[2024-01-24 11:43:25,084] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:43:25,086] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:43:25,086] [INFO] DQC Reference Directory: /var/lib/cwl/stg68b3e92a-7344-43e2-86d6-fa64a8d3127d/dqc_reference
[2024-01-24 11:43:30,064] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:43:30,065] [INFO] Task started: Prodigal
[2024-01-24 11:43:30,065] [INFO] Running command: gunzip -c /var/lib/cwl/stg71c2a624-4536-448c-bb4b-ae758a7fe7c9/GCF_019047465.1_ASM1904746v1_genomic.fna.gz | prodigal -d GCF_019047465.1_ASM1904746v1_genomic.fna/cds.fna -a GCF_019047465.1_ASM1904746v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:43:42,573] [INFO] Task succeeded: Prodigal
[2024-01-24 11:43:42,574] [INFO] Task started: HMMsearch
[2024-01-24 11:43:42,574] [INFO] Running command: hmmsearch --tblout GCF_019047465.1_ASM1904746v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg68b3e92a-7344-43e2-86d6-fa64a8d3127d/dqc_reference/reference_markers.hmm GCF_019047465.1_ASM1904746v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:43:42,892] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:43:42,894] [INFO] Found 6/6 markers.
[2024-01-24 11:43:42,932] [INFO] Query marker FASTA was written to GCF_019047465.1_ASM1904746v1_genomic.fna/markers.fasta
[2024-01-24 11:43:42,932] [INFO] Task started: Blastn
[2024-01-24 11:43:42,932] [INFO] Running command: blastn -query GCF_019047465.1_ASM1904746v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg68b3e92a-7344-43e2-86d6-fa64a8d3127d/dqc_reference/reference_markers.fasta -out GCF_019047465.1_ASM1904746v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:43:43,847] [INFO] Task succeeded: Blastn
[2024-01-24 11:43:43,851] [INFO] Selected 15 target genomes.
[2024-01-24 11:43:43,851] [INFO] Target genome list was writen to GCF_019047465.1_ASM1904746v1_genomic.fna/target_genomes.txt
[2024-01-24 11:43:43,860] [INFO] Task started: fastANI
[2024-01-24 11:43:43,860] [INFO] Running command: fastANI --query /var/lib/cwl/stg71c2a624-4536-448c-bb4b-ae758a7fe7c9/GCF_019047465.1_ASM1904746v1_genomic.fna.gz --refList GCF_019047465.1_ASM1904746v1_genomic.fna/target_genomes.txt --output GCF_019047465.1_ASM1904746v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:44:00,137] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:00,138] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg68b3e92a-7344-43e2-86d6-fa64a8d3127d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:44:00,138] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg68b3e92a-7344-43e2-86d6-fa64a8d3127d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:44:00,157] [INFO] Found 15 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 11:44:00,157] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:44:00,157] [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
Lelliottia amnigena	strain=FDAARGOS 1444	GCA_019047465.1	61646	61646	type	True	100.0	1498	1501	95	conclusive
Lelliottia amnigena	strain=NBRC 105700	GCA_001514515.1	61646	61646	type	True	99.9922	1463	1501	95	conclusive
Lelliottia amnigena	strain=LMG 2784	GCA_002553545.1	61646	61646	type	True	99.9877	1416	1501	95	conclusive
Lelliottia aquatilis	strain=6331-17	GCA_002923025.1	2080838	2080838	type	True	85.7823	1192	1501	95	below_threshold
Lelliottia nimipressuralis	strain=CCUG 25894	GCA_004115925.1	69220	69220	type	True	85.7173	1169	1501	95	below_threshold
Enterobacter oligotrophicus	strain=CCA6	GCA_009176645.1	2478464	2478464	type	True	84.0493	1063	1501	95	below_threshold
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	83.9778	1114	1501	95	below_threshold
Enterobacter hormaechei	strain=FDAARGOS 1433	GCA_019048245.1	158836	158836	suspected-type	True	83.8658	1067	1501	95	below_threshold
Enterobacter hormaechei subsp. oharae	strain=DSM 16687	GCA_001729705.1	301102	158836	type	True	83.8459	1088	1501	95	below_threshold
Enterobacter hormaechei subsp. oharae	strain=FDAARGOS_1533	GCA_020097195.1	301102	158836	type	True	83.8365	1099	1501	95	below_threshold
Enterobacter roggenkampii	strain=DSM 16690	GCA_024390995.1	1812935	1812935	type	True	83.806	1031	1501	95	below_threshold
Enterobacter bugandensis		GCA_900324475.1	881260	881260	type	True	83.7839	1085	1501	95	below_threshold
Enterobacter cancerogenus		GCA_900185905.1	69218	69218	type	True	83.6893	1077	1501	95	below_threshold
Enterobacter sichuanensis	strain=WCHECL1597	GCA_025002605.1	2071710	2071710	type	True	83.5897	1079	1501	95	below_threshold
Enterobacter cloacae	strain=DSM 30054	GCA_021469225.1	550	550	type	True	83.5071	1099	1501	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:44:00,159] [INFO] DFAST Taxonomy check result was written to GCF_019047465.1_ASM1904746v1_genomic.fna/tc_result.tsv
