[2024-01-24 13:54:04,189] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:54:04,191] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:54:04,191] [INFO] DQC Reference Directory: /var/lib/cwl/stg3c7839b7-ade6-4749-ab1f-3f2c7fb94721/dqc_reference
[2024-01-24 13:54:05,590] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:54:05,590] [INFO] Task started: Prodigal
[2024-01-24 13:54:05,591] [INFO] Running command: gunzip -c /var/lib/cwl/stge980bb44-51ae-4c91-a4ce-228e0523fe81/GCF_000173735.1_ASM17373v1_genomic.fna.gz | prodigal -d GCF_000173735.1_ASM17373v1_genomic.fna/cds.fna -a GCF_000173735.1_ASM17373v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:54:17,125] [INFO] Task succeeded: Prodigal
[2024-01-24 13:54:17,126] [INFO] Task started: HMMsearch
[2024-01-24 13:54:17,126] [INFO] Running command: hmmsearch --tblout GCF_000173735.1_ASM17373v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3c7839b7-ade6-4749-ab1f-3f2c7fb94721/dqc_reference/reference_markers.hmm GCF_000173735.1_ASM17373v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:54:17,456] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:54:17,458] [INFO] Found 6/6 markers.
[2024-01-24 13:54:17,517] [INFO] Query marker FASTA was written to GCF_000173735.1_ASM17373v1_genomic.fna/markers.fasta
[2024-01-24 13:54:17,517] [INFO] Task started: Blastn
[2024-01-24 13:54:17,517] [INFO] Running command: blastn -query GCF_000173735.1_ASM17373v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3c7839b7-ade6-4749-ab1f-3f2c7fb94721/dqc_reference/reference_markers.fasta -out GCF_000173735.1_ASM17373v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:54:18,469] [INFO] Task succeeded: Blastn
[2024-01-24 13:54:18,472] [INFO] Selected 16 target genomes.
[2024-01-24 13:54:18,472] [INFO] Target genome list was writen to GCF_000173735.1_ASM17373v1_genomic.fna/target_genomes.txt
[2024-01-24 13:54:18,484] [INFO] Task started: fastANI
[2024-01-24 13:54:18,484] [INFO] Running command: fastANI --query /var/lib/cwl/stge980bb44-51ae-4c91-a4ce-228e0523fe81/GCF_000173735.1_ASM17373v1_genomic.fna.gz --refList GCF_000173735.1_ASM17373v1_genomic.fna/target_genomes.txt --output GCF_000173735.1_ASM17373v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:54:35,019] [INFO] Task succeeded: fastANI
[2024-01-24 13:54:35,019] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3c7839b7-ade6-4749-ab1f-3f2c7fb94721/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:54:35,019] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3c7839b7-ade6-4749-ab1f-3f2c7fb94721/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:54:35,038] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:54:35,038] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:54:35,039] [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 aldovae	strain=ATCC 35236	GCA_000173735.1	29483	29483	type	True	100.0	1366	1374	95	conclusive
Yersinia aldovae	strain=IP06005	GCA_001091225.1	29483	29483	type	True	99.971	1367	1374	95	conclusive
Yersinia proxima	strain=IP37424	GCA_902170785.1	2890316	2890316	type	True	85.7628	1035	1374	95	below_threshold
Yersinia enterocolitica	strain=ATCC 9610	GCA_000755055.1	630	630	type	True	85.7203	1058	1374	95	below_threshold
Yersinia enterocolitica subsp. enterocolitica	strain=NBRC 105693	GCA_001598735.1	150052	630	type	True	85.6787	1043	1374	95	below_threshold
Yersinia enterocolitica subsp. enterocolitica	strain=NCTC12982	GCA_901472495.1	150052	630	type	True	85.6777	1056	1374	95	below_threshold
Yersinia thracica	strain=IP34646	GCA_902170565.1	2890319	2890319	type	True	84.685	958	1374	95	below_threshold
Yersinia rochesterensis	strain=ATCC BAA-2637	GCA_003600645.1	1604335	1604335	type	True	84.5358	981	1374	95	below_threshold
Yersinia kristensenii	strain=NCTC11471	GCA_900460525.1	28152	28152	type	True	84.3829	995	1374	95	below_threshold
Yersinia kristensenii	strain=ATCC 33638	GCA_000173715.1	28152	28152	type	True	84.3421	976	1374	95	below_threshold
Yersinia frederiksenii	strain=NCTC11470	GCA_900460425.1	29484	29484	suspected-type	True	83.848	998	1374	95	below_threshold
Yersinia frederiksenii	strain=ATCC 33641	GCA_000168015.1	29484	29484	suspected-type	True	83.8007	1001	1374	95	below_threshold
Serratia entomophila	strain=A1	GCA_021462285.1	42906	42906	type	True	79.1333	416	1374	95	below_threshold
Serratia bockelmannii	strain=S3	GCA_008011855.1	2703793	2703793	type	True	79.0782	379	1374	95	below_threshold
Serratia nevei	strain=S15	GCA_008364245.1	2703794	2703794	type	True	79.0509	401	1374	95	below_threshold
