[2023-06-28 11:10:06,691] [INFO] DFAST_QC pipeline started.
[2023-06-28 11:10:06,693] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 11:10:06,694] [INFO] DQC Reference Directory: /var/lib/cwl/stg7e893132-c8b2-4080-a8be-a377fe9a332f/dqc_reference
[2023-06-28 11:10:08,020] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 11:10:08,021] [INFO] Task started: Prodigal
[2023-06-28 11:10:08,021] [INFO] Running command: gunzip -c /var/lib/cwl/stg4307ec31-bb40-4258-b3e8-bd8067b37b91/GCA_913775745.1_S1C10298_SP242_genomic.fna.gz | prodigal -d GCA_913775745.1_S1C10298_SP242_genomic.fna/cds.fna -a GCA_913775745.1_S1C10298_SP242_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 11:10:19,991] [INFO] Task succeeded: Prodigal
[2023-06-28 11:10:19,991] [INFO] Task started: HMMsearch
[2023-06-28 11:10:19,991] [INFO] Running command: hmmsearch --tblout GCA_913775745.1_S1C10298_SP242_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7e893132-c8b2-4080-a8be-a377fe9a332f/dqc_reference/reference_markers.hmm GCA_913775745.1_S1C10298_SP242_genomic.fna/protein.faa > /dev/null
[2023-06-28 11:10:20,304] [INFO] Task succeeded: HMMsearch
[2023-06-28 11:10:20,306] [INFO] Found 6/6 markers.
[2023-06-28 11:10:20,349] [INFO] Query marker FASTA was written to GCA_913775745.1_S1C10298_SP242_genomic.fna/markers.fasta
[2023-06-28 11:10:20,350] [INFO] Task started: Blastn
[2023-06-28 11:10:20,350] [INFO] Running command: blastn -query GCA_913775745.1_S1C10298_SP242_genomic.fna/markers.fasta -db /var/lib/cwl/stg7e893132-c8b2-4080-a8be-a377fe9a332f/dqc_reference/reference_markers.fasta -out GCA_913775745.1_S1C10298_SP242_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 11:10:21,305] [INFO] Task succeeded: Blastn
[2023-06-28 11:10:21,309] [INFO] Selected 13 target genomes.
[2023-06-28 11:10:21,309] [INFO] Target genome list was writen to GCA_913775745.1_S1C10298_SP242_genomic.fna/target_genomes.txt
[2023-06-28 11:10:21,311] [INFO] Task started: fastANI
[2023-06-28 11:10:21,311] [INFO] Running command: fastANI --query /var/lib/cwl/stg4307ec31-bb40-4258-b3e8-bd8067b37b91/GCA_913775745.1_S1C10298_SP242_genomic.fna.gz --refList GCA_913775745.1_S1C10298_SP242_genomic.fna/target_genomes.txt --output GCA_913775745.1_S1C10298_SP242_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 11:10:36,673] [INFO] Task succeeded: fastANI
[2023-06-28 11:10:36,674] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7e893132-c8b2-4080-a8be-a377fe9a332f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 11:10:36,674] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7e893132-c8b2-4080-a8be-a377fe9a332f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 11:10:36,690] [INFO] Found 13 fastANI hits (3 hits with ANI > threshold)
[2023-06-28 11:10:36,690] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-28 11:10:36,691] [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=DSM 16690	GCA_024390995.1	1812935	1812935	type	True	98.4837	1297	1482	95	conclusive
Enterobacter roggenkampii	strain=FDAARGOS 1430	GCA_019047025.1	1812935	1812935	type	True	98.4564	1396	1482	95	conclusive
Enterobacter roggenkampii	strain=DSM 16690	GCA_001729805.1	1812935	1812935	type	True	98.4393	1395	1482	95	conclusive
Enterobacter vonholyi	strain=E13	GCA_008364555.1	2797505	2797505	type	True	94.3015	1326	1482	95	below_threshold
Enterobacter asburiae	strain=FDAARGOS_892	GCA_016027695.1	61645	61645	type	True	93.2577	1282	1482	95	below_threshold
Enterobacter asburiae	strain=ATCC 35953	GCA_001521715.1	61645	61645	type	True	93.2447	1287	1482	95	below_threshold
Enterobacter chengduensis	strain=WCHECl-C4 = WCHECh050004	GCA_001984825.2	2494701	2494701	type	True	92.781	1317	1482	95	below_threshold
Enterobacter sichuanensis	strain=WCHECL1597	GCA_025002605.1	2071710	2071710	type	True	91.9569	1281	1482	95	below_threshold
Enterobacter sichuanensis	strain=WCHECL1597	GCA_002939185.1	2071710	2071710	type	True	91.8893	1237	1482	95	below_threshold
Enterobacter kobei	strain=DSM 13645	GCA_001729765.1	208224	208224	type	True	90.5884	1268	1482	95	below_threshold
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	88.9806	1243	1482	95	below_threshold
Enterobacter cloacae	strain=DSM 30054	GCA_021469225.1	550	550	type	True	88.9274	1266	1482	95	below_threshold