[2024-01-24 11:44:00,159] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:44:00,159] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:44:00,160] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg68b3e92a-7344-43e2-86d6-fa64a8d3127d/dqc_reference/checkm_data
[2024-01-24 11:44:00,161] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:44:00,202] [INFO] Task started: CheckM
[2024-01-24 11:44:00,203] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019047465.1_ASM1904746v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019047465.1_ASM1904746v1_genomic.fna/checkm_input GCF_019047465.1_ASM1904746v1_genomic.fna/checkm_result
[2024-01-24 11:44:39,930] [INFO] Task succeeded: CheckM
[2024-01-24 11:44:39,931] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 11:44:39,952] [INFO] ===== Completeness check finished =====
[2024-01-24 11:44:39,953] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:44:39,953] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019047465.1_ASM1904746v1_genomic.fna/markers.fasta)
[2024-01-24 11:44:39,954] [INFO] Task started: Blastn
[2024-01-24 11:44:39,954] [INFO] Running command: blastn -query GCF_019047465.1_ASM1904746v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg68b3e92a-7344-43e2-86d6-fa64a8d3127d/dqc_reference/reference_markers_gtdb.fasta -out GCF_019047465.1_ASM1904746v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:41,381] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:41,384] [INFO] Selected 13 target genomes.
[2024-01-24 11:44:41,385] [INFO] Target genome list was writen to GCF_019047465.1_ASM1904746v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:44:41,396] [INFO] Task started: fastANI
[2024-01-24 11:44:41,396] [INFO] Running command: fastANI --query /var/lib/cwl/stg71c2a624-4536-448c-bb4b-ae758a7fe7c9/GCF_019047465.1_ASM1904746v1_genomic.fna.gz --refList GCF_019047465.1_ASM1904746v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019047465.1_ASM1904746v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:44:55,872] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:55,883] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:44:55,883] [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_900635465.1	s__Lelliottia amnigena	99.968	1488	1501	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Lelliottia	95.0	98.81	98.20	0.95	0.91	15	conclusive
GCF_000016325.1	s__Lelliottia sp000016325	93.6974	1338	1501	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Lelliottia	95.0	95.60	95.60	0.93	0.93	2	-
GCA_002271215.1	s__Lelliottia jeotgali	85.8609	1181	1501	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Lelliottia	95.0	98.81	98.80	0.92	0.92	9	-
GCF_004115925.1	s__Lelliottia nimipressuralis	85.7173	1169	1501	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Lelliottia	95.0	98.29	98.00	0.93	0.92	11	-
GCA_009668015.1	s__Lelliottia sp009668015	85.5399	1162	1501	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Lelliottia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009176645.1	s__Enterobacter oligotrophicus	84.0575	1064	1501	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	99.55	99.09	0.97	0.94	3	-
GCF_001652505.2	s__Lelliottia amnigena_A	83.9668	1103	1501	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Lelliottia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009755685.1	s__Enterobacter sp000568095	83.8842	1094	1501	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0476	98.37	98.04	0.95	0.92	11	-
GCF_003634515.1	s__Enterobacter asburiae_A	83.8252	1085	1501	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	96.0274	97.62	96.46	0.91	0.85	7	-
GCF_008080435.1	s__Enterobacter asburiae_C	83.8247	1055	1501	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.5575	N/A	N/A	N/A	N/A	1	-
GCF_900322725.1	s__Enterobacter quasihormaechei	83.7468	1088	1501	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	99.46	97.61	0.96	0.89	41	-
GCF_003594915.1	s__Enterobacter chuandaensis	83.7367	1093	1501	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	83.5804	1102	1501	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	98.05	95.14	0.91	0.80	129	-
--------------------------------------------------------------------------------
[2024-01-24 11:44:55,885] [INFO] GTDB search result was written to GCF_019047465.1_ASM1904746v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:44:55,886] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:44:55,891] [INFO] DFAST_QC result json was written to GCF_019047465.1_ASM1904746v1_genomic.fna/dqc_result.json
[2024-01-24 11:44:55,892] [INFO] DFAST_QC completed!
[2024-01-24 11:44:55,892] [INFO] Total running time: 0h1m31s