[2024-01-25 19:10:35,755] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:10:35,756] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:10:35,756] [INFO] DQC Reference Directory: /var/lib/cwl/stgedf464d6-54ec-49a0-a34a-550a0fb46522/dqc_reference
[2024-01-25 19:10:36,890] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:10:36,890] [INFO] Task started: Prodigal
[2024-01-25 19:10:36,890] [INFO] Running command: gunzip -c /var/lib/cwl/stg683fe933-bb52-496b-aa9c-480c2c26ea70/GCF_026344075.1_ASM2634407v1_genomic.fna.gz | prodigal -d GCF_026344075.1_ASM2634407v1_genomic.fna/cds.fna -a GCF_026344075.1_ASM2634407v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:10:48,126] [INFO] Task succeeded: Prodigal
[2024-01-25 19:10:48,127] [INFO] Task started: HMMsearch
[2024-01-25 19:10:48,127] [INFO] Running command: hmmsearch --tblout GCF_026344075.1_ASM2634407v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgedf464d6-54ec-49a0-a34a-550a0fb46522/dqc_reference/reference_markers.hmm GCF_026344075.1_ASM2634407v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:10:48,406] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:10:48,408] [INFO] Found 6/6 markers.
[2024-01-25 19:10:48,450] [INFO] Query marker FASTA was written to GCF_026344075.1_ASM2634407v1_genomic.fna/markers.fasta
[2024-01-25 19:10:48,450] [INFO] Task started: Blastn
[2024-01-25 19:10:48,450] [INFO] Running command: blastn -query GCF_026344075.1_ASM2634407v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgedf464d6-54ec-49a0-a34a-550a0fb46522/dqc_reference/reference_markers.fasta -out GCF_026344075.1_ASM2634407v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:10:49,351] [INFO] Task succeeded: Blastn
[2024-01-25 19:10:49,354] [INFO] Selected 17 target genomes.
[2024-01-25 19:10:49,354] [INFO] Target genome list was writen to GCF_026344075.1_ASM2634407v1_genomic.fna/target_genomes.txt
[2024-01-25 19:10:49,364] [INFO] Task started: fastANI
[2024-01-25 19:10:49,364] [INFO] Running command: fastANI --query /var/lib/cwl/stg683fe933-bb52-496b-aa9c-480c2c26ea70/GCF_026344075.1_ASM2634407v1_genomic.fna.gz --refList GCF_026344075.1_ASM2634407v1_genomic.fna/target_genomes.txt --output GCF_026344075.1_ASM2634407v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:11:07,843] [INFO] Task succeeded: fastANI
[2024-01-25 19:11:07,844] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgedf464d6-54ec-49a0-a34a-550a0fb46522/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:11:07,844] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgedf464d6-54ec-49a0-a34a-550a0fb46522/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:11:07,854] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:11:07,854] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:11:07,854] [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	95.5973	1414	1560	95	conclusive
Enterobacter bugandensis	strain=FDAARGOS 1427	GCA_019046905.1	881260	881260	type	True	95.5331	1420	1560	95	conclusive
Enterobacter asburiae	strain=ATCC 35953	GCA_001521715.1	61645	61645	type	True	92.0726	1298	1560	95	below_threshold
Enterobacter asburiae	strain=FDAARGOS_892	GCA_016027695.1	61645	61645	type	True	92.0606	1288	1560	95	below_threshold
Enterobacter roggenkampii	strain=DSM 16690	GCA_024390995.1	1812935	1812935	type	True	91.7391	1248	1560	95	below_threshold
Enterobacter roggenkampii	strain=FDAARGOS 1430	GCA_019047025.1	1812935	1812935	type	True	91.6609	1339	1560	95	below_threshold
Enterobacter roggenkampii	strain=DSM 16690	GCA_001729805.1	1812935	1812935	type	True	91.5999	1354	1560	95	below_threshold
Enterobacter kobei	strain=DSM 13645	GCA_001729765.1	208224	208224	type	True	91.2919	1321	1560	95	below_threshold
Enterobacter sichuanensis	strain=WCHECL1597	GCA_002939185.1	2071710	2071710	type	True	90.4638	1240	1560	95	below_threshold
Enterobacter sichuanensis	strain=WCHECL1597	GCA_025002605.1	2071710	2071710	type	True	90.4559	1274	1560	95	below_threshold
Enterobacter quasimori	strain=090044	GCA_003964905.1	2838947	2838947	type	True	90.274	1296	1560	95	below_threshold
Enterobacter mori	strain=LMG 25706	GCA_000211415.1	539813	539813	type	True	89.8002	1286	1560	95	below_threshold
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	89.3456	1268	1560	95	below_threshold
Enterobacter hormaechei subsp. hormaechei	strain=ATCC 49162	GCA_000213995.1	301105	158836	type	True	88.9329	1272	1560	95	below_threshold
Enterobacter cloacae	strain=DSM 30054	GCA_021469225.1	550	550	type	True	88.8822	1328	1560	95	below_threshold
Enterobacter hormaechei	strain=FDAARGOS 1433	GCA_019048245.1	158836	158836	suspected-type	True	88.8819	1286	1560	95	below_threshold
Enterobacter hormaechei subsp. hormaechei	strain=ATCC 49162	GCA_001875655.1	301105	158836	type	True	88.8108	1286	1560	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:11:07,856] [INFO] DFAST Taxonomy check result was written to GCF_026344075.1_ASM2634407v1_genomic.fna/tc_result.tsv
