[2024-01-24 10:57:13,182] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:13,183] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:13,184] [INFO] DQC Reference Directory: /var/lib/cwl/stgb6d71a99-58b0-4235-81bb-88c974d8a289/dqc_reference
[2024-01-24 10:57:14,625] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:14,626] [INFO] Task started: Prodigal
[2024-01-24 10:57:14,627] [INFO] Running command: gunzip -c /var/lib/cwl/stg6f219bc0-77a4-47a8-93ed-9b5c5fb266a1/GCF_002003665.1_ASM200366v1_genomic.fna.gz | prodigal -d GCF_002003665.1_ASM200366v1_genomic.fna/cds.fna -a GCF_002003665.1_ASM200366v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:20,664] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:20,665] [INFO] Task started: HMMsearch
[2024-01-24 10:57:20,665] [INFO] Running command: hmmsearch --tblout GCF_002003665.1_ASM200366v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb6d71a99-58b0-4235-81bb-88c974d8a289/dqc_reference/reference_markers.hmm GCF_002003665.1_ASM200366v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:20,971] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:20,972] [INFO] Found 6/6 markers.
[2024-01-24 10:57:20,996] [INFO] Query marker FASTA was written to GCF_002003665.1_ASM200366v1_genomic.fna/markers.fasta
[2024-01-24 10:57:20,996] [INFO] Task started: Blastn
[2024-01-24 10:57:20,996] [INFO] Running command: blastn -query GCF_002003665.1_ASM200366v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb6d71a99-58b0-4235-81bb-88c974d8a289/dqc_reference/reference_markers.fasta -out GCF_002003665.1_ASM200366v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:21,724] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:21,727] [INFO] Selected 15 target genomes.
[2024-01-24 10:57:21,728] [INFO] Target genome list was writen to GCF_002003665.1_ASM200366v1_genomic.fna/target_genomes.txt
[2024-01-24 10:57:21,733] [INFO] Task started: fastANI
[2024-01-24 10:57:21,734] [INFO] Running command: fastANI --query /var/lib/cwl/stg6f219bc0-77a4-47a8-93ed-9b5c5fb266a1/GCF_002003665.1_ASM200366v1_genomic.fna.gz --refList GCF_002003665.1_ASM200366v1_genomic.fna/target_genomes.txt --output GCF_002003665.1_ASM200366v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:57:28,831] [INFO] Task succeeded: fastANI
[2024-01-24 10:57:28,832] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb6d71a99-58b0-4235-81bb-88c974d8a289/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:57:28,832] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb6d71a99-58b0-4235-81bb-88c974d8a289/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:57:28,841] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:57:28,841] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:57:28,842] [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 intestini	strain=R-52487	GCA_002003665.1	1539051	1539051	type	True	100.0	668	668	95	conclusive
Bombella favorum	strain=TMW 2.1880	GCA_014048475.1	2039164	2039164	type	True	94.2498	627	668	95	below_threshold
Bombella apis	strain=MRM1	GCA_018221685.1	1785988	1785988	type	True	83.1123	519	668	95	below_threshold
Bombella apis	strain=MRM1	GCA_014878255.1	1785988	1785988	type	True	83.047	549	668	95	below_threshold
Saccharibacter floricola	strain=DSM 15669	GCA_000378165.1	231053	231053	type	True	77.8072	98	668	95	below_threshold
Gluconobacter frateurii	strain=NBRC 3264	GCA_002723955.1	38308	38308	suspected-type	True	77.4235	86	668	95	below_threshold
Neokomagataea thailandica	strain=NBRC 106555	GCA_001598495.1	661190	661190	type	True	77.0005	57	668	95	below_threshold
Asaia lannensis	strain=NBRC 102526	GCA_024054035.1	415421	415421	type	True	76.9417	61	668	95	below_threshold
Acetobacter papayae	strain=JCM 25143	GCA_000613285.1	1076592	1076592	type	True	76.4429	54	668	95	below_threshold
Acidomonas methanolica	strain=NBRC 104435	GCA_007988925.1	437	437	type	True	76.3328	51	668	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:57:28,843] [INFO] DFAST Taxonomy check result was written to GCF_002003665.1_ASM200366v1_genomic.fna/tc_result.tsv
[2024-01-24 10:57:28,844] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:57:28,844] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:57:28,844] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb6d71a99-58b0-4235-81bb-88c974d8a289/dqc_reference/checkm_data
[2024-01-24 10:57:28,845] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:57:28,871] [INFO] Task started: CheckM
[2024-01-24 10:57:28,871] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002003665.1_ASM200366v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002003665.1_ASM200366v1_genomic.fna/checkm_input GCF_002003665.1_ASM200366v1_genomic.fna/checkm_result
[2024-01-24 10:57:53,152] [INFO] Task succeeded: CheckM
[2024-01-24 10:57:53,154] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:57:53,175] [INFO] ===== Completeness check finished =====
[2024-01-24 10:57:53,175] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:57:53,176] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002003665.1_ASM200366v1_genomic.fna/markers.fasta)
[2024-01-24 10:57:53,176] [INFO] Task started: Blastn
[2024-01-24 10:57:53,176] [INFO] Running command: blastn -query GCF_002003665.1_ASM200366v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb6d71a99-58b0-4235-81bb-88c974d8a289/dqc_reference/reference_markers_gtdb.fasta -out GCF_002003665.1_ASM200366v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:54,141] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:54,144] [INFO] Selected 9 target genomes.
[2024-01-24 10:57:54,145] [INFO] Target genome list was writen to GCF_002003665.1_ASM200366v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:57:54,152] [INFO] Task started: fastANI
[2024-01-24 10:57:54,153] [INFO] Running command: fastANI --query /var/lib/cwl/stg6f219bc0-77a4-47a8-93ed-9b5c5fb266a1/GCF_002003665.1_ASM200366v1_genomic.fna.gz --refList GCF_002003665.1_ASM200366v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002003665.1_ASM200366v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:57:58,913] [INFO] Task succeeded: fastANI
[2024-01-24 10:57:58,921] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:57:58,922] [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_002003665.1	s__Bombella intestini	100.0	668	668	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Bombella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014048475.1	s__Bombella favorum	94.2498	627	668	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	83.1007	520	668	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Bombella	95.0	99.16	98.65	0.96	0.94	13	-
GCF_014048465.1	s__Bombella mellum	82.251	478	668	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	78.8202	253	668	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	78.7036	248	668	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Bombella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004346035.1	s__Acidomonas methanolica	76.3211	50	668	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acidomonas	95.0	99.93	99.80	0.99	0.98	4	-
--------------------------------------------------------------------------------
[2024-01-24 10:57:58,924] [INFO] GTDB search result was written to GCF_002003665.1_ASM200366v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:57:58,924] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:57:58,927] [INFO] DFAST_QC result json was written to GCF_002003665.1_ASM200366v1_genomic.fna/dqc_result.json
[2024-01-24 10:57:58,928] [INFO] DFAST_QC completed!
[2024-01-24 10:57:58,928] [INFO] Total running time: 0h0m46s