[2024-01-25 18:49:35,425] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:49:35,429] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:49:35,429] [INFO] DQC Reference Directory: /var/lib/cwl/stg8f9345b8-af8a-40da-a5e7-2836a7cfc6d1/dqc_reference
[2024-01-25 18:49:36,592] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:49:36,592] [INFO] Task started: Prodigal
[2024-01-25 18:49:36,593] [INFO] Running command: gunzip -c /var/lib/cwl/stg060956a2-9546-4fc7-a58c-e8ba5b2e183a/GCF_020097195.1_ASM2009719v1_genomic.fna.gz | prodigal -d GCF_020097195.1_ASM2009719v1_genomic.fna/cds.fna -a GCF_020097195.1_ASM2009719v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:49:48,044] [INFO] Task succeeded: Prodigal
[2024-01-25 18:49:48,045] [INFO] Task started: HMMsearch
[2024-01-25 18:49:48,045] [INFO] Running command: hmmsearch --tblout GCF_020097195.1_ASM2009719v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8f9345b8-af8a-40da-a5e7-2836a7cfc6d1/dqc_reference/reference_markers.hmm GCF_020097195.1_ASM2009719v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:49:48,354] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:49:48,355] [INFO] Found 6/6 markers.
[2024-01-25 18:49:48,398] [INFO] Query marker FASTA was written to GCF_020097195.1_ASM2009719v1_genomic.fna/markers.fasta
[2024-01-25 18:49:48,398] [INFO] Task started: Blastn
[2024-01-25 18:49:48,399] [INFO] Running command: blastn -query GCF_020097195.1_ASM2009719v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8f9345b8-af8a-40da-a5e7-2836a7cfc6d1/dqc_reference/reference_markers.fasta -out GCF_020097195.1_ASM2009719v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:49:49,237] [INFO] Task succeeded: Blastn
[2024-01-25 18:49:49,239] [INFO] Selected 13 target genomes.
[2024-01-25 18:49:49,240] [INFO] Target genome list was writen to GCF_020097195.1_ASM2009719v1_genomic.fna/target_genomes.txt
[2024-01-25 18:49:49,247] [INFO] Task started: fastANI
[2024-01-25 18:49:49,247] [INFO] Running command: fastANI --query /var/lib/cwl/stg060956a2-9546-4fc7-a58c-e8ba5b2e183a/GCF_020097195.1_ASM2009719v1_genomic.fna.gz --refList GCF_020097195.1_ASM2009719v1_genomic.fna/target_genomes.txt --output GCF_020097195.1_ASM2009719v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:50:05,646] [INFO] Task succeeded: fastANI
[2024-01-25 18:50:05,646] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8f9345b8-af8a-40da-a5e7-2836a7cfc6d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:50:05,647] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8f9345b8-af8a-40da-a5e7-2836a7cfc6d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:50:05,655] [INFO] Found 13 fastANI hits (7 hits with ANI > threshold)
[2024-01-25 18:50:05,656] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:50:05,656] [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 hormaechei subsp. oharae	strain=FDAARGOS_1533	GCA_020097195.1	301102	158836	type	True	100.0	1572	1575	95	conclusive
Enterobacter hormaechei subsp. oharae	strain=DSM 16687	GCA_001729705.1	301102	158836	type	True	99.9998	1571	1575	95	conclusive
Enterobacter hormaechei subsp. steigerwaltii	strain=DSM 16691	GCA_001729725.1	299766	158836	type	True	97.5314	1419	1575	95	conclusive
Enterobacter hormaechei subsp. xiangfangensis	strain=LMG27195	GCA_001729785.1	1296536	158836	type	True	97.1292	1417	1575	95	conclusive
Enterobacter hormaechei subsp. hoffmannii	strain=DSM 14563	GCA_001729745.1	1812934	158836	type	True	95.9116	1388	1575	95	conclusive
Enterobacter hormaechei subsp. hormaechei	strain=ATCC 49162	GCA_001875655.1	301105	158836	type	True	95.1603	1401	1575	95	conclusive
Enterobacter hormaechei	strain=FDAARGOS 1433	GCA_019048245.1	158836	158836	suspected-type	True	95.1592	1406	1575	95	conclusive
Enterobacter roggenkampii	strain=DSM 16690	GCA_024390995.1	1812935	1812935	type	True	88.4761	1231	1575	95	below_threshold
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	88.3809	1272	1575	95	below_threshold
Enterobacter sichuanensis	strain=WCHECL1597	GCA_025002605.1	2071710	2071710	type	True	87.8526	1206	1575	95	below_threshold
Enterobacter cloacae	strain=DSM 30054	GCA_021469225.1	550	550	type	True	87.7371	1310	1575	95	below_threshold
Leclercia pneumoniae	strain=49125	GCA_017348915.1	2815358	2815358	type	True	84.3659	1069	1575	95	below_threshold
Leclercia pneumoniae	strain=49125	GCA_018987305.1	2815358	2815358	type	True	84.3524	1064	1575	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:50:05,658] [INFO] DFAST Taxonomy check result was written to GCF_020097195.1_ASM2009719v1_genomic.fna/tc_result.tsv
