[2024-01-24 12:42:08,766] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:42:08,768] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:42:08,768] [INFO] DQC Reference Directory: /var/lib/cwl/stgf99397e7-5b17-4fe4-96a2-3bb74a8b7d5f/dqc_reference
[2024-01-24 12:42:10,098] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:42:10,100] [INFO] Task started: Prodigal
[2024-01-24 12:42:10,100] [INFO] Running command: gunzip -c /var/lib/cwl/stg71de36b5-9ac3-4d7a-89a3-9611e7f7a7b0/GCF_902170785.1_IP37424_genomic.fna.gz | prodigal -d GCF_902170785.1_IP37424_genomic.fna/cds.fna -a GCF_902170785.1_IP37424_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:42:22,421] [INFO] Task succeeded: Prodigal
[2024-01-24 12:42:22,421] [INFO] Task started: HMMsearch
[2024-01-24 12:42:22,421] [INFO] Running command: hmmsearch --tblout GCF_902170785.1_IP37424_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf99397e7-5b17-4fe4-96a2-3bb74a8b7d5f/dqc_reference/reference_markers.hmm GCF_902170785.1_IP37424_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:42:22,738] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:42:22,740] [INFO] Found 6/6 markers.
[2024-01-24 12:42:22,782] [INFO] Query marker FASTA was written to GCF_902170785.1_IP37424_genomic.fna/markers.fasta
[2024-01-24 12:42:22,783] [INFO] Task started: Blastn
[2024-01-24 12:42:22,783] [INFO] Running command: blastn -query GCF_902170785.1_IP37424_genomic.fna/markers.fasta -db /var/lib/cwl/stgf99397e7-5b17-4fe4-96a2-3bb74a8b7d5f/dqc_reference/reference_markers.fasta -out GCF_902170785.1_IP37424_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:42:23,607] [INFO] Task succeeded: Blastn
[2024-01-24 12:42:23,611] [INFO] Selected 13 target genomes.
[2024-01-24 12:42:23,611] [INFO] Target genome list was writen to GCF_902170785.1_IP37424_genomic.fna/target_genomes.txt
[2024-01-24 12:42:23,618] [INFO] Task started: fastANI
[2024-01-24 12:42:23,618] [INFO] Running command: fastANI --query /var/lib/cwl/stg71de36b5-9ac3-4d7a-89a3-9611e7f7a7b0/GCF_902170785.1_IP37424_genomic.fna.gz --refList GCF_902170785.1_IP37424_genomic.fna/target_genomes.txt --output GCF_902170785.1_IP37424_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:42:37,304] [INFO] Task succeeded: fastANI
[2024-01-24 12:42:37,305] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf99397e7-5b17-4fe4-96a2-3bb74a8b7d5f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:42:37,306] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf99397e7-5b17-4fe4-96a2-3bb74a8b7d5f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:42:37,322] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:42:37,322] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:42:37,323] [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 proxima	strain=IP37424	GCA_902170785.1	2890316	2890316	type	True	100.0	1564	1565	95	conclusive
Yersinia artesiana	strain=IP42281	GCA_902726545.1	2890315	2890315	type	True	94.7568	1268	1565	95	below_threshold
Yersinia enterocolitica subsp. enterocolitica	strain=NBRC 105693	GCA_001598735.1	150052	630	type	True	93.9051	1273	1565	95	below_threshold
Yersinia enterocolitica subsp. enterocolitica	strain=NCTC12982	GCA_901472495.1	150052	630	type	True	93.8909	1292	1565	95	below_threshold
Yersinia enterocolitica	strain=ATCC 9610	GCA_000755055.1	630	630	type	True	93.8794	1299	1565	95	below_threshold
Yersinia enterocolitica subsp. palearctica	strain=NCTC13769	GCA_900637005.1	150053	630	type	True	93.8026	1255	1565	95	below_threshold
Yersinia enterocolitica subsp. palearctica	strain=Y11	GCA_000253175.1	150053	630	type	True	93.7629	1261	1565	95	below_threshold
Yersinia aldovae	strain=IP06005	GCA_001091225.1	29483	29483	type	True	85.9021	1046	1565	95	below_threshold
Yersinia frederiksenii	strain=ATCC 33641	GCA_000168015.1	29484	29484	suspected-type	True	85.4568	1155	1565	95	below_threshold
Serratia entomophila	strain=A1	GCA_021462285.1	42906	42906	type	True	79.1376	416	1565	95	below_threshold
