[2024-01-24 13:46:10,947] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:10,948] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:10,948] [INFO] DQC Reference Directory: /var/lib/cwl/stg7cef1628-7b10-41d0-b259-c8474e20c73b/dqc_reference
[2024-01-24 13:46:12,277] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:12,277] [INFO] Task started: Prodigal
[2024-01-24 13:46:12,278] [INFO] Running command: gunzip -c /var/lib/cwl/stg137b03c2-a94c-4489-8a78-5dc83e268c48/GCF_000613285.1_ASM61328v1_genomic.fna.gz | prodigal -d GCF_000613285.1_ASM61328v1_genomic.fna/cds.fna -a GCF_000613285.1_ASM61328v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:21,454] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:21,455] [INFO] Task started: HMMsearch
[2024-01-24 13:46:21,455] [INFO] Running command: hmmsearch --tblout GCF_000613285.1_ASM61328v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7cef1628-7b10-41d0-b259-c8474e20c73b/dqc_reference/reference_markers.hmm GCF_000613285.1_ASM61328v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:21,695] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:21,697] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg137b03c2-a94c-4489-8a78-5dc83e268c48/GCF_000613285.1_ASM61328v1_genomic.fna.gz]
[2024-01-24 13:46:21,726] [INFO] Query marker FASTA was written to GCF_000613285.1_ASM61328v1_genomic.fna/markers.fasta
[2024-01-24 13:46:21,726] [INFO] Task started: Blastn
[2024-01-24 13:46:21,726] [INFO] Running command: blastn -query GCF_000613285.1_ASM61328v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7cef1628-7b10-41d0-b259-c8474e20c73b/dqc_reference/reference_markers.fasta -out GCF_000613285.1_ASM61328v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:22,548] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:22,552] [INFO] Selected 15 target genomes.
[2024-01-24 13:46:22,552] [INFO] Target genome list was writen to GCF_000613285.1_ASM61328v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:22,579] [INFO] Task started: fastANI
[2024-01-24 13:46:22,579] [INFO] Running command: fastANI --query /var/lib/cwl/stg137b03c2-a94c-4489-8a78-5dc83e268c48/GCF_000613285.1_ASM61328v1_genomic.fna.gz --refList GCF_000613285.1_ASM61328v1_genomic.fna/target_genomes.txt --output GCF_000613285.1_ASM61328v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:31,930] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:31,931] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7cef1628-7b10-41d0-b259-c8474e20c73b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:31,931] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7cef1628-7b10-41d0-b259-c8474e20c73b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:31,942] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:46:31,942] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:46:31,942] [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 papayae	strain=JCM 25143	GCA_000613285.1	1076592	1076592	type	True	100.0	917	923	95	conclusive
Acetobacter peroxydans	strain=NBRC 13755	GCA_006539345.1	104098	104098	type	True	86.4028	680	923	95	below_threshold
Acetobacter peroxydans	strain=LMG 1635	GCA_011516745.1	104098	104098	type	True	86.3106	681	923	95	below_threshold
Acetobacter garciniae	strain=TBRC 12339	GCA_017377735.1	2817435	2817435	type	True	80.4433	414	923	95	below_threshold
Acetobacter lovaniensis	strain=LMG 1617	GCA_011516875.1	104100	104100	type	True	79.8932	395	923	95	below_threshold
Acetobacter lovaniensis	strain=DSM 4491	GCA_014207635.1	104100	104100	type	True	79.8732	387	923	95	below_threshold
Acetobacter fabarum	strain=LMG 24244	GCA_011516925.1	483199	483199	type	True	79.7146	402	923	95	below_threshold
Acetobacter lambici	strain=LMG 27439	GCA_011516885.1	1332824	1332824	type	True	79.3786	377	923	95	below_threshold
Acetobacter malorum	strain=LMG 1746	GCA_001580615.1	178901	178901	suspected-type	True	78.4453	291	923	95	below_threshold
Acetobacter persici	strain=JCM 25330	GCA_000613905.1	1076596	1076596	type	True	78.3974	284	923	95	below_threshold
Acetobacter tropicalis	strain=NBRC 16470	GCA_007989245.1	104102	104102	type	True	78.3009	280	923	95	below_threshold
Asaia lannensis	strain=NBRC 102526	GCA_024054035.1	415421	415421	type	True	77.2887	107	923	95	below_threshold
