[2024-01-24 12:30:18,324] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:30:18,326] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:30:18,327] [INFO] DQC Reference Directory: /var/lib/cwl/stg80e50f3b-e4a7-4947-9499-4ac97426ab73/dqc_reference
[2024-01-24 12:30:19,661] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:30:19,662] [INFO] Task started: Prodigal
[2024-01-24 12:30:19,662] [INFO] Running command: gunzip -c /var/lib/cwl/stg30e67ab1-e0b0-4c99-8346-3fa7e77791ba/GCF_016862575.1_ASM1686257v1_genomic.fna.gz | prodigal -d GCF_016862575.1_ASM1686257v1_genomic.fna/cds.fna -a GCF_016862575.1_ASM1686257v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:30:45,599] [INFO] Task succeeded: Prodigal
[2024-01-24 12:30:45,600] [INFO] Task started: HMMsearch
[2024-01-24 12:30:45,600] [INFO] Running command: hmmsearch --tblout GCF_016862575.1_ASM1686257v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg80e50f3b-e4a7-4947-9499-4ac97426ab73/dqc_reference/reference_markers.hmm GCF_016862575.1_ASM1686257v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:30:45,929] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:30:45,930] [INFO] Found 6/6 markers.
[2024-01-24 12:30:45,998] [INFO] Query marker FASTA was written to GCF_016862575.1_ASM1686257v1_genomic.fna/markers.fasta
[2024-01-24 12:30:45,999] [INFO] Task started: Blastn
[2024-01-24 12:30:45,999] [INFO] Running command: blastn -query GCF_016862575.1_ASM1686257v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg80e50f3b-e4a7-4947-9499-4ac97426ab73/dqc_reference/reference_markers.fasta -out GCF_016862575.1_ASM1686257v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:30:47,264] [INFO] Task succeeded: Blastn
[2024-01-24 12:30:47,268] [INFO] Selected 7 target genomes.
[2024-01-24 12:30:47,268] [INFO] Target genome list was writen to GCF_016862575.1_ASM1686257v1_genomic.fna/target_genomes.txt
[2024-01-24 12:30:47,272] [INFO] Task started: fastANI
[2024-01-24 12:30:47,272] [INFO] Running command: fastANI --query /var/lib/cwl/stg30e67ab1-e0b0-4c99-8346-3fa7e77791ba/GCF_016862575.1_ASM1686257v1_genomic.fna.gz --refList GCF_016862575.1_ASM1686257v1_genomic.fna/target_genomes.txt --output GCF_016862575.1_ASM1686257v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:31:05,521] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:05,521] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg80e50f3b-e4a7-4947-9499-4ac97426ab73/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:31:05,522] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg80e50f3b-e4a7-4947-9499-4ac97426ab73/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:31:05,529] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:31:05,529] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:31:05,529] [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 chokoriensis	strain=2-25(1)	GCA_011297315.1	310353	310353	type	True	86.8728	1965	2882	95	below_threshold
Catellatospora citrea	strain=NBRC 14495	GCA_016862615.1	53366	53366	type	True	86.8608	2007	2882	95	below_threshold
Catellatospora vulcania	strain=NEAU-JM1	GCA_009720385.1	1460450	1460450	type	True	86.7845	2075	2882	95	below_threshold
Catellatospora paridis	strain=NEAU-CL2	GCA_009720365.1	1617086	1617086	type	True	86.6878	2024	2882	95	below_threshold
Catellatospora methionotrophica	strain=NBRC 14553	GCA_016862655.1	121620	121620	type	True	86.6211	1904	2882	95	below_threshold
Catellatospora sichuanensis	strain=H14505	GCA_007483665.1	1969805	1969805	type	True	86.5933	2057	2882	95	below_threshold
Catellatospora methionotrophica	strain=IMSNU 22006	GCA_011297335.1	121620	121620	type	True	86.5237	1913	2882	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:31:05,530] [INFO] DFAST Taxonomy check result was written to GCF_016862575.1_ASM1686257v1_genomic.fna/tc_result.tsv
[2024-01-24 12:31:05,531] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:31:05,531] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:31:05,531] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg80e50f3b-e4a7-4947-9499-4ac97426ab73/dqc_reference/checkm_data
[2024-01-24 12:31:05,532] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:31:05,608] [INFO] Task started: CheckM
[2024-01-24 12:31:05,609] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016862575.1_ASM1686257v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016862575.1_ASM1686257v1_genomic.fna/checkm_input GCF_016862575.1_ASM1686257v1_genomic.fna/checkm_result
[2024-01-24 12:32:24,460] [INFO] Task succeeded: CheckM
[2024-01-24 12:32:24,461] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:32:24,484] [INFO] ===== Completeness check finished =====
[2024-01-24 12:32:24,484] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:32:24,484] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016862575.1_ASM1686257v1_genomic.fna/markers.fasta)
[2024-01-24 12:32:24,485] [INFO] Task started: Blastn
[2024-01-24 12:32:24,485] [INFO] Running command: blastn -query GCF_016862575.1_ASM1686257v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg80e50f3b-e4a7-4947-9499-4ac97426ab73/dqc_reference/reference_markers_gtdb.fasta -out GCF_016862575.1_ASM1686257v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:26,493] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:26,496] [INFO] Selected 7 target genomes.
[2024-01-24 12:32:26,496] [INFO] Target genome list was writen to GCF_016862575.1_ASM1686257v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:32:26,501] [INFO] Task started: fastANI
[2024-01-24 12:32:26,501] [INFO] Running command: fastANI --query /var/lib/cwl/stg30e67ab1-e0b0-4c99-8346-3fa7e77791ba/GCF_016862575.1_ASM1686257v1_genomic.fna.gz --refList GCF_016862575.1_ASM1686257v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016862575.1_ASM1686257v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:32:45,621] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:45,628] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:32:45,628] [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_016862575.1	s__Catellatospora bangladeshensis	100.0	2874	2882	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Catellatospora	95.0	95.24	95.24	0.85	0.85	2	conclusive
GCF_016862635.1	s__Catellatospora coxensis	87.0375	2082	2882	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	86.7997	2071	2882	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	86.7581	2034	2882	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Catellatospora	95.0	97.34	95.99	0.88	0.83	4	-
GCF_009720365.1	s__Catellatospora paridis	86.6644	2027	2882	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Catellatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007483665.1	s__Catellatospora sichuanensis	86.6187	2054	2882	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	86.5507	1909	2882	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Catellatospora	95.0	99.99	99.99	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:32:45,631] [INFO] GTDB search result was written to GCF_016862575.1_ASM1686257v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:32:45,631] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:32:45,634] [INFO] DFAST_QC result json was written to GCF_016862575.1_ASM1686257v1_genomic.fna/dqc_result.json
[2024-01-24 12:32:45,634] [INFO] DFAST_QC completed!
[2024-01-24 12:32:45,634] [INFO] Total running time: 0h2m27s