[2024-01-25 18:50:05,659] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:50:05,659] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:50:05,659] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8f9345b8-af8a-40da-a5e7-2836a7cfc6d1/dqc_reference/checkm_data
[2024-01-25 18:50:05,660] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:50:05,706] [INFO] Task started: CheckM
[2024-01-25 18:50:05,707] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020097195.1_ASM2009719v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020097195.1_ASM2009719v1_genomic.fna/checkm_input GCF_020097195.1_ASM2009719v1_genomic.fna/checkm_result
[2024-01-25 18:50:40,854] [INFO] Task succeeded: CheckM
[2024-01-25 18:50:40,855] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:50:40,873] [INFO] ===== Completeness check finished =====
[2024-01-25 18:50:40,873] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:50:40,874] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020097195.1_ASM2009719v1_genomic.fna/markers.fasta)
[2024-01-25 18:50:40,874] [INFO] Task started: Blastn
[2024-01-25 18:50:40,874] [INFO] Running command: blastn -query GCF_020097195.1_ASM2009719v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8f9345b8-af8a-40da-a5e7-2836a7cfc6d1/dqc_reference/reference_markers_gtdb.fasta -out GCF_020097195.1_ASM2009719v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:50:41,948] [INFO] Task succeeded: Blastn
[2024-01-25 18:50:41,952] [INFO] Selected 12 target genomes.
[2024-01-25 18:50:41,952] [INFO] Target genome list was writen to GCF_020097195.1_ASM2009719v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:50:41,961] [INFO] Task started: fastANI
[2024-01-25 18:50:41,961] [INFO] Running command: fastANI --query /var/lib/cwl/stg060956a2-9546-4fc7-a58c-e8ba5b2e183a/GCF_020097195.1_ASM2009719v1_genomic.fna.gz --refList GCF_020097195.1_ASM2009719v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020097195.1_ASM2009719v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:50:56,794] [INFO] Task succeeded: fastANI
[2024-01-25 18:50:56,803] [INFO] Found 12 fastANI hits (3 hits with ANI > circumscription radius)
[2024-01-25 18:50:56,803] [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_001729745.1	s__Enterobacter hormaechei_A	95.9142	1389	1575	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	96.63	95.22	0.89	0.83	1867	inconclusive
GCF_001875655.1	s__Enterobacter hormaechei	95.1603	1401	1575	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	99.46	98.52	0.92	0.86	32	inconclusive
GCF_011078175.1	s__Enterobacter cloacae_Q	95.0784	1324	1575	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	100.00	100.00	1.00	1.00	2	inconclusive
GCF_900322725.1	s__Enterobacter quasihormaechei	93.7388	1386	1575	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	91.4732	1361	1575	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	98.68	98.59	0.94	0.92	6	-
GCF_900324475.1	s__Enterobacter bugandensis	89.1733	1292	1575	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	98.49	95.52	0.94	0.88	115	-
GCF_003594915.1	s__Enterobacter chuandaensis	88.9345	1271	1575	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	98.38	98.32	0.92	0.92	3	-
GCF_000025565.1	s__Enterobacter cloacae	87.8316	1322	1575	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	98.05	95.14	0.91	0.80	129	-
GCF_017348915.1	s__UBA7405 sp000755535	84.3715	1068	1575	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__UBA7405	95.0	98.56	97.85	0.93	0.89	10	-
GCF_009363175.1	s__Citrobacter_A telavivensis	82.2933	915	1575	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter_A	95.0	99.99	99.99	1.00	1.00	2	-
GCF_004353845.1	s__Citrobacter freundii_E	81.9423	891	1575	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter	95.0	99.27	99.27	0.92	0.92	2	-
GCF_010231475.1	s__Citrobacter sp010231475	81.463	835	1575	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:50:56,804] [INFO] GTDB search result was written to GCF_020097195.1_ASM2009719v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:50:56,805] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:50:56,808] [INFO] DFAST_QC result json was written to GCF_020097195.1_ASM2009719v1_genomic.fna/dqc_result.json
[2024-01-25 18:50:56,808] [INFO] DFAST_QC completed!
[2024-01-25 18:50:56,808] [INFO] Total running time: 0h1m21s