[2024-01-24 13:55:41,223] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:55:41,225] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:55:41,225] [INFO] DQC Reference Directory: /var/lib/cwl/stg58750900-2acb-4e51-8cb5-6fd34ed0da1b/dqc_reference
[2024-01-24 13:55:42,505] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:55:42,506] [INFO] Task started: Prodigal
[2024-01-24 13:55:42,506] [INFO] Running command: gunzip -c /var/lib/cwl/stg4507ffe5-129b-42fb-b972-1a5f1e126041/GCF_902726565.1_IP38594v1_genomic.fna.gz | prodigal -d GCF_902726565.1_IP38594v1_genomic.fna/cds.fna -a GCF_902726565.1_IP38594v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:55:54,636] [INFO] Task succeeded: Prodigal
[2024-01-24 13:55:54,636] [INFO] Task started: HMMsearch
[2024-01-24 13:55:54,636] [INFO] Running command: hmmsearch --tblout GCF_902726565.1_IP38594v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg58750900-2acb-4e51-8cb5-6fd34ed0da1b/dqc_reference/reference_markers.hmm GCF_902726565.1_IP38594v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:55:54,915] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:55:54,917] [INFO] Found 6/6 markers.
[2024-01-24 13:55:54,972] [INFO] Query marker FASTA was written to GCF_902726565.1_IP38594v1_genomic.fna/markers.fasta
[2024-01-24 13:55:54,973] [INFO] Task started: Blastn
[2024-01-24 13:55:54,973] [INFO] Running command: blastn -query GCF_902726565.1_IP38594v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg58750900-2acb-4e51-8cb5-6fd34ed0da1b/dqc_reference/reference_markers.fasta -out GCF_902726565.1_IP38594v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:55:55,787] [INFO] Task succeeded: Blastn
[2024-01-24 13:55:55,791] [INFO] Selected 13 target genomes.
[2024-01-24 13:55:55,791] [INFO] Target genome list was writen to GCF_902726565.1_IP38594v1_genomic.fna/target_genomes.txt
[2024-01-24 13:55:55,810] [INFO] Task started: fastANI
[2024-01-24 13:55:55,811] [INFO] Running command: fastANI --query /var/lib/cwl/stg4507ffe5-129b-42fb-b972-1a5f1e126041/GCF_902726565.1_IP38594v1_genomic.fna.gz --refList GCF_902726565.1_IP38594v1_genomic.fna/target_genomes.txt --output GCF_902726565.1_IP38594v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:56:08,902] [INFO] Task succeeded: fastANI
[2024-01-24 13:56:08,903] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg58750900-2acb-4e51-8cb5-6fd34ed0da1b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:56:08,904] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg58750900-2acb-4e51-8cb5-6fd34ed0da1b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:56:08,918] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:56:08,919] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:56:08,919] [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 vastinensis	strain=IP38594	GCA_902726565.1	2890318	2890318	type	True	100.0	1486	1488	95	conclusive
Yersinia alsatica	strain=IP38850	GCA_902170305.1	2890317	2890317	type	True	87.5793	1281	1488	95	below_threshold
Yersinia frederiksenii	strain=ATCC 33641	GCA_000754805.1	29484	29484	suspected-type	True	87.1448	1245	1488	95	below_threshold
Yersinia frederiksenii	strain=ATCC 33641	GCA_000168015.1	29484	29484	suspected-type	True	87.1278	1206	1488	95	below_threshold
Yersinia frederiksenii	strain=NCTC11470	GCA_900460425.1	29484	29484	suspected-type	True	87.0956	1254	1488	95	below_threshold
Yersinia proxima	strain=IP37424	GCA_902170785.1	2890316	2890316	type	True	85.1223	1150	1488	95	below_threshold
Yersinia intermedia	strain=NCTC11469	GCA_900635455.1	631	631	type	True	84.2509	1082	1488	95	below_threshold
Yersinia intermedia	strain=ATCC 29909	GCA_000168035.1	631	631	type	True	84.2366	1057	1488	95	below_threshold
Yersinia aldovae	strain=IP06005	GCA_001091225.1	29483	29483	type	True	83.687	970	1488	95	below_threshold
Serratia entomophila	strain=A1	GCA_021462285.1	42906	42906	type	True	79.344	375	1488	95	below_threshold
Serratia nevei	strain=S15	GCA_008364245.1	2703794	2703794	type	True	79.111	361	1488	95	below_threshold
Serratia bockelmannii	strain=S3	GCA_008011855.1	2703793	2703793	type	True	78.9749	359	1488	95	below_threshold
[Pantoea] beijingensis	strain=JZB2120001	GCA_022647505.1	1324864	1324864	type	True	78.2836	214	1488	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:56:08,920] [INFO] DFAST Taxonomy check result was written to GCF_902726565.1_IP38594v1_genomic.fna/tc_result.tsv
