[2024-01-24 11:43:42,333] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:43:42,340] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:43:42,341] [INFO] DQC Reference Directory: /var/lib/cwl/stg8a8ec1cb-77e3-42d6-9afb-6f386a030047/dqc_reference
[2024-01-24 11:43:43,688] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:43:43,689] [INFO] Task started: Prodigal
[2024-01-24 11:43:43,690] [INFO] Running command: gunzip -c /var/lib/cwl/stge9b95e7a-acdb-41ef-ab6c-353112634ee5/GCF_016027695.1_ASM1602769v1_genomic.fna.gz | prodigal -d GCF_016027695.1_ASM1602769v1_genomic.fna/cds.fna -a GCF_016027695.1_ASM1602769v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:43:58,577] [INFO] Task succeeded: Prodigal
[2024-01-24 11:43:58,577] [INFO] Task started: HMMsearch
[2024-01-24 11:43:58,577] [INFO] Running command: hmmsearch --tblout GCF_016027695.1_ASM1602769v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8a8ec1cb-77e3-42d6-9afb-6f386a030047/dqc_reference/reference_markers.hmm GCF_016027695.1_ASM1602769v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:43:59,000] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:43:59,001] [INFO] Found 6/6 markers.
[2024-01-24 11:43:59,041] [INFO] Query marker FASTA was written to GCF_016027695.1_ASM1602769v1_genomic.fna/markers.fasta
[2024-01-24 11:43:59,042] [INFO] Task started: Blastn
[2024-01-24 11:43:59,042] [INFO] Running command: blastn -query GCF_016027695.1_ASM1602769v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8a8ec1cb-77e3-42d6-9afb-6f386a030047/dqc_reference/reference_markers.fasta -out GCF_016027695.1_ASM1602769v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:43:59,907] [INFO] Task succeeded: Blastn
[2024-01-24 11:43:59,911] [INFO] Selected 12 target genomes.
[2024-01-24 11:43:59,911] [INFO] Target genome list was writen to GCF_016027695.1_ASM1602769v1_genomic.fna/target_genomes.txt
[2024-01-24 11:43:59,925] [INFO] Task started: fastANI
[2024-01-24 11:43:59,925] [INFO] Running command: fastANI --query /var/lib/cwl/stge9b95e7a-acdb-41ef-ab6c-353112634ee5/GCF_016027695.1_ASM1602769v1_genomic.fna.gz --refList GCF_016027695.1_ASM1602769v1_genomic.fna/target_genomes.txt --output GCF_016027695.1_ASM1602769v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:44:17,048] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:17,049] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8a8ec1cb-77e3-42d6-9afb-6f386a030047/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:44:17,049] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8a8ec1cb-77e3-42d6-9afb-6f386a030047/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:44:17,059] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:44:17,059] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:44:17,060] [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 asburiae	strain=FDAARGOS_892	GCA_016027695.1	61645	61645	type	True	100.0	1585	1587	95	conclusive
Enterobacter asburiae	strain=ATCC 35953	GCA_001521715.1	61645	61645	type	True	99.9931	1581	1587	95	conclusive
Enterobacter vonholyi	strain=E13	GCA_008364555.1	2797505	2797505	type	True	94.2993	1326	1587	95	below_threshold
Enterobacter roggenkampii	strain=DSM 16690	GCA_001729805.1	1812935	1812935	type	True	93.4028	1342	1587	95	below_threshold
Enterobacter roggenkampii	strain=FDAARGOS 1430	GCA_019047025.1	1812935	1812935	type	True	93.3936	1344	1587	95	below_threshold
Enterobacter roggenkampii	strain=DSM 16690	GCA_024390995.1	1812935	1812935	type	True	93.3402	1267	1587	95	below_threshold
Enterobacter chengduensis	strain=WCHECl-C4 = WCHECh050004	GCA_001984825.2	2494701	2494701	type	True	93.34	1319	1587	95	below_threshold
Enterobacter sichuanensis	strain=WCHECL1597	GCA_025002605.1	2071710	2071710	type	True	91.7319	1281	1587	95	below_threshold
Enterobacter kobei	strain=DSM 13645	GCA_001729765.1	208224	208224	type	True	91.1073	1281	1587	95	below_threshold
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	89.664	1226	1587	95	below_threshold
Enterobacter cloacae	strain=DSM 30054	GCA_021469225.1	550	550	type	True	89.0418	1257	1587	95	below_threshold
Enterobacter hormaechei	strain=FDAARGOS 1433	GCA_019048245.1	158836	158836	suspected-type	True	88.3746	1214	1587	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:44:17,061] [INFO] DFAST Taxonomy check result was written to GCF_016027695.1_ASM1602769v1_genomic.fna/tc_result.tsv
