[2024-01-25 20:19:35,446] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:19:35,448] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:19:35,448] [INFO] DQC Reference Directory: /var/lib/cwl/stg4206e5e5-7c7d-4cc8-a03d-6adc70a1ae2b/dqc_reference
[2024-01-25 20:19:36,609] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:19:36,610] [INFO] Task started: Prodigal
[2024-01-25 20:19:36,610] [INFO] Running command: gunzip -c /var/lib/cwl/stg8b8bff71-6db9-487a-bfe3-95597e1d6b48/GCF_026283945.1_ASM2628394v1_genomic.fna.gz | prodigal -d GCF_026283945.1_ASM2628394v1_genomic.fna/cds.fna -a GCF_026283945.1_ASM2628394v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:19:50,831] [INFO] Task succeeded: Prodigal
[2024-01-25 20:19:50,832] [INFO] Task started: HMMsearch
[2024-01-25 20:19:50,832] [INFO] Running command: hmmsearch --tblout GCF_026283945.1_ASM2628394v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4206e5e5-7c7d-4cc8-a03d-6adc70a1ae2b/dqc_reference/reference_markers.hmm GCF_026283945.1_ASM2628394v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:19:51,055] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:19:51,056] [INFO] Found 6/6 markers.
[2024-01-25 20:19:51,094] [INFO] Query marker FASTA was written to GCF_026283945.1_ASM2628394v1_genomic.fna/markers.fasta
[2024-01-25 20:19:51,094] [INFO] Task started: Blastn
[2024-01-25 20:19:51,094] [INFO] Running command: blastn -query GCF_026283945.1_ASM2628394v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4206e5e5-7c7d-4cc8-a03d-6adc70a1ae2b/dqc_reference/reference_markers.fasta -out GCF_026283945.1_ASM2628394v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:19:52,058] [INFO] Task succeeded: Blastn
[2024-01-25 20:19:52,062] [INFO] Selected 10 target genomes.
[2024-01-25 20:19:52,062] [INFO] Target genome list was writen to GCF_026283945.1_ASM2628394v1_genomic.fna/target_genomes.txt
[2024-01-25 20:19:52,064] [INFO] Task started: fastANI
[2024-01-25 20:19:52,064] [INFO] Running command: fastANI --query /var/lib/cwl/stg8b8bff71-6db9-487a-bfe3-95597e1d6b48/GCF_026283945.1_ASM2628394v1_genomic.fna.gz --refList GCF_026283945.1_ASM2628394v1_genomic.fna/target_genomes.txt --output GCF_026283945.1_ASM2628394v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:20:01,256] [INFO] Task succeeded: fastANI
[2024-01-25 20:20:01,256] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4206e5e5-7c7d-4cc8-a03d-6adc70a1ae2b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:20:01,257] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4206e5e5-7c7d-4cc8-a03d-6adc70a1ae2b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:20:01,264] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 20:20:01,264] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 20:20:01,264] [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
Dyella kyungheensis	strain=THG-B117	GCA_016905005.1	1242174	1242174	type	True	82.5903	877	1519	95	below_threshold
Dyella solisilvae	strain=DHG54	GCA_003351225.1	1920168	1920168	type	True	82.5587	916	1519	95	below_threshold
Dyella japonica	strain=DSM 16301	GCA_001010355.1	231455	231455	type	True	82.3474	756	1519	95	below_threshold
Dyella amyloliquefaciens	strain=DHC06	GCA_004296575.1	1770545	1770545	type	True	82.252	906	1519	95	below_threshold
Dyella telluris	strain=G9	GCA_014297575.1	2763498	2763498	type	True	82.1578	895	1519	95	below_threshold
Fulvimonas soli	strain=LMG 19981	GCA_006352285.1	155197	155197	type	True	80.6507	609	1519	95	below_threshold
Fulvimonas soli	strain=DSM 14263	GCA_003148905.1	155197	155197	type	True	80.5976	663	1519	95	below_threshold
Dyella acidiphila	strain=7MK23	GCA_014863405.1	2775866	2775866	type	True	80.1879	626	1519	95	below_threshold
Frateuria flava	strain=MAH-13	GCA_017837635.1	2821489	2821489	type	True	80.0856	545	1519	95	below_threshold
Tahibacter caeni	strain=BUT-6	GCA_024609805.1	1453545	1453545	type	True	78.0081	281	1519	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:20:01,265] [INFO] DFAST Taxonomy check result was written to GCF_026283945.1_ASM2628394v1_genomic.fna/tc_result.tsv
