[2024-01-25 17:47:51,048] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:47:51,049] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:47:51,050] [INFO] DQC Reference Directory: /var/lib/cwl/stgc7c490ae-5cc6-4609-9fda-1df049d6968c/dqc_reference
[2024-01-25 17:47:52,257] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:47:52,257] [INFO] Task started: Prodigal
[2024-01-25 17:47:52,258] [INFO] Running command: gunzip -c /var/lib/cwl/stg923b5609-2e5c-406e-980f-37f30a734c0e/GCF_026385525.1_ASM2638552v1_genomic.fna.gz | prodigal -d GCF_026385525.1_ASM2638552v1_genomic.fna/cds.fna -a GCF_026385525.1_ASM2638552v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:47:57,418] [INFO] Task succeeded: Prodigal
[2024-01-25 17:47:57,419] [INFO] Task started: HMMsearch
[2024-01-25 17:47:57,419] [INFO] Running command: hmmsearch --tblout GCF_026385525.1_ASM2638552v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc7c490ae-5cc6-4609-9fda-1df049d6968c/dqc_reference/reference_markers.hmm GCF_026385525.1_ASM2638552v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:47:57,603] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:47:57,604] [INFO] Found 6/6 markers.
[2024-01-25 17:47:57,624] [INFO] Query marker FASTA was written to GCF_026385525.1_ASM2638552v1_genomic.fna/markers.fasta
[2024-01-25 17:47:57,624] [INFO] Task started: Blastn
[2024-01-25 17:47:57,624] [INFO] Running command: blastn -query GCF_026385525.1_ASM2638552v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc7c490ae-5cc6-4609-9fda-1df049d6968c/dqc_reference/reference_markers.fasta -out GCF_026385525.1_ASM2638552v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:47:58,302] [INFO] Task succeeded: Blastn
[2024-01-25 17:47:58,304] [INFO] Selected 18 target genomes.
[2024-01-25 17:47:58,305] [INFO] Target genome list was writen to GCF_026385525.1_ASM2638552v1_genomic.fna/target_genomes.txt
[2024-01-25 17:47:58,321] [INFO] Task started: fastANI
[2024-01-25 17:47:58,322] [INFO] Running command: fastANI --query /var/lib/cwl/stg923b5609-2e5c-406e-980f-37f30a734c0e/GCF_026385525.1_ASM2638552v1_genomic.fna.gz --refList GCF_026385525.1_ASM2638552v1_genomic.fna/target_genomes.txt --output GCF_026385525.1_ASM2638552v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:48:07,987] [INFO] Task succeeded: fastANI
[2024-01-25 17:48:07,987] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc7c490ae-5cc6-4609-9fda-1df049d6968c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:48:07,987] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc7c490ae-5cc6-4609-9fda-1df049d6968c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:48:07,995] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 17:48:07,995] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 17:48:07,995] [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
Bombella apis	strain=MRM1	GCA_018221685.1	1785988	1785988	type	True	83.4991	506	665	95	below_threshold
Bombella apis	strain=MRM1	GCA_014878255.1	1785988	1785988	type	True	83.4333	521	665	95	below_threshold
Bombella favorum	strain=TMW 2.1880	GCA_014048475.1	2039164	2039164	type	True	83.0152	509	665	95	below_threshold
Bombella intestini	strain=R-52487	GCA_002003665.1	1539051	1539051	type	True	82.826	498	665	95	below_threshold
Gluconobacter aidae	strain=AC10	GCA_009547075.1	2662454	2662454	type	True	77.4413	100	665	95	below_threshold
Gluconobacter oxydans	strain=NBRC 14819	GCA_006539685.1	442	442	type	True	77.4161	108	665	95	below_threshold
Gluconobacter roseus	strain=NBRC 3990	GCA_006538885.1	586239	586239	type	True	77.388	104	665	95	below_threshold
Gluconobacter vitians	strain=LMG 31484	GCA_015244565.1	2728102	2728102	type	True	77.337	108	665	95	below_threshold
Gluconobacter cerevisiae	strain=DSM 27644	GCA_018811965.1	1379734	1379734	type	True	77.0538	95	665	95	below_threshold
Gluconobacter cerevisiae	strain=LMG 27748	GCA_015244675.1	1379734	1379734	type	True	76.9992	99	665	95	below_threshold
Acidomonas methanolica	strain=NBRC 104435	GCA_007988925.1	437	437	type	True	76.663	70	665	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:48:07,996] [INFO] DFAST Taxonomy check result was written to GCF_026385525.1_ASM2638552v1_genomic.fna/tc_result.tsv
