[2024-01-24 13:13:39,335] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:13:39,338] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:13:39,338] [INFO] DQC Reference Directory: /var/lib/cwl/stg19c97660-3b97-4bde-be78-f3beeebef6e5/dqc_reference
[2024-01-24 13:13:40,644] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:13:40,645] [INFO] Task started: Prodigal
[2024-01-24 13:13:40,645] [INFO] Running command: gunzip -c /var/lib/cwl/stg3103fad6-58b1-4aaf-880e-e80b57c01bb5/GCF_009831415.1_ASM983141v1_genomic.fna.gz | prodigal -d GCF_009831415.1_ASM983141v1_genomic.fna/cds.fna -a GCF_009831415.1_ASM983141v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:53,348] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:53,349] [INFO] Task started: HMMsearch
[2024-01-24 13:13:53,349] [INFO] Running command: hmmsearch --tblout GCF_009831415.1_ASM983141v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg19c97660-3b97-4bde-be78-f3beeebef6e5/dqc_reference/reference_markers.hmm GCF_009831415.1_ASM983141v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:53,614] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:53,615] [INFO] Found 6/6 markers.
[2024-01-24 13:13:53,652] [INFO] Query marker FASTA was written to GCF_009831415.1_ASM983141v1_genomic.fna/markers.fasta
[2024-01-24 13:13:53,653] [INFO] Task started: Blastn
[2024-01-24 13:13:53,653] [INFO] Running command: blastn -query GCF_009831415.1_ASM983141v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg19c97660-3b97-4bde-be78-f3beeebef6e5/dqc_reference/reference_markers.fasta -out GCF_009831415.1_ASM983141v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:54,400] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:54,403] [INFO] Selected 26 target genomes.
[2024-01-24 13:13:54,403] [INFO] Target genome list was writen to GCF_009831415.1_ASM983141v1_genomic.fna/target_genomes.txt
[2024-01-24 13:13:54,408] [INFO] Task started: fastANI
[2024-01-24 13:13:54,408] [INFO] Running command: fastANI --query /var/lib/cwl/stg3103fad6-58b1-4aaf-880e-e80b57c01bb5/GCF_009831415.1_ASM983141v1_genomic.fna.gz --refList GCF_009831415.1_ASM983141v1_genomic.fna/target_genomes.txt --output GCF_009831415.1_ASM983141v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:14:18,734] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:18,735] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg19c97660-3b97-4bde-be78-f3beeebef6e5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:14:18,735] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg19c97660-3b97-4bde-be78-f3beeebef6e5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:14:18,752] [INFO] Found 24 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:14:18,752] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:14:18,753] [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 canariae	strain=NCTC 14382	GCA_009831415.1	2607663	2607663	type	True	100.0	1569	1570	95	conclusive
Yersinia hibernica	strain=CFS1934	GCA_004124235.1	2339259	2339259	type	True	90.0733	1327	1570	95	below_threshold
Yersinia enterocolitica subsp. enterocolitica	strain=NCTC12982	GCA_901472495.1	150052	630	type	True	87.793	1248	1570	95	below_threshold
Yersinia thracica	strain=IP34646	GCA_902170565.1	2890319	2890319	type	True	87.7859	1170	1570	95	below_threshold
Yersinia enterocolitica	strain=ATCC 9610	GCA_000755055.1	630	630	type	True	87.7449	1254	1570	95	below_threshold
Yersinia enterocolitica subsp. palearctica	strain=Y11	GCA_000253175.1	150053	630	type	True	87.7415	1234	1570	95	below_threshold
Yersinia enterocolitica subsp. enterocolitica	strain=NBRC 105693	GCA_001598735.1	150052	630	type	True	87.7167	1220	1570	95	below_threshold
Yersinia rochesterensis	strain=ATCC BAA-2637	GCA_003600645.1	1604335	1604335	type	True	87.7048	1236	1570	95	below_threshold
Yersinia kristensenii	strain=NCTC11471	GCA_900460525.1	28152	28152	type	True	87.6992	1251	1570	95	below_threshold
Yersinia kristensenii	strain=ATCC 33638	GCA_000173715.1	28152	28152	type	True	87.5751	1221	1570	95	below_threshold
Yersinia alsatica	strain=IP38850	GCA_902170305.1	2890317	2890317	type	True	86.0188	1219	1570	95	below_threshold
Yersinia frederiksenii	strain=NCTC11470	GCA_900460425.1	29484	29484	suspected-type	True	85.8117	1244	1570	95	below_threshold
Yersinia frederiksenii	strain=ATCC 33641	GCA_000754805.1	29484	29484	suspected-type	True	85.7004	1262	1570	95	below_threshold
Yersinia frederiksenii	strain=ATCC 33641	GCA_000168015.1	29484	29484	suspected-type	True	85.6715	1194	1570	95	below_threshold
Yersinia rohdei	strain=ATCC 43380	GCA_000173775.1	29485	29485	type	True	85.2408	1106	1570	95	below_threshold
Yersinia intermedia	strain=NCTC11469	GCA_900635455.1	631	631	type	True	84.6788	1172	1570	95	below_threshold
Yersinia aldovae	strain=IP06005	GCA_001091225.1	29483	29483	type	True	84.584	1034	1570	95	below_threshold
Yersinia intermedia	strain=ATCC 29909	GCA_000168035.1	631	631	type	True	84.53	1128	1570	95	below_threshold
Serratia entomophila	strain=A1	GCA_021462285.1	42906	42906	type	True	79.7567	398	1570	95	below_threshold
Serratia bockelmannii	strain=S3	GCA_008011855.1	2703793	2703793	type	True	79.2716	364	1570	95	below_threshold
Serratia nevei	strain=S15	GCA_008364245.1	2703794	2703794	type	True	79.175	372	1570	95	below_threshold
