[2024-01-24 12:29:39,466] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:29:39,470] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:29:39,470] [INFO] DQC Reference Directory: /var/lib/cwl/stg5192a405-18d1-40f5-8b2e-6e7df9e9674b/dqc_reference
[2024-01-24 12:29:42,403] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:29:42,404] [INFO] Task started: Prodigal
[2024-01-24 12:29:42,404] [INFO] Running command: gunzip -c /var/lib/cwl/stgcc99111a-db6a-4696-9a45-91a3547fafa9/GCF_019083965.1_ASM1908396v1_genomic.fna.gz | prodigal -d GCF_019083965.1_ASM1908396v1_genomic.fna/cds.fna -a GCF_019083965.1_ASM1908396v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:30:13,764] [INFO] Task succeeded: Prodigal
[2024-01-24 12:30:13,765] [INFO] Task started: HMMsearch
[2024-01-24 12:30:13,765] [INFO] Running command: hmmsearch --tblout GCF_019083965.1_ASM1908396v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5192a405-18d1-40f5-8b2e-6e7df9e9674b/dqc_reference/reference_markers.hmm GCF_019083965.1_ASM1908396v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:30:14,127] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:30:14,128] [INFO] Found 6/6 markers.
[2024-01-24 12:30:14,197] [INFO] Query marker FASTA was written to GCF_019083965.1_ASM1908396v1_genomic.fna/markers.fasta
[2024-01-24 12:30:14,198] [INFO] Task started: Blastn
[2024-01-24 12:30:14,198] [INFO] Running command: blastn -query GCF_019083965.1_ASM1908396v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5192a405-18d1-40f5-8b2e-6e7df9e9674b/dqc_reference/reference_markers.fasta -out GCF_019083965.1_ASM1908396v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:30:15,656] [INFO] Task succeeded: Blastn
[2024-01-24 12:30:15,661] [INFO] Selected 8 target genomes.
[2024-01-24 12:30:15,662] [INFO] Target genome list was writen to GCF_019083965.1_ASM1908396v1_genomic.fna/target_genomes.txt
[2024-01-24 12:30:15,674] [INFO] Task started: fastANI
[2024-01-24 12:30:15,675] [INFO] Running command: fastANI --query /var/lib/cwl/stgcc99111a-db6a-4696-9a45-91a3547fafa9/GCF_019083965.1_ASM1908396v1_genomic.fna.gz --refList GCF_019083965.1_ASM1908396v1_genomic.fna/target_genomes.txt --output GCF_019083965.1_ASM1908396v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:30:37,110] [INFO] Task succeeded: fastANI
[2024-01-24 12:30:37,111] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5192a405-18d1-40f5-8b2e-6e7df9e9674b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:30:37,111] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5192a405-18d1-40f5-8b2e-6e7df9e9674b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:30:37,124] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:30:37,124] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:30:37,124] [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
Catellatospora tritici	strain=NEAU-YM18	GCA_019083965.1	2851566	2851566	type	True	100.0	3091	3172	95	conclusive
Catellatospora vulcania	strain=NEAU-JM1	GCA_009720385.1	1460450	1460450	type	True	83.8808	1903	3172	95	below_threshold
Catellatospora chokoriensis	strain=2-25(1)	GCA_011297315.1	310353	310353	type	True	83.7826	1824	3172	95	below_threshold
Catellatospora paridis	strain=NEAU-CL2	GCA_009720365.1	1617086	1617086	type	True	83.7654	1861	3172	95	below_threshold
Catellatospora methionotrophica	strain=IMSNU 22006	GCA_011297335.1	121620	121620	type	True	83.7254	1751	3172	95	below_threshold
Catellatospora citrea	strain=NBRC 14495	GCA_016862615.1	53366	53366	type	True	83.6846	1865	3172	95	below_threshold
Catellatospora sichuanensis	strain=H14505	GCA_007483665.1	1969805	1969805	type	True	83.6723	1846	3172	95	below_threshold
Catellatospora methionotrophica	strain=NBRC 14553	GCA_016862655.1	121620	121620	type	True	83.6375	1783	3172	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:30:37,126] [INFO] DFAST Taxonomy check result was written to GCF_019083965.1_ASM1908396v1_genomic.fna/tc_result.tsv
[2024-01-24 12:30:37,127] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:30:37,127] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:30:37,128] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5192a405-18d1-40f5-8b2e-6e7df9e9674b/dqc_reference/checkm_data
[2024-01-24 12:30:37,130] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:30:37,220] [INFO] Task started: CheckM
[2024-01-24 12:30:37,221] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019083965.1_ASM1908396v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019083965.1_ASM1908396v1_genomic.fna/checkm_input GCF_019083965.1_ASM1908396v1_genomic.fna/checkm_result
[2024-01-24 12:32:20,377] [INFO] Task succeeded: CheckM
[2024-01-24 12:32:20,379] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:32:20,406] [INFO] ===== Completeness check finished =====
[2024-01-24 12:32:20,406] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:32:20,407] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019083965.1_ASM1908396v1_genomic.fna/markers.fasta)
[2024-01-24 12:32:20,407] [INFO] Task started: Blastn
[2024-01-24 12:32:20,407] [INFO] Running command: blastn -query GCF_019083965.1_ASM1908396v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5192a405-18d1-40f5-8b2e-6e7df9e9674b/dqc_reference/reference_markers_gtdb.fasta -out GCF_019083965.1_ASM1908396v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:22,677] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:22,682] [INFO] Selected 9 target genomes.
[2024-01-24 12:32:22,682] [INFO] Target genome list was writen to GCF_019083965.1_ASM1908396v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:32:22,698] [INFO] Task started: fastANI
[2024-01-24 12:32:22,698] [INFO] Running command: fastANI --query /var/lib/cwl/stgcc99111a-db6a-4696-9a45-91a3547fafa9/GCF_019083965.1_ASM1908396v1_genomic.fna.gz --refList GCF_019083965.1_ASM1908396v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019083965.1_ASM1908396v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:32:46,959] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:46,969] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:32:46,969] [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_019083965.1	s__Catellatospora sp019083965	100.0	3083	3172	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Catellatospora	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_018327705.1	s__Catellatospora sp018327705	89.8517	2215	3172	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Catellatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862575.1	s__Catellatospora bangladeshensis	84.0742	1817	3172	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Catellatospora	95.0	95.24	95.24	0.85	0.85	2	-
GCF_016862635.1	s__Catellatospora coxensis	83.9776	1828	3172	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Catellatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009720385.1	s__Catellatospora vulcania	83.8859	1903	3172	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Catellatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011297335.1	s__Catellatospora methionotrophica	83.7438	1746	3172	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Catellatospora	95.0	99.99	99.99	0.99	0.99	2	-
GCF_007483665.1	s__Catellatospora sichuanensis	83.7216	1838	3172	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Catellatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009720365.1	s__Catellatospora paridis	83.721	1869	3172	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Catellatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003610235.1	s__Catellatospora citrea	83.677	1881	3172	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Catellatospora	95.0	97.34	95.99	0.88	0.83	4	-
--------------------------------------------------------------------------------
[2024-01-24 12:32:46,971] [INFO] GTDB search result was written to GCF_019083965.1_ASM1908396v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:32:46,971] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:32:46,976] [INFO] DFAST_QC result json was written to GCF_019083965.1_ASM1908396v1_genomic.fna/dqc_result.json
[2024-01-24 12:32:46,976] [INFO] DFAST_QC completed!
[2024-01-24 12:32:46,976] [INFO] Total running time: 0h3m8s