Roseomonas haemaphysalidis	strain=546	GCA_017355405.1	2768162	2768162	type	True	76.3397	60	923	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:31,943] [INFO] DFAST Taxonomy check result was written to GCF_000613285.1_ASM61328v1_genomic.fna/tc_result.tsv
[2024-01-24 13:46:31,944] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:31,944] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:31,944] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7cef1628-7b10-41d0-b259-c8474e20c73b/dqc_reference/checkm_data
[2024-01-24 13:46:31,945] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:31,976] [INFO] Task started: CheckM
[2024-01-24 13:46:31,977] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000613285.1_ASM61328v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000613285.1_ASM61328v1_genomic.fna/checkm_input GCF_000613285.1_ASM61328v1_genomic.fna/checkm_result
[2024-01-24 13:47:02,861] [INFO] Task succeeded: CheckM
[2024-01-24 13:47:02,862] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.46%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:47:02,884] [INFO] ===== Completeness check finished =====
[2024-01-24 13:47:02,885] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:47:02,885] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000613285.1_ASM61328v1_genomic.fna/markers.fasta)
[2024-01-24 13:47:02,886] [INFO] Task started: Blastn
[2024-01-24 13:47:02,886] [INFO] Running command: blastn -query GCF_000613285.1_ASM61328v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7cef1628-7b10-41d0-b259-c8474e20c73b/dqc_reference/reference_markers_gtdb.fasta -out GCF_000613285.1_ASM61328v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:04,149] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:04,154] [INFO] Selected 11 target genomes.
[2024-01-24 13:47:04,154] [INFO] Target genome list was writen to GCF_000613285.1_ASM61328v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:47:04,167] [INFO] Task started: fastANI
[2024-01-24 13:47:04,167] [INFO] Running command: fastANI --query /var/lib/cwl/stg137b03c2-a94c-4489-8a78-5dc83e268c48/GCF_000613285.1_ASM61328v1_genomic.fna.gz --refList GCF_000613285.1_ASM61328v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000613285.1_ASM61328v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:47:11,367] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:11,381] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:47:11,381] [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_000613285.1	s__Acetobacter papayae	100.0	917	923	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_017377745.1	s__Acetobacter suratthaniensis	87.0244	748	923	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006539345.1	s__Acetobacter peroxydans	86.4028	680	923	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	100.00	100.00	1.00	1.00	3	-
GCF_017377735.1	s__Acetobacter sp017377735	80.4524	413	923	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008365315.1	s__Acetobacter sp008365315	79.9078	406	923	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014207635.1	s__Acetobacter lovaniensis	79.8732	387	923	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_011516925.1	s__Acetobacter fabarum	79.714	402	923	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	97.96	97.82	0.89	0.87	4	-
GCF_011516885.1	s__Acetobacter lambici	79.3654	378	923	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002153605.1	s__Acetobacter malorum_A	78.7102	264	923	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	96.53	96.53	0.89	0.89	2	-
GCF_001580615.1	s__Acetobacter malorum	78.4452	291	923	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	95.98	95.83	0.82	0.80	5	-
GCF_000613905.1	s__Acetobacter persici	78.3969	284	923	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	96.00	95.85	0.80	0.79	8	-
--------------------------------------------------------------------------------
[2024-01-24 13:47:11,383] [INFO] GTDB search result was written to GCF_000613285.1_ASM61328v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:47:11,383] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:47:11,388] [INFO] DFAST_QC result json was written to GCF_000613285.1_ASM61328v1_genomic.fna/dqc_result.json
[2024-01-24 13:47:11,388] [INFO] DFAST_QC completed!
[2024-01-24 13:47:11,388] [INFO] Total running time: 0h1m0s