[2024-01-24 12:36:24,720] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:36:24,723] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:36:24,723] [INFO] DQC Reference Directory: /var/lib/cwl/stg5b23b3ea-9c2a-4d4b-9272-e4f41cd85e97/dqc_reference
[2024-01-24 12:36:26,068] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:36:26,069] [INFO] Task started: Prodigal
[2024-01-24 12:36:26,069] [INFO] Running command: gunzip -c /var/lib/cwl/stgdf538d37-6ee8-4b7a-baf6-5b5382bc19f3/GCF_019047025.1_ASM1904702v1_genomic.fna.gz | prodigal -d GCF_019047025.1_ASM1904702v1_genomic.fna/cds.fna -a GCF_019047025.1_ASM1904702v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:36:39,790] [INFO] Task succeeded: Prodigal
[2024-01-24 12:36:39,790] [INFO] Task started: HMMsearch
[2024-01-24 12:36:39,790] [INFO] Running command: hmmsearch --tblout GCF_019047025.1_ASM1904702v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5b23b3ea-9c2a-4d4b-9272-e4f41cd85e97/dqc_reference/reference_markers.hmm GCF_019047025.1_ASM1904702v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:36:40,079] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:36:40,081] [INFO] Found 6/6 markers.
[2024-01-24 12:36:40,121] [INFO] Query marker FASTA was written to GCF_019047025.1_ASM1904702v1_genomic.fna/markers.fasta
[2024-01-24 12:36:40,122] [INFO] Task started: Blastn
[2024-01-24 12:36:40,122] [INFO] Running command: blastn -query GCF_019047025.1_ASM1904702v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5b23b3ea-9c2a-4d4b-9272-e4f41cd85e97/dqc_reference/reference_markers.fasta -out GCF_019047025.1_ASM1904702v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:36:41,032] [INFO] Task succeeded: Blastn
[2024-01-24 12:36:41,038] [INFO] Selected 13 target genomes.
[2024-01-24 12:36:41,038] [INFO] Target genome list was writen to GCF_019047025.1_ASM1904702v1_genomic.fna/target_genomes.txt
[2024-01-24 12:36:41,048] [INFO] Task started: fastANI
[2024-01-24 12:36:41,048] [INFO] Running command: fastANI --query /var/lib/cwl/stgdf538d37-6ee8-4b7a-baf6-5b5382bc19f3/GCF_019047025.1_ASM1904702v1_genomic.fna.gz --refList GCF_019047025.1_ASM1904702v1_genomic.fna/target_genomes.txt --output GCF_019047025.1_ASM1904702v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:36:56,578] [INFO] Task succeeded: fastANI
[2024-01-24 12:36:56,579] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5b23b3ea-9c2a-4d4b-9272-e4f41cd85e97/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:36:56,579] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5b23b3ea-9c2a-4d4b-9272-e4f41cd85e97/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:36:56,591] [INFO] Found 13 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 12:36:56,592] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:36:56,592] [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
Enterobacter roggenkampii	strain=FDAARGOS 1430	GCA_019047025.1	1812935	1812935	type	True	100.0	1636	1637	95	conclusive
Enterobacter roggenkampii	strain=DSM 16690	GCA_001729805.1	1812935	1812935	type	True	99.9963	1632	1637	95	conclusive
Enterobacter roggenkampii	strain=DSM 16690	GCA_024390995.1	1812935	1812935	type	True	98.456	1355	1637	95	conclusive
Enterobacter vonholyi	strain=E13	GCA_008364555.1	2797505	2797505	type	True	94.405	1371	1637	95	below_threshold
Enterobacter asburiae	strain=FDAARGOS_892	GCA_016027695.1	61645	61645	type	True	93.3603	1350	1637	95	below_threshold
Enterobacter asburiae	strain=ATCC 35953	GCA_001521715.1	61645	61645	type	True	93.3502	1346	1637	95	below_threshold
Enterobacter chengduensis	strain=WCHECl-C4 = WCHECh050004	GCA_001984825.2	2494701	2494701	type	True	92.7735	1370	1637	95	below_threshold
Enterobacter sichuanensis	strain=WCHECL1597	GCA_025002605.1	2071710	2071710	type	True	91.8757	1333	1637	95	below_threshold
Enterobacter sichuanensis	strain=WCHECL1597	GCA_002939185.1	2071710	2071710	type	True	91.8664	1289	1637	95	below_threshold
Enterobacter kobei	strain=DSM 13645	GCA_001729765.1	208224	208224	type	True	90.6477	1328	1637	95	below_threshold
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	89.0579	1276	1637	95	below_threshold
Enterobacter cloacae	strain=DSM 30054	GCA_021469225.1	550	550	type	True	88.9118	1305	1637	95	below_threshold
Enterobacter hormaechei	strain=FDAARGOS 1433	GCA_019048245.1	158836	158836	suspected-type	True	88.2734	1255	1637	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:36:56,595] [INFO] DFAST Taxonomy check result was written to GCF_019047025.1_ASM1904702v1_genomic.fna/tc_result.tsv
