[2024-01-24 12:44:43,763] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:44:43,765] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:44:43,768] [INFO] DQC Reference Directory: /var/lib/cwl/stg7a0b118b-f24b-4128-ae1e-8f2bf9ef933b/dqc_reference
[2024-01-24 12:44:45,218] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:44:45,219] [INFO] Task started: Prodigal
[2024-01-24 12:44:45,220] [INFO] Running command: gunzip -c /var/lib/cwl/stgf1663c20-ca17-4307-a0b0-7703e7e72761/GCF_025995455.1_ASM2599545v1_genomic.fna.gz | prodigal -d GCF_025995455.1_ASM2599545v1_genomic.fna/cds.fna -a GCF_025995455.1_ASM2599545v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:44:54,572] [INFO] Task succeeded: Prodigal
[2024-01-24 12:44:54,572] [INFO] Task started: HMMsearch
[2024-01-24 12:44:54,572] [INFO] Running command: hmmsearch --tblout GCF_025995455.1_ASM2599545v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7a0b118b-f24b-4128-ae1e-8f2bf9ef933b/dqc_reference/reference_markers.hmm GCF_025995455.1_ASM2599545v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:44:54,915] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:44:54,916] [INFO] Found 6/6 markers.
[2024-01-24 12:44:54,951] [INFO] Query marker FASTA was written to GCF_025995455.1_ASM2599545v1_genomic.fna/markers.fasta
[2024-01-24 12:44:54,952] [INFO] Task started: Blastn
[2024-01-24 12:44:54,952] [INFO] Running command: blastn -query GCF_025995455.1_ASM2599545v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7a0b118b-f24b-4128-ae1e-8f2bf9ef933b/dqc_reference/reference_markers.fasta -out GCF_025995455.1_ASM2599545v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:44:55,661] [INFO] Task succeeded: Blastn
[2024-01-24 12:44:55,665] [INFO] Selected 23 target genomes.
[2024-01-24 12:44:55,666] [INFO] Target genome list was writen to GCF_025995455.1_ASM2599545v1_genomic.fna/target_genomes.txt
[2024-01-24 12:44:55,676] [INFO] Task started: fastANI
[2024-01-24 12:44:55,676] [INFO] Running command: fastANI --query /var/lib/cwl/stgf1663c20-ca17-4307-a0b0-7703e7e72761/GCF_025995455.1_ASM2599545v1_genomic.fna.gz --refList GCF_025995455.1_ASM2599545v1_genomic.fna/target_genomes.txt --output GCF_025995455.1_ASM2599545v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:45:11,470] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:11,471] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7a0b118b-f24b-4128-ae1e-8f2bf9ef933b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:45:11,471] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7a0b118b-f24b-4128-ae1e-8f2bf9ef933b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:45:11,480] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:45:11,480] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:45:11,481] [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
Acetobacter pomorum	strain=LHT 2458	GCA_002738225.1	65959	65959	suspected-type	True	99.9672	925	943	95	conclusive
Acetobacter oryzoeni	strain=B6	GCA_004014775.2	2500548	2500548	type	True	89.0789	702	943	95	below_threshold
Acetobacter pasteurianus subsp. pasteurianus	strain=IFO 3191	GCA_000241625.2	481145	438	type	True	88.9196	657	943	95	below_threshold
Acetobacter pasteurianus subsp. pasteurianus	strain=type strain:LMG 1262	GCA_000285275.1	481145	438	type	True	88.9011	679	943	95	below_threshold
Acetobacter pasteurianus subsp. pasteurianus	strain=NBRC 106471	GCA_003850805.1	481145	438	type	True	88.8966	684	943	95	below_threshold
Acetobacter ascendens	strain=LMG 1590	GCA_001766235.1	481146	481146	type	True	88.0428	672	943	95	below_threshold
Acetobacter oryzifermentans	strain=SLV-7	GCA_001628715.1	1633874	1633874	type	True	88.0142	700	943	95	below_threshold
Gluconobacter potus	strain=R-71646	GCA_015244705.1	2724927	2724927	type	True	77.8153	66	943	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:45:11,483] [INFO] DFAST Taxonomy check result was written to GCF_025995455.1_ASM2599545v1_genomic.fna/tc_result.tsv
[2024-01-24 12:45:11,483] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:45:11,483] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:45:11,484] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7a0b118b-f24b-4128-ae1e-8f2bf9ef933b/dqc_reference/checkm_data
[2024-01-24 12:45:11,485] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:45:11,522] [INFO] Task started: CheckM
[2024-01-24 12:45:11,522] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025995455.1_ASM2599545v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025995455.1_ASM2599545v1_genomic.fna/checkm_input GCF_025995455.1_ASM2599545v1_genomic.fna/checkm_result
[2024-01-24 12:45:45,027] [INFO] Task succeeded: CheckM
[2024-01-24 12:45:45,029] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:45:45,047] [INFO] ===== Completeness check finished =====
[2024-01-24 12:45:45,048] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:45:45,048] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025995455.1_ASM2599545v1_genomic.fna/markers.fasta)
[2024-01-24 12:45:45,048] [INFO] Task started: Blastn
[2024-01-24 12:45:45,049] [INFO] Running command: blastn -query GCF_025995455.1_ASM2599545v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7a0b118b-f24b-4128-ae1e-8f2bf9ef933b/dqc_reference/reference_markers_gtdb.fasta -out GCF_025995455.1_ASM2599545v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:45,906] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:45,910] [INFO] Selected 14 target genomes.
[2024-01-24 12:45:45,910] [INFO] Target genome list was writen to GCF_025995455.1_ASM2599545v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:45:45,933] [INFO] Task started: fastANI
[2024-01-24 12:45:45,934] [INFO] Running command: fastANI --query /var/lib/cwl/stgf1663c20-ca17-4307-a0b0-7703e7e72761/GCF_025995455.1_ASM2599545v1_genomic.fna.gz --refList GCF_025995455.1_ASM2599545v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025995455.1_ASM2599545v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:45:53,311] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:53,319] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:45:53,319] [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_002738225.1	s__Acetobacter pomorum	99.9672	925	943	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	97.71	97.71	0.83	0.83	2	conclusive
GCF_004014775.2	s__Acetobacter oryzoeni	89.0789	702	943	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	97.72	97.29	0.89	0.84	4	-
GCF_000723785.2	s__Acetobacter pasteurianus	89.0559	709	943	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	98.11	97.27	0.89	0.78	27	-
GCF_001766235.1	s__Acetobacter ascendens	88.0262	673	943	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	98.38	98.13	0.85	0.83	6	-
GCF_001628715.1	s__Acetobacter oryzifermentans	88.0175	699	943	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	98.28	98.04	0.87	0.83	24	-
--------------------------------------------------------------------------------
[2024-01-24 12:45:53,322] [INFO] GTDB search result was written to GCF_025995455.1_ASM2599545v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:45:53,322] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:45:53,325] [INFO] DFAST_QC result json was written to GCF_025995455.1_ASM2599545v1_genomic.fna/dqc_result.json
[2024-01-24 12:45:53,325] [INFO] DFAST_QC completed!
[2024-01-24 12:45:53,325] [INFO] Total running time: 0h1m10s