Buttiauxella massiliensis	strain=Marseille-P9829	GCA_902500225.1	2831590	2831590	type	True	78.5234	270	1570	95	below_threshold
Aeromonas sobria	strain=CECT 4245	GCA_000820145.1	646	646	suspected-type	True	76.7424	51	1570	95	below_threshold
Aeromonas sobria	strain=CIP 74.33	GCA_018359945.1	646	646	suspected-type	True	76.6696	54	1570	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:14:18,754] [INFO] DFAST Taxonomy check result was written to GCF_009831415.1_ASM983141v1_genomic.fna/tc_result.tsv
[2024-01-24 13:14:18,755] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:14:18,755] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:14:18,755] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg19c97660-3b97-4bde-be78-f3beeebef6e5/dqc_reference/checkm_data
[2024-01-24 13:14:18,756] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:14:18,799] [INFO] Task started: CheckM
[2024-01-24 13:14:18,799] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009831415.1_ASM983141v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009831415.1_ASM983141v1_genomic.fna/checkm_input GCF_009831415.1_ASM983141v1_genomic.fna/checkm_result
[2024-01-24 13:15:00,063] [INFO] Task succeeded: CheckM
[2024-01-24 13:15:00,064] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:15:00,092] [INFO] ===== Completeness check finished =====
[2024-01-24 13:15:00,092] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:15:00,093] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009831415.1_ASM983141v1_genomic.fna/markers.fasta)
[2024-01-24 13:15:00,093] [INFO] Task started: Blastn
[2024-01-24 13:15:00,093] [INFO] Running command: blastn -query GCF_009831415.1_ASM983141v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg19c97660-3b97-4bde-be78-f3beeebef6e5/dqc_reference/reference_markers_gtdb.fasta -out GCF_009831415.1_ASM983141v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:15:01,018] [INFO] Task succeeded: Blastn
[2024-01-24 13:15:01,021] [INFO] Selected 17 target genomes.
[2024-01-24 13:15:01,021] [INFO] Target genome list was writen to GCF_009831415.1_ASM983141v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:15:01,035] [INFO] Task started: fastANI
[2024-01-24 13:15:01,035] [INFO] Running command: fastANI --query /var/lib/cwl/stg3103fad6-58b1-4aaf-880e-e80b57c01bb5/GCF_009831415.1_ASM983141v1_genomic.fna.gz --refList GCF_009831415.1_ASM983141v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009831415.1_ASM983141v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:15:19,090] [INFO] Task succeeded: fastANI
[2024-01-24 13:15:19,103] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:15:19,104] [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_009831415.1	s__Yersinia canariae	100.0	1569	1570	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	98.93	98.81	0.93	0.92	3	conclusive
GCF_004124235.1	s__Yersinia hibernica	90.0695	1326	1570	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	98.98	98.46	0.91	0.87	4	-
GCF_001123825.1	s__Yersinia kristensenii_C	87.8678	1182	1570	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.60	99.58	0.95	0.93	4	-
GCF_901472495.1	s__Yersinia enterocolitica	87.7884	1248	1570	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	97.11	96.22	0.89	0.83	185	-
GCF_003600645.1	s__Yersinia rochesterensis	87.7141	1237	1570	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.46	98.81	0.94	0.91	13	-
GCF_902726525.1	s__Yersinia enterocolitica_H	87.6898	1203	1570	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.97	99.97	0.99	0.99	3	-
GCF_900460525.1	s__Yersinia kristensenii	87.6869	1251	1570	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	98.20	97.89	0.92	0.89	22	-
GCF_001995075.1	s__Yersinia enterocolitica_F	87.6861	1232	1570	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.25	99.14	0.94	0.92	3	-
GCF_001098625.1	s__Yersinia frederiksenii_C	85.9626	1222	1570	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	98.63	97.69	0.93	0.89	21	-
GCF_000754805.1	s__Yersinia frederiksenii	85.7048	1261	1570	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.36	98.91	0.95	0.85	11	-
GCF_000173775.1	s__Yersinia rohdei	85.2408	1106	1570	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.41	99.12	0.94	0.89	12	-
GCF_002082245.2	s__Yersinia enterocolitica_E	84.8277	1193	1570	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900635455.1	s__Yersinia intermedia	84.6829	1171	1570	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.02	97.82	0.92	0.88	29	-
GCF_001006005.1	s__Serratia_A fonticola	79.943	463	1570	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia_A	95.0	96.10	95.03	0.87	0.81	45	-
GCF_001976145.1	s__Chania oryzae	79.37	451	1570	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Chania	95.0	98.90	98.79	0.94	0.94	3	-
GCF_000496755.2	s__Serratia_A sp000496755	78.9872	297	1570	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:15:19,105] [INFO] GTDB search result was written to GCF_009831415.1_ASM983141v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:15:19,106] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:15:19,110] [INFO] DFAST_QC result json was written to GCF_009831415.1_ASM983141v1_genomic.fna/dqc_result.json
[2024-01-24 13:15:19,110] [INFO] DFAST_QC completed!
[2024-01-24 13:15:19,110] [INFO] Total running time: 0h1m40s