[2024-01-25 18:07:20,552] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:07:20,554] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:07:20,554] [INFO] DQC Reference Directory: /var/lib/cwl/stgda93d8d5-44e8-4c59-b995-93d058d638ea/dqc_reference
[2024-01-25 18:07:21,665] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:07:21,665] [INFO] Task started: Prodigal
[2024-01-25 18:07:21,666] [INFO] Running command: gunzip -c /var/lib/cwl/stgb60c9895-f758-46c3-8bf2-c4fc61574fb2/GCF_000439375.1_06-3099_v1_genomic.fna.gz | prodigal -d GCF_000439375.1_06-3099_v1_genomic.fna/cds.fna -a GCF_000439375.1_06-3099_v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:07:28,772] [INFO] Task succeeded: Prodigal
[2024-01-25 18:07:28,773] [INFO] Task started: HMMsearch
[2024-01-25 18:07:28,773] [INFO] Running command: hmmsearch --tblout GCF_000439375.1_06-3099_v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgda93d8d5-44e8-4c59-b995-93d058d638ea/dqc_reference/reference_markers.hmm GCF_000439375.1_06-3099_v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:07:29,000] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:07:29,001] [INFO] Found 6/6 markers.
[2024-01-25 18:07:29,027] [INFO] Query marker FASTA was written to GCF_000439375.1_06-3099_v1_genomic.fna/markers.fasta
[2024-01-25 18:07:29,027] [INFO] Task started: Blastn
[2024-01-25 18:07:29,027] [INFO] Running command: blastn -query GCF_000439375.1_06-3099_v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgda93d8d5-44e8-4c59-b995-93d058d638ea/dqc_reference/reference_markers.fasta -out GCF_000439375.1_06-3099_v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:07:29,758] [INFO] Task succeeded: Blastn
[2024-01-25 18:07:29,760] [INFO] Selected 13 target genomes.
[2024-01-25 18:07:29,761] [INFO] Target genome list was writen to GCF_000439375.1_06-3099_v1_genomic.fna/target_genomes.txt
[2024-01-25 18:07:29,781] [INFO] Task started: fastANI
[2024-01-25 18:07:29,781] [INFO] Running command: fastANI --query /var/lib/cwl/stgb60c9895-f758-46c3-8bf2-c4fc61574fb2/GCF_000439375.1_06-3099_v1_genomic.fna.gz --refList GCF_000439375.1_06-3099_v1_genomic.fna/target_genomes.txt --output GCF_000439375.1_06-3099_v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:07:39,724] [INFO] Task succeeded: fastANI
[2024-01-25 18:07:39,725] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgda93d8d5-44e8-4c59-b995-93d058d638ea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:07:39,725] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgda93d8d5-44e8-4c59-b995-93d058d638ea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:07:39,733] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:07:39,733] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:07:39,733] [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
Tatumella saanichensis	strain=NML 06-3099	GCA_000439375.1	480813	480813	type	True	100.0	1071	1075	95	conclusive
Tatumella ptyseos	strain=ATCC 33301	GCA_000439895.1	82987	82987	type	True	80.5931	504	1075	95	below_threshold
Tatumella ptyseos	strain=NCTC11468	GCA_900478715.1	82987	82987	type	True	80.5456	521	1075	95	below_threshold
Tatumella ptyseos	strain=ATCC 33301	GCA_000735525.1	82987	82987	type	True	80.5374	516	1075	95	below_threshold
Tatumella citrea	strain=DSM 13699	GCA_002163585.1	53336	53336	type	True	80.111	417	1075	95	below_threshold
Tatumella morbirosei	strain=LMG 23360	GCA_000757425.2	642227	642227	type	True	79.9976	438	1075	95	below_threshold
Erwinia iniecta	strain=B120	GCA_001267535.1	1560201	1560201	type	True	78.8183	270	1075	95	below_threshold
Erwinia aphidicola	strain=X001	GCA_024169515.1	68334	68334	type	True	78.5155	240	1075	95	below_threshold
Enterobacter cloacae	strain=DSM 30054	GCA_021469225.1	550	550	type	True	78.3268	206	1075	95	below_threshold
Enterobacter hormaechei	strain=FDAARGOS 1433	GCA_019048245.1	158836	158836	suspected-type	True	78.2831	196	1075	95	below_threshold
Enterobacter roggenkampii	strain=DSM 16690	GCA_024390995.1	1812935	1812935	type	True	78.2603	195	1075	95	below_threshold
Leclercia pneumoniae	strain=49125	GCA_018987305.1	2815358	2815358	type	True	78.2498	189	1075	95	below_threshold