Enterobacter hormaechei	strain=FDAARGOS 1433	GCA_019048245.1	158836	158836	suspected-type	True	88.054	1215	1482	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 11:10:36,693] [INFO] DFAST Taxonomy check result was written to GCA_913775745.1_S1C10298_SP242_genomic.fna/tc_result.tsv
[2023-06-28 11:10:36,693] [INFO] ===== Taxonomy check completed =====
[2023-06-28 11:10:36,693] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 11:10:36,693] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7e893132-c8b2-4080-a8be-a377fe9a332f/dqc_reference/checkm_data
[2023-06-28 11:10:36,694] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 11:10:36,744] [INFO] Task started: CheckM
[2023-06-28 11:10:36,745] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_913775745.1_S1C10298_SP242_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_913775745.1_S1C10298_SP242_genomic.fna/checkm_input GCA_913775745.1_S1C10298_SP242_genomic.fna/checkm_result
[2023-06-28 11:11:15,785] [INFO] Task succeeded: CheckM
[2023-06-28 11:11:15,786] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 11:11:15,807] [INFO] ===== Completeness check finished =====
[2023-06-28 11:11:15,807] [INFO] ===== Start GTDB Search =====
[2023-06-28 11:11:15,808] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_913775745.1_S1C10298_SP242_genomic.fna/markers.fasta)
[2023-06-28 11:11:15,808] [INFO] Task started: Blastn
[2023-06-28 11:11:15,808] [INFO] Running command: blastn -query GCA_913775745.1_S1C10298_SP242_genomic.fna/markers.fasta -db /var/lib/cwl/stg7e893132-c8b2-4080-a8be-a377fe9a332f/dqc_reference/reference_markers_gtdb.fasta -out GCA_913775745.1_S1C10298_SP242_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 11:11:17,293] [INFO] Task succeeded: Blastn
[2023-06-28 11:11:17,310] [INFO] Selected 13 target genomes.
[2023-06-28 11:11:17,311] [INFO] Target genome list was writen to GCA_913775745.1_S1C10298_SP242_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 11:11:17,314] [INFO] Task started: fastANI
[2023-06-28 11:11:17,314] [INFO] Running command: fastANI --query /var/lib/cwl/stg4307ec31-bb40-4258-b3e8-bd8067b37b91/GCA_913775745.1_S1C10298_SP242_genomic.fna.gz --refList GCA_913775745.1_S1C10298_SP242_genomic.fna/target_genomes_gtdb.txt --output GCA_913775745.1_S1C10298_SP242_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 11:11:32,123] [INFO] Task succeeded: fastANI
[2023-06-28 11:11:32,136] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 11:11:32,137] [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	98.4393	1395	1482	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	94.3015	1326	1482	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	94.2207	1336	1482	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0476	98.37	98.04	0.95	0.92	11	-
GCF_008364625.1	s__Enterobacter dykesii	93.3872	1289	1482	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	96.5795	99.13	97.97	0.97	0.95	7	-
GCF_007035645.1	s__Enterobacter asburiae_B	93.3168	1317	1482	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	96.8818	98.31	97.34	0.92	0.85	70	-
GCF_003634515.1	s__Enterobacter asburiae_A	93.2578	1332	1482	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	93.207	1312	1482	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	93.0438	1311	1482	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	92.781	1317	1482	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	92.503	1324	1482	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	91.8893	1237	1482	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	98.38	97.99	0.90	0.85	19	-
GCF_011754535.1	s__Enterobacter cloacae_N	91.7461	1313	1482	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	99.03	98.99	0.93	0.91	4	-
GCF_001729765.1	s__Enterobacter kobei	90.5884	1268	1482	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	98.81	98.45	0.89	0.85	141	-
--------------------------------------------------------------------------------
[2023-06-28 11:11:32,139] [INFO] GTDB search result was written to GCA_913775745.1_S1C10298_SP242_genomic.fna/result_gtdb.tsv
[2023-06-28 11:11:32,139] [INFO] ===== GTDB Search completed =====
[2023-06-28 11:11:32,143] [INFO] DFAST_QC result json was written to GCA_913775745.1_S1C10298_SP242_genomic.fna/dqc_result.json
[2023-06-28 11:11:32,143] [INFO] DFAST_QC completed!
[2023-06-28 11:11:32,143] [INFO] Total running time: 0h1m25s