[2024-01-24 13:08:58,073] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:08:58,094] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:08:58,094] [INFO] DQC Reference Directory: /var/lib/cwl/stg808c0ed2-6467-4aee-91de-15a5c3fa0bda/dqc_reference
[2024-01-24 13:08:59,359] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:08:59,360] [INFO] Task started: Prodigal
[2024-01-24 13:08:59,360] [INFO] Running command: gunzip -c /var/lib/cwl/stgfd7191a9-0c6c-48ab-90b4-2f81ffb82c67/GCF_000735515.1_GLAD_DRAFTv1_genomic.fna.gz | prodigal -d GCF_000735515.1_GLAD_DRAFTv1_genomic.fna/cds.fna -a GCF_000735515.1_GLAD_DRAFTv1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:09:12,275] [INFO] Task succeeded: Prodigal
[2024-01-24 13:09:12,275] [INFO] Task started: HMMsearch
[2024-01-24 13:09:12,275] [INFO] Running command: hmmsearch --tblout GCF_000735515.1_GLAD_DRAFTv1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg808c0ed2-6467-4aee-91de-15a5c3fa0bda/dqc_reference/reference_markers.hmm GCF_000735515.1_GLAD_DRAFTv1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:09:12,561] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:09:12,562] [INFO] Found 6/6 markers.
[2024-01-24 13:09:12,613] [INFO] Query marker FASTA was written to GCF_000735515.1_GLAD_DRAFTv1_genomic.fna/markers.fasta
[2024-01-24 13:09:12,614] [INFO] Task started: Blastn
[2024-01-24 13:09:12,614] [INFO] Running command: blastn -query GCF_000735515.1_GLAD_DRAFTv1_genomic.fna/markers.fasta -db /var/lib/cwl/stg808c0ed2-6467-4aee-91de-15a5c3fa0bda/dqc_reference/reference_markers.fasta -out GCF_000735515.1_GLAD_DRAFTv1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:09:13,477] [INFO] Task succeeded: Blastn
[2024-01-24 13:09:13,480] [INFO] Selected 23 target genomes.
[2024-01-24 13:09:13,480] [INFO] Target genome list was writen to GCF_000735515.1_GLAD_DRAFTv1_genomic.fna/target_genomes.txt
[2024-01-24 13:09:13,569] [INFO] Task started: fastANI
[2024-01-24 13:09:13,569] [INFO] Running command: fastANI --query /var/lib/cwl/stgfd7191a9-0c6c-48ab-90b4-2f81ffb82c67/GCF_000735515.1_GLAD_DRAFTv1_genomic.fna.gz --refList GCF_000735515.1_GLAD_DRAFTv1_genomic.fna/target_genomes.txt --output GCF_000735515.1_GLAD_DRAFTv1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:09:35,476] [INFO] Task succeeded: fastANI
[2024-01-24 13:09:35,476] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg808c0ed2-6467-4aee-91de-15a5c3fa0bda/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:09:35,477] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg808c0ed2-6467-4aee-91de-15a5c3fa0bda/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:09:35,496] [INFO] Found 20 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:09:35,496] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:09:35,496] [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
Leclercia adecarboxylata	strain=ATCC 23216	GCA_000735515.1	83655	83655	suspected-type	True	100.0	1592	1597	95	conclusive
Leclercia adecarboxylata	strain=FDAARGOS_1505	GCA_020097395.1	83655	83655	suspected-type	True	99.9959	1596	1597	95	conclusive
Leclercia adecarboxylata	strain=NBRC 102595	GCA_001515505.1	83655	83655	suspected-type	True	99.9901	1581	1597	95	conclusive
Enterobacter roggenkampii	strain=DSM 16690	GCA_024390995.1	1812935	1812935	type	True	84.4856	1046	1597	95	below_threshold
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	84.2609	1098	1597	95	below_threshold
Enterobacter bugandensis	strain=FDAARGOS 1427	GCA_019046905.1	881260	881260	type	True	84.246	1072	1597	95	below_threshold
Enterobacter roggenkampii	strain=FDAARGOS 1430	GCA_019047025.1	1812935	1812935	type	True	84.2233	1080	1597	95	below_threshold
Enterobacter chengduensis	strain=WCHECl-C4 = WCHECh050004	GCA_001984825.2	2494701	2494701	type	True	84.2231	1087	1597	95	below_threshold
Enterobacter bugandensis		GCA_900324475.1	881260	881260	type	True	84.2138	1086	1597	95	below_threshold
Leclercia pneumoniae	strain=49125	GCA_017348915.1	2815358	2815358	type	True	84.2133	1120	1597	95	below_threshold
Enterobacter hormaechei	strain=FDAARGOS 1433	GCA_019048245.1	158836	158836	suspected-type	True	84.1492	1084	1597	95	below_threshold
Leclercia pneumoniae	strain=49125	GCA_018987305.1	2815358	2815358	type	True	84.147	1124	1597	95	below_threshold
Enterobacter cloacae	strain=DSM 30054	GCA_021469225.1	550	550	type	True	84.0837	1078	1597	95	below_threshold
Enterobacter cancerogenus	strain=FDAARGOS 1428	GCA_019047785.1	69218	69218	type	True	84.0057	1052	1597	95	below_threshold
Enterobacter sichuanensis	strain=WCHECL1597	GCA_002939185.1	2071710	2071710	type	True	83.9953	1027	1597	95	below_threshold
Enterobacter cancerogenus		GCA_900185905.1	69218	69218	type	True	83.9503	1063	1597	95	below_threshold
Enterobacter kobei	strain=DSM 13645	GCA_001729765.1	208224	208224	type	True	83.9428	1045	1597	95	below_threshold