[2024-01-25 20:20:01,266] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:20:01,266] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:20:01,266] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4206e5e5-7c7d-4cc8-a03d-6adc70a1ae2b/dqc_reference/checkm_data
[2024-01-25 20:20:01,267] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:20:01,309] [INFO] Task started: CheckM
[2024-01-25 20:20:01,309] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_026283945.1_ASM2628394v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_026283945.1_ASM2628394v1_genomic.fna/checkm_input GCF_026283945.1_ASM2628394v1_genomic.fna/checkm_result
[2024-01-25 20:20:44,746] [INFO] Task succeeded: CheckM
[2024-01-25 20:20:44,747] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:20:44,765] [INFO] ===== Completeness check finished =====
[2024-01-25 20:20:44,766] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:20:44,767] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_026283945.1_ASM2628394v1_genomic.fna/markers.fasta)
[2024-01-25 20:20:44,767] [INFO] Task started: Blastn
[2024-01-25 20:20:44,767] [INFO] Running command: blastn -query GCF_026283945.1_ASM2628394v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4206e5e5-7c7d-4cc8-a03d-6adc70a1ae2b/dqc_reference/reference_markers_gtdb.fasta -out GCF_026283945.1_ASM2628394v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:20:46,688] [INFO] Task succeeded: Blastn
[2024-01-25 20:20:46,692] [INFO] Selected 14 target genomes.
[2024-01-25 20:20:46,692] [INFO] Target genome list was writen to GCF_026283945.1_ASM2628394v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:20:46,695] [INFO] Task started: fastANI
[2024-01-25 20:20:46,695] [INFO] Running command: fastANI --query /var/lib/cwl/stg8b8bff71-6db9-487a-bfe3-95597e1d6b48/GCF_026283945.1_ASM2628394v1_genomic.fna.gz --refList GCF_026283945.1_ASM2628394v1_genomic.fna/target_genomes_gtdb.txt --output GCF_026283945.1_ASM2628394v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:21:01,724] [INFO] Task succeeded: fastANI
[2024-01-25 20:21:01,732] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 20:21:01,733] [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_003332825.1	s__Dyella sp003332825	82.78	873	1519	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016905005.1	s__Dyella kyungheensis	82.6025	874	1519	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003351225.1	s__Dyella solisilvae	82.5514	917	1519	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003201105.1	s__Dyella jiangningensis_B	82.5142	897	1519	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	99.99	99.99	0.99	0.99	2	-
GCF_000725385.1	s__Dyella japonica_C	82.466	885	1519	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003264855.1	s__Dyella jiangningensis_C	82.3675	897	1519	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001010355.1	s__Dyella japonica	82.3658	754	1519	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016586165.1	s__Dyella sp016586165	82.2962	887	1519	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000632805.1	s__Dyella jiangningensis	82.2553	868	1519	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004296575.1	s__Dyella sp004296575	82.2276	909	1519	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003688835.1	s__Dyella sp003688835	82.1803	910	1519	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014297575.1	s__Dyella sp014297575	82.1568	895	1519	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003121485.1	s__Dyella sp003121485	81.978	827	1519	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012275375.1	s__Dyella sp012275375	81.6884	730	1519	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	96.64	95.58	0.92	0.90	4	-
--------------------------------------------------------------------------------
[2024-01-25 20:21:01,734] [INFO] GTDB search result was written to GCF_026283945.1_ASM2628394v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:21:01,735] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:21:01,737] [INFO] DFAST_QC result json was written to GCF_026283945.1_ASM2628394v1_genomic.fna/dqc_result.json
[2024-01-25 20:21:01,737] [INFO] DFAST_QC completed!
[2024-01-25 20:21:01,737] [INFO] Total running time: 0h1m26s