[2024-01-25 19:11:07,856] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:11:07,857] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:11:07,857] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgedf464d6-54ec-49a0-a34a-550a0fb46522/dqc_reference/checkm_data
[2024-01-25 19:11:07,857] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:11:07,902] [INFO] Task started: CheckM
[2024-01-25 19:11:07,902] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_026344075.1_ASM2634407v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_026344075.1_ASM2634407v1_genomic.fna/checkm_input GCF_026344075.1_ASM2634407v1_genomic.fna/checkm_result
[2024-01-25 19:11:42,789] [INFO] Task succeeded: CheckM
[2024-01-25 19:11:42,790] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:11:42,809] [INFO] ===== Completeness check finished =====
[2024-01-25 19:11:42,809] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:11:42,809] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_026344075.1_ASM2634407v1_genomic.fna/markers.fasta)
[2024-01-25 19:11:42,809] [INFO] Task started: Blastn
[2024-01-25 19:11:42,810] [INFO] Running command: blastn -query GCF_026344075.1_ASM2634407v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgedf464d6-54ec-49a0-a34a-550a0fb46522/dqc_reference/reference_markers_gtdb.fasta -out GCF_026344075.1_ASM2634407v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:11:44,280] [INFO] Task succeeded: Blastn
[2024-01-25 19:11:44,282] [INFO] Selected 16 target genomes.
[2024-01-25 19:11:44,282] [INFO] Target genome list was writen to GCF_026344075.1_ASM2634407v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:11:44,298] [INFO] Task started: fastANI
[2024-01-25 19:11:44,298] [INFO] Running command: fastANI --query /var/lib/cwl/stg683fe933-bb52-496b-aa9c-480c2c26ea70/GCF_026344075.1_ASM2634407v1_genomic.fna.gz --refList GCF_026344075.1_ASM2634407v1_genomic.fna/target_genomes_gtdb.txt --output GCF_026344075.1_ASM2634407v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:12:02,807] [INFO] Task succeeded: fastANI
[2024-01-25 19:12:02,817] [INFO] Found 16 fastANI hits (2 hits with ANI > circumscription radius)
[2024-01-25 19:12:02,817] [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	95.5973	1414	1560	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	98.49	95.52	0.94	0.88	115	inconclusive
GCF_011754535.1	s__Enterobacter cloacae_N	95.0151	1425	1560	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	99.03	98.99	0.93	0.91	4	inconclusive
GCF_003594915.1	s__Enterobacter chuandaensis	94.4113	1362	1560	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	92.091	1333	1560	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	96.8818	98.31	97.34	0.92	0.85	70	-
GCF_001521715.1	s__Enterobacter asburiae	92.0726	1298	1560	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	92.0371	1370	1560	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	96.0274	97.62	96.46	0.91	0.85	7	-
GCF_008364625.1	s__Enterobacter dykesii	91.932	1326	1560	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	96.5795	99.13	97.97	0.97	0.95	7	-
GCF_000493015.1	s__Enterobacter sp000493015	91.761	1344	1560	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	91.6835	1332	1560	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.5575	N/A	N/A	N/A	N/A	1	-
GCF_001729805.1	s__Enterobacter roggenkampii	91.6055	1353	1560	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	98.21	95.50	0.89	0.83	197	-
GCF_008364555.1	s__Enterobacter vonholyi	91.4984	1330	1560	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	98.34	98.09	0.94	0.93	8	-
GCF_001729765.1	s__Enterobacter kobei	91.2851	1322	1560	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	98.81	98.45	0.89	0.85	141	-
GCF_002939185.1	s__Enterobacter sichuanensis	90.4638	1240	1560	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	98.38	97.99	0.90	0.85	19	-
GCF_000211415.1	s__Enterobacter mori	89.7925	1288	1560	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	97.59	96.13	0.88	0.85	23	-
GCF_900322725.1	s__Enterobacter quasihormaechei	89.0119	1263	1560	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	99.46	97.61	0.96	0.89	41	-
GCF_013375935.1	s__Enterobacter cloacae_O	88.8468	1298	1560	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 19:12:02,819] [INFO] GTDB search result was written to GCF_026344075.1_ASM2634407v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:12:02,819] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:12:02,823] [INFO] DFAST_QC result json was written to GCF_026344075.1_ASM2634407v1_genomic.fna/dqc_result.json
[2024-01-25 19:12:02,823] [INFO] DFAST_QC completed!
[2024-01-25 19:12:02,823] [INFO] Total running time: 0h1m27s