[2024-01-24 12:29:29,030] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:29:29,035] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:29:29,036] [INFO] DQC Reference Directory: /var/lib/cwl/stg73343993-ae0d-4ec7-b51e-f467f4d0897d/dqc_reference
[2024-01-24 12:29:30,346] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:29:30,347] [INFO] Task started: Prodigal
[2024-01-24 12:29:30,347] [INFO] Running command: gunzip -c /var/lib/cwl/stg42ee154b-18d3-490f-9d53-9a11f7c3f6c5/GCF_030160155.1_ASM3016015v1_genomic.fna.gz | prodigal -d GCF_030160155.1_ASM3016015v1_genomic.fna/cds.fna -a GCF_030160155.1_ASM3016015v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:29:41,395] [INFO] Task succeeded: Prodigal
[2024-01-24 12:29:41,395] [INFO] Task started: HMMsearch
[2024-01-24 12:29:41,395] [INFO] Running command: hmmsearch --tblout GCF_030160155.1_ASM3016015v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg73343993-ae0d-4ec7-b51e-f467f4d0897d/dqc_reference/reference_markers.hmm GCF_030160155.1_ASM3016015v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:29:41,779] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:29:41,780] [INFO] Found 6/6 markers.
[2024-01-24 12:29:41,819] [INFO] Query marker FASTA was written to GCF_030160155.1_ASM3016015v1_genomic.fna/markers.fasta
[2024-01-24 12:29:41,820] [INFO] Task started: Blastn
[2024-01-24 12:29:41,820] [INFO] Running command: blastn -query GCF_030160155.1_ASM3016015v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg73343993-ae0d-4ec7-b51e-f467f4d0897d/dqc_reference/reference_markers.fasta -out GCF_030160155.1_ASM3016015v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:29:42,626] [INFO] Task succeeded: Blastn
[2024-01-24 12:29:42,630] [INFO] Selected 18 target genomes.
[2024-01-24 12:29:42,630] [INFO] Target genome list was writen to GCF_030160155.1_ASM3016015v1_genomic.fna/target_genomes.txt
[2024-01-24 12:29:42,640] [INFO] Task started: fastANI
[2024-01-24 12:29:42,640] [INFO] Running command: fastANI --query /var/lib/cwl/stg42ee154b-18d3-490f-9d53-9a11f7c3f6c5/GCF_030160155.1_ASM3016015v1_genomic.fna.gz --refList GCF_030160155.1_ASM3016015v1_genomic.fna/target_genomes.txt --output GCF_030160155.1_ASM3016015v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:29:53,849] [INFO] Task succeeded: fastANI
[2024-01-24 12:29:53,849] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg73343993-ae0d-4ec7-b51e-f467f4d0897d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:29:53,850] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg73343993-ae0d-4ec7-b51e-f467f4d0897d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:29:53,860] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:29:53,861] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:29:53,861] [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
Gluconobacter cerinus	strain=NBRC 3267	GCA_002723935.1	38307	38307	type	True	99.9744	1161	1178	95	conclusive
Gluconobacter thailandicus	strain=NBRC 100600	GCA_007990185.1	257438	257438	type	True	83.4782	643	1178	95	below_threshold
Gluconobacter thailandicus	strain=F149-1	GCA_000964465.1	257438	257438	type	True	83.4604	650	1178	95	below_threshold
Gluconobacter frateurii	strain=NBRC 3264	GCA_002723955.1	38308	38308	suspected-type	True	83.4438	661	1178	95	below_threshold
Gluconobacter japonicus	strain=NBRC 3271	GCA_002723975.1	376620	376620	type	True	83.0141	630	1178	95	below_threshold
Gluconobacter oxydans	strain=DSM 3503	GCA_004346605.1	442	442	type	True	80.7227	401	1178	95	below_threshold
Gluconobacter aidae	strain=AC10	GCA_009547075.1	2662454	2662454	type	True	80.709	407	1178	95	below_threshold
Gluconobacter potus	strain=R-71646	GCA_015244705.1	2724927	2724927	type	True	79.8756	390	1178	95	below_threshold
Gluconobacter oxydans	strain=NBRC 14819	GCA_006539685.1	442	442	type	True	79.8022	361	1178	95	below_threshold
Gluconobacter morbifer	strain=G707	GCA_000234355.2	479935	479935	type	True	79.0918	335	1178	95	below_threshold
Asaia platycodi	strain=JCM 25414	GCA_000614545.1	610243	610243	type	True	77.9689	108	1178	95	below_threshold
Neokomagataea anthophila	strain=TBRC 2177	GCA_018122595.1	2826925	2826925	type	True	77.741	127	1178	95	below_threshold