[2024-01-24 12:36:56,596] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:36:56,596] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:36:56,596] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5b23b3ea-9c2a-4d4b-9272-e4f41cd85e97/dqc_reference/checkm_data
[2024-01-24 12:36:56,599] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:36:56,646] [INFO] Task started: CheckM
[2024-01-24 12:36:56,646] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019047025.1_ASM1904702v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019047025.1_ASM1904702v1_genomic.fna/checkm_input GCF_019047025.1_ASM1904702v1_genomic.fna/checkm_result
[2024-01-24 12:37:39,171] [INFO] Task succeeded: CheckM
[2024-01-24 12:37:39,172] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:37:39,198] [INFO] ===== Completeness check finished =====
[2024-01-24 12:37:39,199] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:37:39,199] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019047025.1_ASM1904702v1_genomic.fna/markers.fasta)
[2024-01-24 12:37:39,200] [INFO] Task started: Blastn
[2024-01-24 12:37:39,200] [INFO] Running command: blastn -query GCF_019047025.1_ASM1904702v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5b23b3ea-9c2a-4d4b-9272-e4f41cd85e97/dqc_reference/reference_markers_gtdb.fasta -out GCF_019047025.1_ASM1904702v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:40,647] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:40,651] [INFO] Selected 13 target genomes.
[2024-01-24 12:37:40,651] [INFO] Target genome list was writen to GCF_019047025.1_ASM1904702v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:37:40,660] [INFO] Task started: fastANI
[2024-01-24 12:37:40,661] [INFO] Running command: fastANI --query /var/lib/cwl/stgdf538d37-6ee8-4b7a-baf6-5b5382bc19f3/GCF_019047025.1_ASM1904702v1_genomic.fna.gz --refList GCF_019047025.1_ASM1904702v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019047025.1_ASM1904702v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:37:56,634] [INFO] Task succeeded: fastANI
[2024-01-24 12:37:56,653] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:37:56,653] [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_001729805.1	s__Enterobacter roggenkampii	99.9963	1632	1637	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	98.21	95.50	0.89	0.83	197	conclusive
GCF_008364555.1	s__Enterobacter vonholyi	94.405	1371	1637	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	98.34	98.09	0.94	0.93	8	-
GCF_009755685.1	s__Enterobacter sp000568095	94.2667	1411	1637	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0476	98.37	98.04	0.95	0.92	11	-
GCF_007035645.1	s__Enterobacter asburiae_B	93.4272	1375	1637	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	96.8818	98.31	97.34	0.92	0.85	70	-
GCF_008364625.1	s__Enterobacter dykesii	93.4138	1331	1637	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	96.5795	99.13	97.97	0.97	0.95	7	-
GCF_001521715.1	s__Enterobacter asburiae	93.3502	1346	1637	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	96.8818	98.42	96.92	0.89	0.84	32	-
GCF_003634515.1	s__Enterobacter asburiae_A	93.3025	1372	1637	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	96.0274	97.62	96.46	0.91	0.85	7	-
GCF_000493015.1	s__Enterobacter sp000493015	93.1974	1380	1637	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.7595	98.68	98.68	0.92	0.92	2	-
GCF_008080435.1	s__Enterobacter asburiae_C	93.0556	1360	1637	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.5575	N/A	N/A	N/A	N/A	1	-
GCF_001984825.2	s__Enterobacter chengduensis	92.7827	1369	1637	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	97.11	95.58	0.88	0.79	24	-
GCF_001022965.1	s__Enterobacter cloacae_L	92.3886	1381	1637	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	97.51	97.16	0.91	0.90	5	-
GCF_002939185.1	s__Enterobacter sichuanensis	91.8742	1288	1637	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	98.38	97.99	0.90	0.85	19	-
GCF_001729765.1	s__Enterobacter kobei	90.6452	1326	1637	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	98.81	98.45	0.89	0.85	141	-
--------------------------------------------------------------------------------
[2024-01-24 12:37:56,655] [INFO] GTDB search result was written to GCF_019047025.1_ASM1904702v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:37:56,656] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:37:56,659] [INFO] DFAST_QC result json was written to GCF_019047025.1_ASM1904702v1_genomic.fna/dqc_result.json
[2024-01-24 12:37:56,659] [INFO] DFAST_QC completed!
[2024-01-24 12:37:56,660] [INFO] Total running time: 0h1m32s