Serratia nevei	strain=S15	GCA_008364245.1	2703794	2703794	type	True	78.928	400	1565	95	below_threshold
Serratia bockelmannii	strain=S3	GCA_008011855.1	2703793	2703793	type	True	78.9134	385	1565	95	below_threshold
Rahnella ecdela	strain=FRB 231	GCA_019049625.1	2816250	2816250	type	True	78.9122	368	1565	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:42:37,324] [INFO] DFAST Taxonomy check result was written to GCF_902170785.1_IP37424_genomic.fna/tc_result.tsv
[2024-01-24 12:42:37,325] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:42:37,325] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:42:37,325] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf99397e7-5b17-4fe4-96a2-3bb74a8b7d5f/dqc_reference/checkm_data
[2024-01-24 12:42:37,326] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:42:37,377] [INFO] Task started: CheckM
[2024-01-24 12:42:37,377] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_902170785.1_IP37424_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_902170785.1_IP37424_genomic.fna/checkm_input GCF_902170785.1_IP37424_genomic.fna/checkm_result
[2024-01-24 12:43:18,173] [INFO] Task succeeded: CheckM
[2024-01-24 12:43:18,175] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:43:18,197] [INFO] ===== Completeness check finished =====
[2024-01-24 12:43:18,197] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:43:18,198] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_902170785.1_IP37424_genomic.fna/markers.fasta)
[2024-01-24 12:43:18,198] [INFO] Task started: Blastn
[2024-01-24 12:43:18,198] [INFO] Running command: blastn -query GCF_902170785.1_IP37424_genomic.fna/markers.fasta -db /var/lib/cwl/stgf99397e7-5b17-4fe4-96a2-3bb74a8b7d5f/dqc_reference/reference_markers_gtdb.fasta -out GCF_902170785.1_IP37424_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:43:19,449] [INFO] Task succeeded: Blastn
[2024-01-24 12:43:19,452] [INFO] Selected 11 target genomes.
[2024-01-24 12:43:19,452] [INFO] Target genome list was writen to GCF_902170785.1_IP37424_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:43:19,461] [INFO] Task started: fastANI
[2024-01-24 12:43:19,462] [INFO] Running command: fastANI --query /var/lib/cwl/stg71de36b5-9ac3-4d7a-89a3-9611e7f7a7b0/GCF_902170785.1_IP37424_genomic.fna.gz --refList GCF_902170785.1_IP37424_genomic.fna/target_genomes_gtdb.txt --output GCF_902170785.1_IP37424_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:43:32,110] [INFO] Task succeeded: fastANI
[2024-01-24 12:43:32,124] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:43:32,125] [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_001995075.1	s__Yersinia enterocolitica_F	99.1723	1466	1565	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.25	99.14	0.94	0.92	3	conclusive
GCF_902726525.1	s__Yersinia enterocolitica_H	94.5325	1326	1565	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.97	99.97	0.99	0.99	3	-
GCF_901472495.1	s__Yersinia enterocolitica	93.8909	1292	1565	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	87.896	1181	1565	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	87.8503	1205	1565	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	87.6972	1249	1565	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	86.3441	1216	1565	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	85.8947	1032	1565	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	85.6581	1189	1565	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	85.4931	1174	1565	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.36	98.91	0.95	0.85	11	-
GCF_001047675.1	s__Yersinia aleksiciae	85.0534	986	1565	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 12:43:32,128] [INFO] GTDB search result was written to GCF_902170785.1_IP37424_genomic.fna/result_gtdb.tsv
[2024-01-24 12:43:32,129] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:43:32,133] [INFO] DFAST_QC result json was written to GCF_902170785.1_IP37424_genomic.fna/dqc_result.json
[2024-01-24 12:43:32,133] [INFO] DFAST_QC completed!
[2024-01-24 12:43:32,133] [INFO] Total running time: 0h1m23s