Enterobacter sichuanensis	strain=WCHECL1597	GCA_025002605.1	2071710	2071710	type	True	83.9333	1056	1597	95	below_threshold
Shewanella khirikhana	strain=TH2012	GCA_003957745.1	1965282	1965282	type	True	77.0104	75	1597	95	below_threshold
Oceanimonas marisflavi	strain=102-Na3	GCA_003049725.1	2059724	2059724	type	True	76.4188	90	1597	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:09:35,498] [INFO] DFAST Taxonomy check result was written to GCF_000735515.1_GLAD_DRAFTv1_genomic.fna/tc_result.tsv
[2024-01-24 13:09:35,498] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:09:35,498] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:09:35,499] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg808c0ed2-6467-4aee-91de-15a5c3fa0bda/dqc_reference/checkm_data
[2024-01-24 13:09:35,500] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:09:35,549] [INFO] Task started: CheckM
[2024-01-24 13:09:35,550] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000735515.1_GLAD_DRAFTv1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000735515.1_GLAD_DRAFTv1_genomic.fna/checkm_input GCF_000735515.1_GLAD_DRAFTv1_genomic.fna/checkm_result
[2024-01-24 13:10:15,895] [INFO] Task succeeded: CheckM
[2024-01-24 13:10:15,896] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:10:15,914] [INFO] ===== Completeness check finished =====
[2024-01-24 13:10:15,915] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:10:15,915] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000735515.1_GLAD_DRAFTv1_genomic.fna/markers.fasta)
[2024-01-24 13:10:15,916] [INFO] Task started: Blastn
[2024-01-24 13:10:15,916] [INFO] Running command: blastn -query GCF_000735515.1_GLAD_DRAFTv1_genomic.fna/markers.fasta -db /var/lib/cwl/stg808c0ed2-6467-4aee-91de-15a5c3fa0bda/dqc_reference/reference_markers_gtdb.fasta -out GCF_000735515.1_GLAD_DRAFTv1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:17,084] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:17,088] [INFO] Selected 12 target genomes.
[2024-01-24 13:10:17,088] [INFO] Target genome list was writen to GCF_000735515.1_GLAD_DRAFTv1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:10:17,100] [INFO] Task started: fastANI
[2024-01-24 13:10:17,101] [INFO] Running command: fastANI --query /var/lib/cwl/stgfd7191a9-0c6c-48ab-90b4-2f81ffb82c67/GCF_000735515.1_GLAD_DRAFTv1_genomic.fna.gz --refList GCF_000735515.1_GLAD_DRAFTv1_genomic.fna/target_genomes_gtdb.txt --output GCF_000735515.1_GLAD_DRAFTv1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:10:30,584] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:30,595] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:10:30,595] [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
GCA_901472455.1	s__Leclercia adecarboxylata	99.7858	1597	1597	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Leclercia	95.0	98.53	98.09	0.95	0.87	86	conclusive
GCF_006874705.1	s__Leclercia adecarboxylata_C	91.717	1333	1597	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Leclercia	95.0	98.71	98.25	0.93	0.90	13	-
GCF_011290365.1	s__Leclercia sp003024485	91.6751	1347	1597	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Leclercia	95.0	98.06	98.06	0.90	0.90	2	-
GCA_002360945.1	s__Leclercia adecarboxylata_B	91.5602	1298	1597	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Leclercia	95.0	99.97	99.97	0.98	0.98	2	-
GCF_006171285.1	s__Leclercia adecarboxylata_A	89.5331	1346	1597	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Leclercia	95.0	97.80	96.55	0.92	0.89	4	-
GCF_002902985.1	s__Leclercia sp002902985	88.9748	1325	1597	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Leclercia	95.0	98.13	96.37	0.93	0.86	16	-
GCF_013927005.1	s__Enterobacter sp013927005	83.8252	1111	1597	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018323985.1	s__Enterobacter_D kobei_A	82.3274	943	1597	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter_D	95.0	99.37	98.44	0.98	0.93	6	-
GCF_000735365.1	s__Kluyvera ascorbata	82.1497	866	1597	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kluyvera	95.0	98.94	97.70	0.94	0.89	5	-
GCF_002915575.1	s__Superficieibacter electus	81.2263	788	1597	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Superficieibacter	95.0	99.98	99.98	1.00	1.00	2	-
GCF_014155765.1	s__Pantoea dispersa	79.6057	551	1597	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	97.93	96.36	0.92	0.86	38	-
GCA_002386445.1	s__Pseudomonas_E sp002386445	79.1442	86	1597	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:10:30,596] [INFO] GTDB search result was written to GCF_000735515.1_GLAD_DRAFTv1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:10:30,597] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:10:30,603] [INFO] DFAST_QC result json was written to GCF_000735515.1_GLAD_DRAFTv1_genomic.fna/dqc_result.json
[2024-01-24 13:10:30,603] [INFO] DFAST_QC completed!
[2024-01-24 13:10:30,604] [INFO] Total running time: 0h1m33s