[2024-01-24 14:03:08,186] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:03:08,188] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:03:08,188] [INFO] DQC Reference Directory: /var/lib/cwl/stg2bd36920-5be0-41fc-8cf0-b1c179ee2649/dqc_reference
[2024-01-24 14:03:09,672] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:03:09,673] [INFO] Task started: Prodigal
[2024-01-24 14:03:09,674] [INFO] Running command: gunzip -c /var/lib/cwl/stgd32f09c4-c124-4e83-b5d9-7e2e0f75dc48/GCF_014202765.1_ASM1420276v1_genomic.fna.gz | prodigal -d GCF_014202765.1_ASM1420276v1_genomic.fna/cds.fna -a GCF_014202765.1_ASM1420276v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:03:27,155] [INFO] Task succeeded: Prodigal
[2024-01-24 14:03:27,156] [INFO] Task started: HMMsearch
[2024-01-24 14:03:27,156] [INFO] Running command: hmmsearch --tblout GCF_014202765.1_ASM1420276v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2bd36920-5be0-41fc-8cf0-b1c179ee2649/dqc_reference/reference_markers.hmm GCF_014202765.1_ASM1420276v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:03:27,517] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:03:27,519] [INFO] Found 6/6 markers.
[2024-01-24 14:03:27,574] [INFO] Query marker FASTA was written to GCF_014202765.1_ASM1420276v1_genomic.fna/markers.fasta
[2024-01-24 14:03:27,574] [INFO] Task started: Blastn
[2024-01-24 14:03:27,574] [INFO] Running command: blastn -query GCF_014202765.1_ASM1420276v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2bd36920-5be0-41fc-8cf0-b1c179ee2649/dqc_reference/reference_markers.fasta -out GCF_014202765.1_ASM1420276v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:03:28,339] [INFO] Task succeeded: Blastn
[2024-01-24 14:03:28,343] [INFO] Selected 15 target genomes.
[2024-01-24 14:03:28,343] [INFO] Target genome list was writen to GCF_014202765.1_ASM1420276v1_genomic.fna/target_genomes.txt
[2024-01-24 14:03:28,354] [INFO] Task started: fastANI
[2024-01-24 14:03:28,354] [INFO] Running command: fastANI --query /var/lib/cwl/stgd32f09c4-c124-4e83-b5d9-7e2e0f75dc48/GCF_014202765.1_ASM1420276v1_genomic.fna.gz --refList GCF_014202765.1_ASM1420276v1_genomic.fna/target_genomes.txt --output GCF_014202765.1_ASM1420276v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:03:42,532] [INFO] Task succeeded: fastANI
[2024-01-24 14:03:42,533] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2bd36920-5be0-41fc-8cf0-b1c179ee2649/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:03:42,533] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2bd36920-5be0-41fc-8cf0-b1c179ee2649/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:03:42,542] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:03:42,542] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:03:42,543] [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
Silvimonas terrae	strain=DSM 18233	GCA_014202765.1	300266	300266	type	True	100.0	1600	1600	95	conclusive
Silvimonas iriomotensis	strain=CGMCC 1.8859	GCA_014645535.1	449662	449662	type	True	85.3305	1242	1600	95	below_threshold
Silvimonas amylolytica	strain=CGMCC 1.8860	GCA_014645555.1	449663	449663	type	True	84.2587	1198	1600	95	below_threshold
Andreprevotia lacus	strain=DSM 23236	GCA_900176275.1	1121000	1121000	type	True	78.2483	362	1600	95	below_threshold
Andreprevotia chitinilytica	strain=DSM 18519	GCA_000711875.1	396808	396808	type	True	77.9706	338	1600	95	below_threshold
Jeongeupia chitinilytica	strain=KCTC 23701	GCA_014652315.1	1041641	1041641	type	True	77.8165	287	1600	95	below_threshold
Chitinilyticum litopenaei	strain=DSM 21440	GCA_000428145.1	1121276	1121276	type	True	77.6754	251	1600	95	below_threshold
Chitinilyticum piscinae	strain=4Y14	GCA_015223195.1	2866724	2866724	type	True	77.4629	237	1600	95	below_threshold
Formivibrio citricus	strain=DSM 6150	GCA_900115065.1	83765	83765	type	True	77.1273	188	1600	95	below_threshold
Crenobacter cavernae	strain=K1W11S-77	GCA_003355495.1	2290923	2290923	type	True	76.6934	128	1600	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:03:42,544] [INFO] DFAST Taxonomy check result was written to GCF_014202765.1_ASM1420276v1_genomic.fna/tc_result.tsv
