[2024-01-25 17:49:50,524] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:49:50,526] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:49:50,526] [INFO] DQC Reference Directory: /var/lib/cwl/stg1c7159d1-af0d-4564-9d55-cdd7e8719189/dqc_reference
[2024-01-25 17:49:51,678] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:49:51,678] [INFO] Task started: Prodigal
[2024-01-25 17:49:51,679] [INFO] Running command: gunzip -c /var/lib/cwl/stg54369abc-5c73-4c2a-915d-09f56cecdf75/GCF_900324475.1_EB-247_genomic.fna.gz | prodigal -d GCF_900324475.1_EB-247_genomic.fna/cds.fna -a GCF_900324475.1_EB-247_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:50:02,987] [INFO] Task succeeded: Prodigal
[2024-01-25 17:50:02,987] [INFO] Task started: HMMsearch
[2024-01-25 17:50:02,988] [INFO] Running command: hmmsearch --tblout GCF_900324475.1_EB-247_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1c7159d1-af0d-4564-9d55-cdd7e8719189/dqc_reference/reference_markers.hmm GCF_900324475.1_EB-247_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:50:03,249] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:50:03,254] [INFO] Found 6/6 markers.
[2024-01-25 17:50:03,293] [INFO] Query marker FASTA was written to GCF_900324475.1_EB-247_genomic.fna/markers.fasta
[2024-01-25 17:50:03,294] [INFO] Task started: Blastn
[2024-01-25 17:50:03,294] [INFO] Running command: blastn -query GCF_900324475.1_EB-247_genomic.fna/markers.fasta -db /var/lib/cwl/stg1c7159d1-af0d-4564-9d55-cdd7e8719189/dqc_reference/reference_markers.fasta -out GCF_900324475.1_EB-247_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:50:04,178] [INFO] Task succeeded: Blastn
[2024-01-25 17:50:04,180] [INFO] Selected 18 target genomes.
[2024-01-25 17:50:04,180] [INFO] Target genome list was writen to GCF_900324475.1_EB-247_genomic.fna/target_genomes.txt
[2024-01-25 17:50:04,195] [INFO] Task started: fastANI
[2024-01-25 17:50:04,195] [INFO] Running command: fastANI --query /var/lib/cwl/stg54369abc-5c73-4c2a-915d-09f56cecdf75/GCF_900324475.1_EB-247_genomic.fna.gz --refList GCF_900324475.1_EB-247_genomic.fna/target_genomes.txt --output GCF_900324475.1_EB-247_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:50:25,158] [INFO] Task succeeded: fastANI
[2024-01-25 17:50:25,158] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1c7159d1-af0d-4564-9d55-cdd7e8719189/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:50:25,159] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1c7159d1-af0d-4564-9d55-cdd7e8719189/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:50:25,169] [INFO] Found 18 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 17:50:25,170] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:50:25,170] [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 bugandensis		GCA_900324475.1	881260	881260	type	True	100.0	1572	1572	95	conclusive
Enterobacter bugandensis	strain=FDAARGOS 1427	GCA_019046905.1	881260	881260	type	True	99.9963	1571	1572	95	conclusive
Enterobacter asburiae	strain=ATCC 35953	GCA_001521715.1	61645	61645	type	True	91.9024	1314	1572	95	below_threshold
Enterobacter asburiae	strain=FDAARGOS_892	GCA_016027695.1	61645	61645	type	True	91.8621	1319	1572	95	below_threshold
Enterobacter roggenkampii	strain=FDAARGOS 1430	GCA_019047025.1	1812935	1812935	type	True	91.8351	1366	1572	95	below_threshold
Enterobacter roggenkampii	strain=DSM 16690	GCA_024390995.1	1812935	1812935	type	True	91.7409	1283	1572	95	below_threshold
Enterobacter chengduensis	strain=WCHECl-C4 = WCHECh050004	GCA_001984825.2	2494701	2494701	type	True	91.1349	1357	1572	95	below_threshold
Enterobacter kobei	strain=DSM 13645	GCA_001729765.1	208224	208224	type	True	91.1337	1313	1572	95	below_threshold
Enterobacter sichuanensis	strain=WCHECL1597	GCA_002939185.1	2071710	2071710	type	True	90.3323	1257	1572	95	below_threshold
Enterobacter sichuanensis	strain=WCHECL1597	GCA_025002605.1	2071710	2071710	type	True	90.301	1318	1572	95	below_threshold
Enterobacter quasimori	strain=090044	GCA_003964905.1	2838947	2838947	type	True	90.0412	1323	1572	95	below_threshold
Enterobacter mori	strain=LMG 25706	GCA_000211415.1	539813	539813	type	True	89.6137	1298	1572	95	below_threshold
Enterobacter hormaechei subsp. oharae	strain=FDAARGOS_1533	GCA_020097195.1	301102	158836	type	True	89.2111	1288	1572	95	below_threshold
Enterobacter hormaechei subsp. xiangfangensis	strain=LMG27195	GCA_001729785.1	1296536	158836	type	True	89.2094	1282	1572	95	below_threshold
Enterobacter hormaechei subsp. oharae	strain=DSM 16687	GCA_001729705.1	301102	158836	type	True	89.1414	1298	1572	95	below_threshold
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	89.0761	1288	1572	95	below_threshold
Enterobacter hormaechei	strain=FDAARGOS 1433	GCA_019048245.1	158836	158836	suspected-type	True	89.0315	1299	1572	95	below_threshold