Neokomagataea thailandica	strain=NBRC 106555	GCA_001598495.1	661190	661190	type	True	77.5007	120	1178	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:29:53,863] [INFO] DFAST Taxonomy check result was written to GCF_030160155.1_ASM3016015v1_genomic.fna/tc_result.tsv
[2024-01-24 12:29:53,863] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:29:53,863] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:29:53,864] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg73343993-ae0d-4ec7-b51e-f467f4d0897d/dqc_reference/checkm_data
[2024-01-24 12:29:53,865] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:29:53,905] [INFO] Task started: CheckM
[2024-01-24 12:29:53,905] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030160155.1_ASM3016015v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030160155.1_ASM3016015v1_genomic.fna/checkm_input GCF_030160155.1_ASM3016015v1_genomic.fna/checkm_result
[2024-01-24 12:30:30,475] [INFO] Task succeeded: CheckM
[2024-01-24 12:30:30,477] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:30:30,506] [INFO] ===== Completeness check finished =====
[2024-01-24 12:30:30,506] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:30:30,507] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030160155.1_ASM3016015v1_genomic.fna/markers.fasta)
[2024-01-24 12:30:30,507] [INFO] Task started: Blastn
[2024-01-24 12:30:30,507] [INFO] Running command: blastn -query GCF_030160155.1_ASM3016015v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg73343993-ae0d-4ec7-b51e-f467f4d0897d/dqc_reference/reference_markers_gtdb.fasta -out GCF_030160155.1_ASM3016015v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:30:31,554] [INFO] Task succeeded: Blastn
[2024-01-24 12:30:31,557] [INFO] Selected 14 target genomes.
[2024-01-24 12:30:31,558] [INFO] Target genome list was writen to GCF_030160155.1_ASM3016015v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:30:31,595] [INFO] Task started: fastANI
[2024-01-24 12:30:31,596] [INFO] Running command: fastANI --query /var/lib/cwl/stg42ee154b-18d3-490f-9d53-9a11f7c3f6c5/GCF_030160155.1_ASM3016015v1_genomic.fna.gz --refList GCF_030160155.1_ASM3016015v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030160155.1_ASM3016015v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:30:40,152] [INFO] Task succeeded: fastANI
[2024-01-24 12:30:40,161] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:30:40,162] [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_002723935.1	s__Gluconobacter_A cerinus	99.9744	1161	1178	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter_A	95.0	96.40	95.61	0.88	0.86	20	conclusive
GCF_014132155.1	s__Gluconobacter_A sp014132155	93.4721	888	1178	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter_A	95.0	97.46	96.68	0.90	0.89	4	-
GCF_002723955.1	s__Gluconobacter_A frateurii	83.4438	661	1178	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter_A	95.0	97.06	97.06	0.93	0.93	2	-
GCF_000964465.1	s__Gluconobacter_A thailandicus	83.4371	652	1178	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter_A	95.0	98.77	97.43	0.93	0.88	11	-
GCF_002723975.1	s__Gluconobacter_A japonicus	83.0113	631	1178	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter_A	95.0	96.84	95.27	0.89	0.85	9	-
GCF_018256155.1	s__Gluconobacter sp018256155	81.4682	434	1178	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006539685.1	s__Gluconobacter oxydans	79.7876	362	1178	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	98.14	96.18	0.93	0.85	13	-
GCF_000234355.1	s__Gluconobacter_C morbifer	79.1059	334	1178	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018122595.1	s__Neokomagataea sp018122595	77.741	127	1178	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Neokomagataea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:30:40,164] [INFO] GTDB search result was written to GCF_030160155.1_ASM3016015v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:30:40,165] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:30:40,170] [INFO] DFAST_QC result json was written to GCF_030160155.1_ASM3016015v1_genomic.fna/dqc_result.json
[2024-01-24 12:30:40,170] [INFO] DFAST_QC completed!
[2024-01-24 12:30:40,170] [INFO] Total running time: 0h1m11s