[2024-01-24 14:03:42,545] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:03:42,545] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:03:42,545] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2bd36920-5be0-41fc-8cf0-b1c179ee2649/dqc_reference/checkm_data
[2024-01-24 14:03:42,546] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:03:42,598] [INFO] Task started: CheckM
[2024-01-24 14:03:42,599] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014202765.1_ASM1420276v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014202765.1_ASM1420276v1_genomic.fna/checkm_input GCF_014202765.1_ASM1420276v1_genomic.fna/checkm_result
[2024-01-24 14:04:33,592] [INFO] Task succeeded: CheckM
[2024-01-24 14:04:33,594] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:04:33,616] [INFO] ===== Completeness check finished =====
[2024-01-24 14:04:33,617] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:04:33,617] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014202765.1_ASM1420276v1_genomic.fna/markers.fasta)
[2024-01-24 14:04:33,617] [INFO] Task started: Blastn
[2024-01-24 14:04:33,618] [INFO] Running command: blastn -query GCF_014202765.1_ASM1420276v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2bd36920-5be0-41fc-8cf0-b1c179ee2649/dqc_reference/reference_markers_gtdb.fasta -out GCF_014202765.1_ASM1420276v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:04:34,687] [INFO] Task succeeded: Blastn
[2024-01-24 14:04:34,691] [INFO] Selected 10 target genomes.
[2024-01-24 14:04:34,691] [INFO] Target genome list was writen to GCF_014202765.1_ASM1420276v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:04:34,701] [INFO] Task started: fastANI
[2024-01-24 14:04:34,702] [INFO] Running command: fastANI --query /var/lib/cwl/stgd32f09c4-c124-4e83-b5d9-7e2e0f75dc48/GCF_014202765.1_ASM1420276v1_genomic.fna.gz --refList GCF_014202765.1_ASM1420276v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014202765.1_ASM1420276v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:04:45,925] [INFO] Task succeeded: fastANI
[2024-01-24 14:04:45,937] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:04:45,937] [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_014202765.1	s__Silvimonas terrae	100.0	1600	1600	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Silvimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014645535.1	s__Silvimonas iriomotensis	85.3377	1240	1600	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Silvimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014645555.1	s__Silvimonas amylolytica	84.2659	1197	1600	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Silvimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001313065.1	s__Amantichitinum sp001313065	79.1692	516	1600	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Amantichitinum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001294205.1	s__Amantichitinum ursilacus	79.0446	663	1600	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Amantichitinum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900176275.1	s__Andreprevotia lacus	78.2788	359	1600	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Andreprevotia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009848685.1	s__Andreprevotia sp009848685	78.244	335	1600	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Andreprevotia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000711875.1	s__Andreprevotia chitinilytica	77.9698	338	1600	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Andreprevotia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014652315.1	s__Jeongeupia chitinilytica	77.8287	286	1600	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Jeongeupia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003355495.1	s__Crenobacter cavernae	76.6775	129	1600	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Crenobacter	95.0	96.17	96.17	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:04:45,939] [INFO] GTDB search result was written to GCF_014202765.1_ASM1420276v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:04:45,939] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:04:45,942] [INFO] DFAST_QC result json was written to GCF_014202765.1_ASM1420276v1_genomic.fna/dqc_result.json
[2024-01-24 14:04:45,943] [INFO] DFAST_QC completed!
[2024-01-24 14:04:45,943] [INFO] Total running time: 0h1m38s