[2024-01-24 11:44:17,062] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:44:17,062] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:44:17,062] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8a8ec1cb-77e3-42d6-9afb-6f386a030047/dqc_reference/checkm_data
[2024-01-24 11:44:17,064] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:44:17,111] [INFO] Task started: CheckM
[2024-01-24 11:44:17,111] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016027695.1_ASM1602769v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016027695.1_ASM1602769v1_genomic.fna/checkm_input GCF_016027695.1_ASM1602769v1_genomic.fna/checkm_result
[2024-01-24 11:45:01,693] [INFO] Task succeeded: CheckM
[2024-01-24 11:45:01,695] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:45:01,718] [INFO] ===== Completeness check finished =====
[2024-01-24 11:45:01,719] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:45:01,719] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016027695.1_ASM1602769v1_genomic.fna/markers.fasta)
[2024-01-24 11:45:01,719] [INFO] Task started: Blastn
[2024-01-24 11:45:01,720] [INFO] Running command: blastn -query GCF_016027695.1_ASM1602769v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8a8ec1cb-77e3-42d6-9afb-6f386a030047/dqc_reference/reference_markers_gtdb.fasta -out GCF_016027695.1_ASM1602769v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:45:02,881] [INFO] Task succeeded: Blastn
[2024-01-24 11:45:02,885] [INFO] Selected 16 target genomes.
[2024-01-24 11:45:02,885] [INFO] Target genome list was writen to GCF_016027695.1_ASM1602769v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:45:02,899] [INFO] Task started: fastANI
[2024-01-24 11:45:02,899] [INFO] Running command: fastANI --query /var/lib/cwl/stge9b95e7a-acdb-41ef-ab6c-353112634ee5/GCF_016027695.1_ASM1602769v1_genomic.fna.gz --refList GCF_016027695.1_ASM1602769v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016027695.1_ASM1602769v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:45:21,623] [INFO] Task succeeded: fastANI
[2024-01-24 11:45:21,638] [INFO] Found 14 fastANI hits (4 hits with ANI > circumscription radius)
[2024-01-24 11:45:21,638] [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_001521715.1	s__Enterobacter asburiae	99.9931	1581	1587	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	96.8818	98.42	96.92	0.89	0.84	32	inconclusive
GCF_007035645.1	s__Enterobacter asburiae_B	96.8992	1362	1587	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	96.8818	98.31	97.34	0.92	0.85	70	inconclusive
GCF_002208095.1	s__Enterobacter cloacae_M	96.7783	1367	1587	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	96.7528	98.28	96.89	0.91	0.85	84	inconclusive
GCF_008364625.1	s__Enterobacter dykesii	96.2234	1309	1587	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	96.5795	99.13	97.97	0.97	0.95	7	-
GCF_003634515.1	s__Enterobacter asburiae_A	96.0364	1336	1587	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	96.0274	97.62	96.46	0.91	0.85	7	inconclusive
GCF_000493015.1	s__Enterobacter sp000493015	95.4765	1338	1587	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	95.2265	1312	1587	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.5575	N/A	N/A	N/A	N/A	1	-
GCF_008364555.1	s__Enterobacter vonholyi	94.2993	1326	1587	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	98.34	98.09	0.94	0.93	8	-
GCF_001022965.1	s__Enterobacter cloacae_L	92.9123	1339	1587	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	91.7572	1260	1587	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	91.1054	1281	1587	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	98.81	98.45	0.89	0.85	141	-
GCF_900322725.1	s__Enterobacter quasihormaechei	88.554	1184	1587	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	88.391	1230	1587	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	98.68	98.59	0.94	0.92	6	-
GCF_000280495.2	s__Kosakonia radicincitans	81.8073	908	1587	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kosakonia	95.7299	99.26	99.13	0.95	0.93	14	-
--------------------------------------------------------------------------------
[2024-01-24 11:45:21,639] [INFO] GTDB search result was written to GCF_016027695.1_ASM1602769v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:45:21,640] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:45:21,643] [INFO] DFAST_QC result json was written to GCF_016027695.1_ASM1602769v1_genomic.fna/dqc_result.json
[2024-01-24 11:45:21,644] [INFO] DFAST_QC completed!
[2024-01-24 11:45:21,644] [INFO] Total running time: 0h1m39s