA_000173715.1	28152	28152	type	True	93.176	1189	1377	95	below_threshold
Yersinia enterocolitica	strain=ATCC 9610	GCA_000755055.1	630	630	type	True	88.3407	1135	1377	95	below_threshold
Yersinia enterocolitica subsp. enterocolitica	strain=NBRC 105693	GCA_001598735.1	150052	630	type	True	88.3304	1134	1377	95	below_threshold
Yersinia enterocolitica subsp. enterocolitica	strain=NCTC12982	GCA_901472495.1	150052	630	type	True	88.3232	1149	1377	95	below_threshold
Yersinia artesiana	strain=IP42281	GCA_902726545.1	2890315	2890315	type	True	88.2438	1113	1377	95	below_threshold
Yersinia enterocolitica subsp. palearctica	strain=Y11	GCA_000253175.1	150053	630	type	True	88.1445	1171	1377	95	below_threshold
Yersinia canariae	strain=NCTC 14382	GCA_009831415.1	2607663	2607663	type	True	87.8614	1151	1377	95	below_threshold
Yersinia hibernica	strain=CFS1934	GCA_004124235.1	2339259	2339259	type	True	86.9111	1139	1377	95	below_threshold
Yersinia aldovae	strain=IP06005	GCA_001091225.1	29483	29483	type	True	84.689	963	1377	95	below_threshold
Serratia nevei	strain=S15	GCA_008364245.1	2703794	2703794	type	True	79.044	407	1377	95	below_threshold
Serratia bockelmannii	strain=S3	GCA_008011855.1	2703793	2703793	type	True	79.0049	389	1377	95	below_threshold
Rahnella ecdela	strain=FRB 231	GCA_019049625.1	2816250	2816250	type	True	78.8438	355	1377	95	below_threshold
Pectobacterium colocasium	strain=LJ1	GCA_020181655.1	2878098	2878098	type	True	78.2443	301	1377	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:14:04,357] [INFO] DFAST Taxonomy check result was written to GCF_902170565.1_IP34646_genomic.fna/tc_result.tsv
[2024-01-24 13:14:04,357] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:14:04,357] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:14:04,358] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3094fae6-af24-4cb2-a605-adb157fcec77/dqc_reference/checkm_data
[2024-01-24 13:14:04,359] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:14:04,402] [INFO] Task started: CheckM
[2024-01-24 13:14:04,403] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_902170565.1_IP34646_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_902170565.1_IP34646_genomic.fna/checkm_input GCF_902170565.1_IP34646_genomic.fna/checkm_result
[2024-01-24 13:14:41,836] [INFO] Task succeeded: CheckM
[2024-01-24 13:14:41,838] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:14:41,857] [INFO] ===== Completeness check finished =====
[2024-01-24 13:14:41,857] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:14:41,857] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_902170565.1_IP34646_genomic.fna/markers.fasta)
[2024-01-24 13:14:41,858] [INFO] Task started: Blastn
[2024-01-24 13:14:41,858] [INFO] Running command: blastn -query GCF_902170565.1_IP34646_genomic.fna/markers.fasta -db /var/lib/cwl/stg3094fae6-af24-4cb2-a605-adb157fcec77/dqc_reference/reference_markers_gtdb.fasta -out GCF_902170565.1_IP34646_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:14:43,080] [INFO] Task succeeded: Blastn
[2024-01-24 13:14:43,084] [INFO] Selected 10 target genomes.
[2024-01-24 13:14:43,084] [INFO] Target genome list was writen to GCF_902170565.1_IP34646_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:14:43,090] [INFO] Task started: fastANI
[2024-01-24 13:14:43,091] [INFO] Running command: fastANI --query /var/lib/cwl/stg1899a99c-9667-4892-81a0-81f88fb64875/GCF_902170565.1_IP34646_genomic.fna.gz --refList GCF_902170565.1_IP34646_genomic.fna/target_genomes_gtdb.txt --output GCF_902170565.1_IP34646_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:14:54,346] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:54,354] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:14:54,355] [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_001123825.1	s__Yersinia kristensenii_C	99.5821	1315	1377	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.60	99.58	0.95	0.93	4	conclusive
GCF_003600645.1	s__Yersinia rochesterensis	94.9926	1212	1377	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	93.2109	1222	1377	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	98.20	97.89	0.92	0.89	22	-
GCF_901472495.1	s__Yersinia enterocolitica	88.3232	1149	1377	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	97.11	96.22	0.89	0.83	185	-
GCF_902726525.1	s__Yersinia enterocolitica_H	88.2483	1136	1377	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.97	99.97	0.99	0.99	3	-
GCF_001995075.1	s__Yersinia enterocolitica_F	88.0925	1123	1377	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.25	99.14	0.94	0.92	3	-
GCF_009831415.1	s__Yersinia canariae	87.8614	1151	1377	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	86.9021	1140	1377	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	98.98	98.46	0.91	0.87	4	-
GCF_001152565.1	s__Yersinia pekkanenii	85.0929	1044	1377	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.90	99.90	0.98	0.98	2	-
GCF_001047675.1	s__Yersinia aleksiciae	85.0096	977	1377	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.22	98.37	0.87	0.82	10	-
--------------------------------------------------------------------------------
[2024-01-24 13:14:54,356] [INFO] GTDB search result was written to GCF_902170565.1_IP34646_genomic.fna/result_gtdb.tsv
[2024-01-24 13:14:54,357] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:14:54,360] [INFO] DFAST_QC result json was written to GCF_902170565.1_IP34646_genomic.fna/dqc_result.json
[2024-01-24 13:14:54,360] [INFO] DFAST_QC completed!
[2024-01-24 13:14:54,361] [INFO] Total running time: 0h1m20s