[2024-01-24 13:56:08,921] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:56:08,921] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:56:08,921] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg58750900-2acb-4e51-8cb5-6fd34ed0da1b/dqc_reference/checkm_data
[2024-01-24 13:56:08,923] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:56:08,968] [INFO] Task started: CheckM
[2024-01-24 13:56:08,968] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_902726565.1_IP38594v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_902726565.1_IP38594v1_genomic.fna/checkm_input GCF_902726565.1_IP38594v1_genomic.fna/checkm_result
[2024-01-24 13:56:47,681] [INFO] Task succeeded: CheckM
[2024-01-24 13:56:47,682] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:56:47,704] [INFO] ===== Completeness check finished =====
[2024-01-24 13:56:47,704] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:56:47,705] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_902726565.1_IP38594v1_genomic.fna/markers.fasta)
[2024-01-24 13:56:47,705] [INFO] Task started: Blastn
[2024-01-24 13:56:47,706] [INFO] Running command: blastn -query GCF_902726565.1_IP38594v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg58750900-2acb-4e51-8cb5-6fd34ed0da1b/dqc_reference/reference_markers_gtdb.fasta -out GCF_902726565.1_IP38594v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:56:48,667] [INFO] Task succeeded: Blastn
[2024-01-24 13:56:48,671] [INFO] Selected 13 target genomes.
[2024-01-24 13:56:48,671] [INFO] Target genome list was writen to GCF_902726565.1_IP38594v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:56:48,693] [INFO] Task started: fastANI
[2024-01-24 13:56:48,694] [INFO] Running command: fastANI --query /var/lib/cwl/stg4507ffe5-129b-42fb-b972-1a5f1e126041/GCF_902726565.1_IP38594v1_genomic.fna.gz --refList GCF_902726565.1_IP38594v1_genomic.fna/target_genomes_gtdb.txt --output GCF_902726565.1_IP38594v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:57:02,243] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:02,258] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:57:02,259] [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_001155565.1	s__Yersinia frederiksenii_A	99.5378	1443	1488	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.53	99.44	0.95	0.92	10	conclusive
GCF_001098625.1	s__Yersinia frederiksenii_C	87.5234	1274	1488	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	87.1415	1246	1488	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	85.414	1102	1488	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.41	99.12	0.94	0.89	12	-
GCF_009831415.1	s__Yersinia canariae	85.2136	1180	1488	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	85.1914	1147	1488	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	98.98	98.46	0.91	0.87	4	-
GCF_901472495.1	s__Yersinia enterocolitica	85.145	1119	1488	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	97.11	96.22	0.89	0.83	185	-
GCF_001995075.1	s__Yersinia enterocolitica_F	85.0695	1151	1488	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.25	99.14	0.94	0.92	3	-
GCF_003600645.1	s__Yersinia rochesterensis	84.9916	1099	1488	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.46	98.81	0.94	0.91	13	-
GCF_001047675.1	s__Yersinia aleksiciae	84.4595	989	1488	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.22	98.37	0.87	0.82	10	-
GCF_001152565.1	s__Yersinia pekkanenii	84.3404	1013	1488	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.90	99.90	0.98	0.98	2	-
GCF_900635455.1	s__Yersinia intermedia	84.2733	1079	1488	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.02	97.82	0.92	0.88	29	-
GCF_013282725.1	s__Yersinia mollaretii	84.2493	1088	1488	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	96.95	95.82	0.92	0.88	25	-
--------------------------------------------------------------------------------
[2024-01-24 13:57:02,261] [INFO] GTDB search result was written to GCF_902726565.1_IP38594v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:57:02,261] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:57:02,265] [INFO] DFAST_QC result json was written to GCF_902726565.1_IP38594v1_genomic.fna/dqc_result.json
[2024-01-24 13:57:02,265] [INFO] DFAST_QC completed!
[2024-01-24 13:57:02,265] [INFO] Total running time: 0h1m21s