[2024-01-25 17:48:07,999] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:48:07,999] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:48:07,999] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc7c490ae-5cc6-4609-9fda-1df049d6968c/dqc_reference/checkm_data
[2024-01-25 17:48:08,000] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:48:08,023] [INFO] Task started: CheckM
[2024-01-25 17:48:08,023] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_026385525.1_ASM2638552v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_026385525.1_ASM2638552v1_genomic.fna/checkm_input GCF_026385525.1_ASM2638552v1_genomic.fna/checkm_result
[2024-01-25 17:48:28,890] [INFO] Task succeeded: CheckM
[2024-01-25 17:48:28,891] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:48:28,907] [INFO] ===== Completeness check finished =====
[2024-01-25 17:48:28,908] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:48:28,908] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_026385525.1_ASM2638552v1_genomic.fna/markers.fasta)
[2024-01-25 17:48:28,908] [INFO] Task started: Blastn
[2024-01-25 17:48:28,908] [INFO] Running command: blastn -query GCF_026385525.1_ASM2638552v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc7c490ae-5cc6-4609-9fda-1df049d6968c/dqc_reference/reference_markers_gtdb.fasta -out GCF_026385525.1_ASM2638552v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:48:30,090] [INFO] Task succeeded: Blastn
[2024-01-25 17:48:30,092] [INFO] Selected 13 target genomes.
[2024-01-25 17:48:30,092] [INFO] Target genome list was writen to GCF_026385525.1_ASM2638552v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:48:30,107] [INFO] Task started: fastANI
[2024-01-25 17:48:30,107] [INFO] Running command: fastANI --query /var/lib/cwl/stg923b5609-2e5c-406e-980f-37f30a734c0e/GCF_026385525.1_ASM2638552v1_genomic.fna.gz --refList GCF_026385525.1_ASM2638552v1_genomic.fna/target_genomes_gtdb.txt --output GCF_026385525.1_ASM2638552v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:48:36,740] [INFO] Task succeeded: fastANI
[2024-01-25 17:48:36,747] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 17:48:36,748] [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_014048465.1	s__Bombella mellum	83.6351	541	665	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Bombella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018221685.1	s__Bombella apis	83.5091	505	665	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Bombella	95.0	99.16	98.65	0.96	0.94	13	-
GCF_014048475.1	s__Bombella favorum	83.0152	509	665	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Bombella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002003665.1	s__Bombella intestini	82.826	498	665	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Bombella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009725755.1	s__Bombella sp009725755	78.7908	260	665	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Bombella	95.0	99.22	99.22	0.99	0.99	2	-
GCF_002592045.1	s__Bombella apium_A	78.7562	253	665	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Bombella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015244565.1	s__Gluconobacter vitians	77.337	108	665	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015244675.1	s__Gluconobacter cerevisiae	76.9992	99	665	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	99.99	99.99	0.99	0.99	2	-
GCF_006542375.1	s__Oecophyllibacter saccharovorans	76.8172	93	665	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Oecophyllibacter	95.0	97.69	97.59	0.98	0.98	3	-
GCF_004346035.1	s__Acidomonas methanolica	76.6021	69	665	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acidomonas	95.0	99.93	99.80	0.99	0.98	4	-
--------------------------------------------------------------------------------
[2024-01-25 17:48:36,749] [INFO] GTDB search result was written to GCF_026385525.1_ASM2638552v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:48:36,749] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:48:36,752] [INFO] DFAST_QC result json was written to GCF_026385525.1_ASM2638552v1_genomic.fna/dqc_result.json
[2024-01-25 17:48:36,752] [INFO] DFAST_QC completed!
[2024-01-25 17:48:36,752] [INFO] Total running time: 0h0m46s