Enterobacter cloacae	strain=DSM 30054	GCA_021469225.1	550	550	type	True	88.8006	1303	1572	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:50:25,171] [INFO] DFAST Taxonomy check result was written to GCF_900324475.1_EB-247_genomic.fna/tc_result.tsv
[2024-01-25 17:50:25,172] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:50:25,172] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:50:25,172] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1c7159d1-af0d-4564-9d55-cdd7e8719189/dqc_reference/checkm_data
[2024-01-25 17:50:25,173] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:50:25,218] [INFO] Task started: CheckM
[2024-01-25 17:50:25,218] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900324475.1_EB-247_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900324475.1_EB-247_genomic.fna/checkm_input GCF_900324475.1_EB-247_genomic.fna/checkm_result
[2024-01-25 17:50:59,745] [INFO] Task succeeded: CheckM
[2024-01-25 17:50:59,746] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:50:59,760] [INFO] ===== Completeness check finished =====
[2024-01-25 17:50:59,760] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:50:59,761] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900324475.1_EB-247_genomic.fna/markers.fasta)
[2024-01-25 17:50:59,761] [INFO] Task started: Blastn
[2024-01-25 17:50:59,761] [INFO] Running command: blastn -query GCF_900324475.1_EB-247_genomic.fna/markers.fasta -db /var/lib/cwl/stg1c7159d1-af0d-4564-9d55-cdd7e8719189/dqc_reference/reference_markers_gtdb.fasta -out GCF_900324475.1_EB-247_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:51:01,187] [INFO] Task succeeded: Blastn
[2024-01-25 17:51:01,189] [INFO] Selected 14 target genomes.
[2024-01-25 17:51:01,189] [INFO] Target genome list was writen to GCF_900324475.1_EB-247_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:51:01,201] [INFO] Task started: fastANI
[2024-01-25 17:51:01,201] [INFO] Running command: fastANI --query /var/lib/cwl/stg54369abc-5c73-4c2a-915d-09f56cecdf75/GCF_900324475.1_EB-247_genomic.fna.gz --refList GCF_900324475.1_EB-247_genomic.fna/target_genomes_gtdb.txt --output GCF_900324475.1_EB-247_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:51:17,413] [INFO] Task succeeded: fastANI
[2024-01-25 17:51:17,422] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:51:17,422] [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_900324475.1	s__Enterobacter bugandensis	100.0	1572	1572	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	98.49	95.52	0.94	0.88	115	conclusive
GCF_011754535.1	s__Enterobacter cloacae_N	94.2301	1424	1572	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	99.03	98.99	0.93	0.91	4	-
GCF_003594915.1	s__Enterobacter chuandaensis	93.9872	1342	1572	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	98.38	98.32	0.92	0.92	3	-
GCF_007035645.1	s__Enterobacter asburiae_B	91.8789	1358	1572	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	96.8818	98.31	97.34	0.92	0.85	70	-
GCF_001729805.1	s__Enterobacter roggenkampii	91.7641	1384	1572	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	98.21	95.50	0.89	0.83	197	-
GCF_003634515.1	s__Enterobacter asburiae_A	91.7469	1373	1572	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	91.6852	1362	1572	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.7595	98.68	98.68	0.92	0.92	2	-
GCF_008364625.1	s__Enterobacter dykesii	91.6212	1324	1572	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	96.5795	99.13	97.97	0.97	0.95	7	-
GCF_008080435.1	s__Enterobacter asburiae_C	91.3976	1327	1572	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.5575	N/A	N/A	N/A	N/A	1	-
GCF_002939185.1	s__Enterobacter sichuanensis	90.3323	1257	1572	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	98.38	97.99	0.90	0.85	19	-
GCF_900322725.1	s__Enterobacter quasihormaechei	89.7052	1283	1572	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	99.46	97.61	0.96	0.89	41	-
GCF_000211415.1	s__Enterobacter mori	89.602	1298	1572	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	97.59	96.13	0.88	0.85	23	-
GCF_001729745.1	s__Enterobacter hormaechei_A	89.0245	1294	1572	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	96.63	95.22	0.89	0.83	1867	-
GCF_013375935.1	s__Enterobacter cloacae_O	88.9295	1315	1572	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	98.68	98.59	0.94	0.92	6	-
--------------------------------------------------------------------------------
[2024-01-25 17:51:17,424] [INFO] GTDB search result was written to GCF_900324475.1_EB-247_genomic.fna/result_gtdb.tsv
[2024-01-25 17:51:17,424] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:51:17,427] [INFO] DFAST_QC result json was written to GCF_900324475.1_EB-247_genomic.fna/dqc_result.json
[2024-01-25 17:51:17,427] [INFO] DFAST_QC completed!
[2024-01-25 17:51:17,427] [INFO] Total running time: 0h1m27s