[2024-01-24 11:05:18,094] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:05:18,097] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:05:18,097] [INFO] DQC Reference Directory: /var/lib/cwl/stg3516d6a5-a732-42b1-881c-9b367d66fac9/dqc_reference
[2024-01-24 11:05:19,306] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:05:19,308] [INFO] Task started: Prodigal
[2024-01-24 11:05:19,308] [INFO] Running command: gunzip -c /var/lib/cwl/stgf8013cde-bad4-4d32-8e00-5ec53e748f33/GCF_007483665.1_ASM748366v1_genomic.fna.gz | prodigal -d GCF_007483665.1_ASM748366v1_genomic.fna/cds.fna -a GCF_007483665.1_ASM748366v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:05:48,166] [INFO] Task succeeded: Prodigal
[2024-01-24 11:05:48,166] [INFO] Task started: HMMsearch
[2024-01-24 11:05:48,167] [INFO] Running command: hmmsearch --tblout GCF_007483665.1_ASM748366v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3516d6a5-a732-42b1-881c-9b367d66fac9/dqc_reference/reference_markers.hmm GCF_007483665.1_ASM748366v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:05:48,653] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:05:48,654] [INFO] Found 6/6 markers.
[2024-01-24 11:05:48,725] [INFO] Query marker FASTA was written to GCF_007483665.1_ASM748366v1_genomic.fna/markers.fasta
[2024-01-24 11:05:48,726] [INFO] Task started: Blastn
[2024-01-24 11:05:48,726] [INFO] Running command: blastn -query GCF_007483665.1_ASM748366v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3516d6a5-a732-42b1-881c-9b367d66fac9/dqc_reference/reference_markers.fasta -out GCF_007483665.1_ASM748366v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:49,989] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:49,993] [INFO] Selected 6 target genomes.
[2024-01-24 11:05:49,993] [INFO] Target genome list was writen to GCF_007483665.1_ASM748366v1_genomic.fna/target_genomes.txt
[2024-01-24 11:05:49,996] [INFO] Task started: fastANI
[2024-01-24 11:05:49,997] [INFO] Running command: fastANI --query /var/lib/cwl/stgf8013cde-bad4-4d32-8e00-5ec53e748f33/GCF_007483665.1_ASM748366v1_genomic.fna.gz --refList GCF_007483665.1_ASM748366v1_genomic.fna/target_genomes.txt --output GCF_007483665.1_ASM748366v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:06:08,834] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:08,834] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3516d6a5-a732-42b1-881c-9b367d66fac9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:06:08,835] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3516d6a5-a732-42b1-881c-9b367d66fac9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:06:08,842] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:06:08,842] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:06:08,842] [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 sichuanensis	strain=H14505	GCA_007483665.1	1969805	1969805	type	True	100.0	3120	3121	95	conclusive
Catellatospora paridis	strain=NEAU-CL2	GCA_009720365.1	1617086	1617086	type	True	92.484	2401	3121	95	below_threshold
Catellatospora chokoriensis	strain=2-25(1)	GCA_011297315.1	310353	310353	type	True	92.0877	2323	3121	95	below_threshold
Catellatospora citrea	strain=NBRC 14495	GCA_016862615.1	53366	53366	type	True	92.057	2380	3121	95	below_threshold
Catellatospora vulcania	strain=NEAU-JM1	GCA_009720385.1	1460450	1460450	type	True	91.597	2355	3121	95	below_threshold
Catellatospora methionotrophica	strain=NBRC 14553	GCA_016862655.1	121620	121620	type	True	90.1766	2137	3121	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:06:08,845] [INFO] DFAST Taxonomy check result was written to GCF_007483665.1_ASM748366v1_genomic.fna/tc_result.tsv
[2024-01-24 11:06:08,846] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:06:08,846] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:06:08,846] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3516d6a5-a732-42b1-881c-9b367d66fac9/dqc_reference/checkm_data
[2024-01-24 11:06:08,848] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:06:08,934] [INFO] Task started: CheckM
[2024-01-24 11:06:08,934] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007483665.1_ASM748366v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007483665.1_ASM748366v1_genomic.fna/checkm_input GCF_007483665.1_ASM748366v1_genomic.fna/checkm_result
[2024-01-24 11:07:42,267] [INFO] Task succeeded: CheckM
[2024-01-24 11:07:42,268] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:07:42,295] [INFO] ===== Completeness check finished =====
[2024-01-24 11:07:42,295] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:07:42,296] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007483665.1_ASM748366v1_genomic.fna/markers.fasta)
[2024-01-24 11:07:42,296] [INFO] Task started: Blastn
[2024-01-24 11:07:42,296] [INFO] Running command: blastn -query GCF_007483665.1_ASM748366v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3516d6a5-a732-42b1-881c-9b367d66fac9/dqc_reference/reference_markers_gtdb.fasta -out GCF_007483665.1_ASM748366v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:07:44,154] [INFO] Task succeeded: Blastn
[2024-01-24 11:07:44,158] [INFO] Selected 7 target genomes.
[2024-01-24 11:07:44,159] [INFO] Target genome list was writen to GCF_007483665.1_ASM748366v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:07:44,174] [INFO] Task started: fastANI
[2024-01-24 11:07:44,174] [INFO] Running command: fastANI --query /var/lib/cwl/stgf8013cde-bad4-4d32-8e00-5ec53e748f33/GCF_007483665.1_ASM748366v1_genomic.fna.gz --refList GCF_007483665.1_ASM748366v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007483665.1_ASM748366v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:08:05,103] [INFO] Task succeeded: fastANI
[2024-01-24 11:08:05,117] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:08:05,117] [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_007483665.1	s__Catellatospora sichuanensis	100.0	3120	3121	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_009720365.1	s__Catellatospora paridis	92.514	2398	3121	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	92.1144	2380	3121	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Catellatospora	95.0	97.34	95.99	0.88	0.83	4	-
GCF_009720385.1	s__Catellatospora vulcania	91.5898	2356	3121	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Catellatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862635.1	s__Catellatospora coxensis	90.6962	2310	3121	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	90.1179	2123	3121	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Catellatospora	95.0	99.99	99.99	0.99	0.99	2	-
GCF_018327705.1	s__Catellatospora sp018327705	83.6863	1801	3121	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Catellatospora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:08:05,120] [INFO] GTDB search result was written to GCF_007483665.1_ASM748366v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:08:05,120] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:08:05,123] [INFO] DFAST_QC result json was written to GCF_007483665.1_ASM748366v1_genomic.fna/dqc_result.json
[2024-01-24 11:08:05,123] [INFO] DFAST_QC completed!
[2024-01-24 11:08:05,124] [INFO] Total running time: 0h2m47s