[2024-01-25 17:50:50,897] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:50:50,898] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:50:50,899] [INFO] DQC Reference Directory: /var/lib/cwl/stg5c11a2b8-9633-4fe6-9a5c-8f3621e2b0e3/dqc_reference
[2024-01-25 17:50:52,021] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:50:52,022] [INFO] Task started: Prodigal
[2024-01-25 17:50:52,022] [INFO] Running command: gunzip -c /var/lib/cwl/stg9933d6ef-e0bf-4190-a4e8-a5e4c9cdce80/GCF_026385475.1_ASM2638547v1_genomic.fna.gz | prodigal -d GCF_026385475.1_ASM2638547v1_genomic.fna/cds.fna -a GCF_026385475.1_ASM2638547v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:50:56,697] [INFO] Task succeeded: Prodigal
[2024-01-25 17:50:56,697] [INFO] Task started: HMMsearch
[2024-01-25 17:50:56,697] [INFO] Running command: hmmsearch --tblout GCF_026385475.1_ASM2638547v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5c11a2b8-9633-4fe6-9a5c-8f3621e2b0e3/dqc_reference/reference_markers.hmm GCF_026385475.1_ASM2638547v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:50:56,868] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:50:56,869] [INFO] Found 6/6 markers.
[2024-01-25 17:50:56,887] [INFO] Query marker FASTA was written to GCF_026385475.1_ASM2638547v1_genomic.fna/markers.fasta
[2024-01-25 17:50:56,887] [INFO] Task started: Blastn
[2024-01-25 17:50:56,887] [INFO] Running command: blastn -query GCF_026385475.1_ASM2638547v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5c11a2b8-9633-4fe6-9a5c-8f3621e2b0e3/dqc_reference/reference_markers.fasta -out GCF_026385475.1_ASM2638547v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:50:57,526] [INFO] Task succeeded: Blastn
[2024-01-25 17:50:57,529] [INFO] Selected 22 target genomes.
[2024-01-25 17:50:57,529] [INFO] Target genome list was writen to GCF_026385475.1_ASM2638547v1_genomic.fna/target_genomes.txt
[2024-01-25 17:50:57,540] [INFO] Task started: fastANI
[2024-01-25 17:50:57,540] [INFO] Running command: fastANI --query /var/lib/cwl/stg9933d6ef-e0bf-4190-a4e8-a5e4c9cdce80/GCF_026385475.1_ASM2638547v1_genomic.fna.gz --refList GCF_026385475.1_ASM2638547v1_genomic.fna/target_genomes.txt --output GCF_026385475.1_ASM2638547v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:51:07,742] [INFO] Task succeeded: fastANI
[2024-01-25 17:51:07,742] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5c11a2b8-9633-4fe6-9a5c-8f3621e2b0e3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:51:07,743] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5c11a2b8-9633-4fe6-9a5c-8f3621e2b0e3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:51:07,747] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 17:51:07,748] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 17:51:07,748] [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_014878255.1	1785988	1785988	type	True	78.7916	233	629	95	below_threshold
Bombella apis	strain=MRM1	GCA_018221685.1	1785988	1785988	type	True	78.7722	225	629	95	below_threshold
Bombella intestini	strain=R-52487	GCA_002003665.1	1539051	1539051	type	True	78.7222	248	629	95	below_threshold
Bombella favorum	strain=TMW 2.1880	GCA_014048475.1	2039164	2039164	type	True	78.6563	259	629	95	below_threshold
Saccharibacter floricola	strain=DSM 15669	GCA_000378165.1	231053	231053	type	True	77.341	108	629	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:51:07,749] [INFO] DFAST Taxonomy check result was written to GCF_026385475.1_ASM2638547v1_genomic.fna/tc_result.tsv
[2024-01-25 17:51:07,749] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:51:07,750] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:51:07,750] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5c11a2b8-9633-4fe6-9a5c-8f3621e2b0e3/dqc_reference/checkm_data
[2024-01-25 17:51:07,751] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:51:07,772] [INFO] Task started: CheckM
[2024-01-25 17:51:07,772] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_026385475.1_ASM2638547v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_026385475.1_ASM2638547v1_genomic.fna/checkm_input GCF_026385475.1_ASM2638547v1_genomic.fna/checkm_result
[2024-01-25 17:51:26,563] [INFO] Task succeeded: CheckM
[2024-01-25 17:51:26,564] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:51:26,578] [INFO] ===== Completeness check finished =====
[2024-01-25 17:51:26,578] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:51:26,579] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_026385475.1_ASM2638547v1_genomic.fna/markers.fasta)
[2024-01-25 17:51:26,579] [INFO] Task started: Blastn
[2024-01-25 17:51:26,579] [INFO] Running command: blastn -query GCF_026385475.1_ASM2638547v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5c11a2b8-9633-4fe6-9a5c-8f3621e2b0e3/dqc_reference/reference_markers_gtdb.fasta -out GCF_026385475.1_ASM2638547v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:51:27,661] [INFO] Task succeeded: Blastn
[2024-01-25 17:51:27,663] [INFO] Selected 14 target genomes.
[2024-01-25 17:51:27,664] [INFO] Target genome list was writen to GCF_026385475.1_ASM2638547v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:51:27,680] [INFO] Task started: fastANI
[2024-01-25 17:51:27,680] [INFO] Running command: fastANI --query /var/lib/cwl/stg9933d6ef-e0bf-4190-a4e8-a5e4c9cdce80/GCF_026385475.1_ASM2638547v1_genomic.fna.gz --refList GCF_026385475.1_ASM2638547v1_genomic.fna/target_genomes_gtdb.txt --output GCF_026385475.1_ASM2638547v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:51:34,810] [INFO] Task succeeded: fastANI
[2024-01-25 17:51:34,815] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:51:34,816] [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_002592045.1	s__Bombella apium_A	99.0639	603	629	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_009725755.1	s__Bombella sp009725755	94.9036	564	629	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Bombella	95.0	99.22	99.22	0.99	0.99	2	-
GCF_018221685.1	s__Bombella apis	78.7722	225	629	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Bombella	95.0	99.16	98.65	0.96	0.94	13	-
GCF_002003665.1	s__Bombella intestini	78.7153	249	629	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Bombella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014048475.1	s__Bombella favorum	78.6563	259	629	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Bombella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014048465.1	s__Bombella mellum	78.5753	217	629	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Bombella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009834765.1	s__Saccharibacter sp009834765	77.4077	107	629	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Saccharibacter	95.0	99.99	99.98	0.99	0.99	3	-
--------------------------------------------------------------------------------
[2024-01-25 17:51:34,817] [INFO] GTDB search result was written to GCF_026385475.1_ASM2638547v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:51:34,818] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:51:34,820] [INFO] DFAST_QC result json was written to GCF_026385475.1_ASM2638547v1_genomic.fna/dqc_result.json
[2024-01-25 17:51:34,820] [INFO] DFAST_QC completed!
[2024-01-25 17:51:34,820] [INFO] Total running time: 0h0m44s