Pectobacterium colocasium	strain=LJ1	GCA_020181655.1	2878098	2878098	type	True	78.3968	290	1374	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:54:35,041] [INFO] DFAST Taxonomy check result was written to GCF_000173735.1_ASM17373v1_genomic.fna/tc_result.tsv
[2024-01-24 13:54:35,042] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:54:35,042] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:54:35,042] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3c7839b7-ade6-4749-ab1f-3f2c7fb94721/dqc_reference/checkm_data
[2024-01-24 13:54:35,044] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:54:35,097] [INFO] Task started: CheckM
[2024-01-24 13:54:35,098] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000173735.1_ASM17373v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000173735.1_ASM17373v1_genomic.fna/checkm_input GCF_000173735.1_ASM17373v1_genomic.fna/checkm_result
[2024-01-24 13:55:12,583] [INFO] Task succeeded: CheckM
[2024-01-24 13:55:12,585] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:55:12,603] [INFO] ===== Completeness check finished =====
[2024-01-24 13:55:12,604] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:55:12,604] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000173735.1_ASM17373v1_genomic.fna/markers.fasta)
[2024-01-24 13:55:12,604] [INFO] Task started: Blastn
[2024-01-24 13:55:12,605] [INFO] Running command: blastn -query GCF_000173735.1_ASM17373v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3c7839b7-ade6-4749-ab1f-3f2c7fb94721/dqc_reference/reference_markers_gtdb.fasta -out GCF_000173735.1_ASM17373v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:55:13,795] [INFO] Task succeeded: Blastn
[2024-01-24 13:55:13,798] [INFO] Selected 12 target genomes.
[2024-01-24 13:55:13,798] [INFO] Target genome list was writen to GCF_000173735.1_ASM17373v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:55:13,829] [INFO] Task started: fastANI
[2024-01-24 13:55:13,829] [INFO] Running command: fastANI --query /var/lib/cwl/stge980bb44-51ae-4c91-a4ce-228e0523fe81/GCF_000173735.1_ASM17373v1_genomic.fna.gz --refList GCF_000173735.1_ASM17373v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000173735.1_ASM17373v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:55:26,090] [INFO] Task succeeded: fastANI
[2024-01-24 13:55:26,101] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:55:26,101] [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_000173735.1	s__Yersinia aldovae	100.0	1366	1374	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.00	96.65	0.94	0.91	11	conclusive
GCF_902726525.1	s__Yersinia enterocolitica_H	85.7654	1009	1374	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	85.7066	1034	1374	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.25	99.14	0.94	0.92	3	-
GCF_901472495.1	s__Yersinia enterocolitica	85.6758	1056	1374	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	97.11	96.22	0.89	0.83	185	-
GCF_001123825.1	s__Yersinia kristensenii_C	84.7125	979	1374	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.60	99.58	0.95	0.93	4	-
GCF_900635455.1	s__Yersinia intermedia	84.7026	1056	1374	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.02	97.82	0.92	0.88	29	-
GCF_003600645.1	s__Yersinia rochesterensis	84.5196	983	1374	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.46	98.81	0.94	0.91	13	-
GCF_009831415.1	s__Yersinia canariae	84.5026	1024	1374	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	98.93	98.81	0.93	0.92	3	-
GCF_900460525.1	s__Yersinia kristensenii	84.3829	995	1374	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	98.20	97.89	0.92	0.89	22	-
GCF_001098625.1	s__Yersinia frederiksenii_C	84.1847	998	1374	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	98.63	97.69	0.93	0.89	21	-
GCF_004124235.1	s__Yersinia hibernica	83.8696	993	1374	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	98.98	98.46	0.91	0.87	4	-
GCF_000754805.1	s__Yersinia frederiksenii	83.7673	1014	1374	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.36	98.91	0.95	0.85	11	-
--------------------------------------------------------------------------------
[2024-01-24 13:55:26,102] [INFO] GTDB search result was written to GCF_000173735.1_ASM17373v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:55:26,103] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:55:26,107] [INFO] DFAST_QC result json was written to GCF_000173735.1_ASM17373v1_genomic.fna/dqc_result.json
[2024-01-24 13:55:26,107] [INFO] DFAST_QC completed!
[2024-01-24 13:55:26,107] [INFO] Total running time: 0h1m22s