Klebsiella pneumoniae	strain=PartO-Kpneumoniae-RM8376	GCA_022869665.1	573	573	type	True	77.9952	186	1075	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:07:39,735] [INFO] DFAST Taxonomy check result was written to GCF_000439375.1_06-3099_v1_genomic.fna/tc_result.tsv
[2024-01-25 18:07:39,735] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:07:39,735] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:07:39,736] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgda93d8d5-44e8-4c59-b995-93d058d638ea/dqc_reference/checkm_data
[2024-01-25 18:07:39,736] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:07:39,771] [INFO] Task started: CheckM
[2024-01-25 18:07:39,771] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000439375.1_06-3099_v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000439375.1_06-3099_v1_genomic.fna/checkm_input GCF_000439375.1_06-3099_v1_genomic.fna/checkm_result
[2024-01-25 18:08:05,756] [INFO] Task succeeded: CheckM
[2024-01-25 18:08:05,758] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:08:05,779] [INFO] ===== Completeness check finished =====
[2024-01-25 18:08:05,780] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:08:05,781] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000439375.1_06-3099_v1_genomic.fna/markers.fasta)
[2024-01-25 18:08:05,781] [INFO] Task started: Blastn
[2024-01-25 18:08:05,781] [INFO] Running command: blastn -query GCF_000439375.1_06-3099_v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgda93d8d5-44e8-4c59-b995-93d058d638ea/dqc_reference/reference_markers_gtdb.fasta -out GCF_000439375.1_06-3099_v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:08:06,867] [INFO] Task succeeded: Blastn
[2024-01-25 18:08:06,870] [INFO] Selected 8 target genomes.
[2024-01-25 18:08:06,870] [INFO] Target genome list was writen to GCF_000439375.1_06-3099_v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:08:06,883] [INFO] Task started: fastANI
[2024-01-25 18:08:06,884] [INFO] Running command: fastANI --query /var/lib/cwl/stgb60c9895-f758-46c3-8bf2-c4fc61574fb2/GCF_000439375.1_06-3099_v1_genomic.fna.gz --refList GCF_000439375.1_06-3099_v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000439375.1_06-3099_v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:08:13,688] [INFO] Task succeeded: fastANI
[2024-01-25 18:08:13,694] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:08:13,694] [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_000439375.1	s__Tatumella saanichensis	100.0	1071	1075	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Tatumella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000735525.1	s__Tatumella ptyseos	80.5404	514	1075	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Tatumella	95.0	99.71	99.17	0.96	0.91	4	-
GCF_018257515.1	s__Tatumella sp018257515	80.494	549	1075	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Tatumella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018257575.1	s__Tatumella sp018257575	80.126	437	1075	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Tatumella	95.0	99.64	99.52	0.95	0.93	6	-
GCF_002163585.1	s__Tatumella citrea	80.0908	416	1075	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Tatumella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000757425.2	s__Tatumella morbirosei	80.0007	437	1075	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Tatumella	95.0	95.37	95.37	0.92	0.92	2	-
GCF_001267535.1	s__Erwinia iniecta	78.8197	267	1075	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	99.95	99.95	0.99	0.99	2	-
GCF_017875465.1	s__Erwinia toletana	78.3693	280	1075	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	99.93	99.93	0.98	0.98	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:08:13,696] [INFO] GTDB search result was written to GCF_000439375.1_06-3099_v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:08:13,696] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:08:13,699] [INFO] DFAST_QC result json was written to GCF_000439375.1_06-3099_v1_genomic.fna/dqc_result.json
[2024-01-25 18:08:13,700] [INFO] DFAST_QC completed!
[2024-01-25 18:08:13,700] [INFO] Total running time: 0h0m53s