[2024-01-25 19:48:05,767] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:48:05,768] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:48:05,768] [INFO] DQC Reference Directory: /var/lib/cwl/stgfb93336f-c8f8-4c3b-88ea-b8adcedb3754/dqc_reference
[2024-01-25 19:48:06,878] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:48:06,879] [INFO] Task started: Prodigal
[2024-01-25 19:48:06,880] [INFO] Running command: gunzip -c /var/lib/cwl/stg76c923b9-b69d-4093-9059-a26ffca692e1/GCF_003610235.1_ASM361023v1_genomic.fna.gz | prodigal -d GCF_003610235.1_ASM361023v1_genomic.fna/cds.fna -a GCF_003610235.1_ASM361023v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:48:34,576] [INFO] Task succeeded: Prodigal
[2024-01-25 19:48:34,576] [INFO] Task started: HMMsearch
[2024-01-25 19:48:34,576] [INFO] Running command: hmmsearch --tblout GCF_003610235.1_ASM361023v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfb93336f-c8f8-4c3b-88ea-b8adcedb3754/dqc_reference/reference_markers.hmm GCF_003610235.1_ASM361023v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:48:35,020] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:48:35,021] [INFO] Found 6/6 markers.
[2024-01-25 19:48:35,098] [INFO] Query marker FASTA was written to GCF_003610235.1_ASM361023v1_genomic.fna/markers.fasta
[2024-01-25 19:48:35,098] [INFO] Task started: Blastn
[2024-01-25 19:48:35,098] [INFO] Running command: blastn -query GCF_003610235.1_ASM361023v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfb93336f-c8f8-4c3b-88ea-b8adcedb3754/dqc_reference/reference_markers.fasta -out GCF_003610235.1_ASM361023v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:48:36,373] [INFO] Task succeeded: Blastn
[2024-01-25 19:48:36,375] [INFO] Selected 7 target genomes.
[2024-01-25 19:48:36,375] [INFO] Target genome list was writen to GCF_003610235.1_ASM361023v1_genomic.fna/target_genomes.txt
[2024-01-25 19:48:36,384] [INFO] Task started: fastANI
[2024-01-25 19:48:36,384] [INFO] Running command: fastANI --query /var/lib/cwl/stg76c923b9-b69d-4093-9059-a26ffca692e1/GCF_003610235.1_ASM361023v1_genomic.fna.gz --refList GCF_003610235.1_ASM361023v1_genomic.fna/target_genomes.txt --output GCF_003610235.1_ASM361023v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:48:56,566] [INFO] Task succeeded: fastANI
[2024-01-25 19:48:56,567] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfb93336f-c8f8-4c3b-88ea-b8adcedb3754/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:48:56,567] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfb93336f-c8f8-4c3b-88ea-b8adcedb3754/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:48:56,573] [INFO] Found 7 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:48:56,573] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-25 19:48:56,573] [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 citrea	strain=NBRC 14495	GCA_016862615.1	53366	53366	type	True	99.9769	3016	3108	95	inconclusive
Catellatospora chokoriensis	strain=2-25(1)	GCA_011297315.1	310353	310353	type	True	95.9921	2535	3108	95	inconclusive
Catellatospora paridis	strain=NEAU-CL2	GCA_009720365.1	1617086	1617086	type	True	94.6489	2558	3108	95	below_threshold
Catellatospora sichuanensis	strain=H14505	GCA_007483665.1	1969805	1969805	type	True	92.1435	2360	3108	95	below_threshold
Catellatospora vulcania	strain=NEAU-JM1	GCA_009720385.1	1460450	1460450	type	True	91.4709	2307	3108	95	below_threshold
Catellatospora methionotrophica	strain=IMSNU 22006	GCA_011297335.1	121620	121620	type	True	90.5914	2132	3108	95	below_threshold
Catellatospora methionotrophica	strain=NBRC 14553	GCA_016862655.1	121620	121620	type	True	90.5826	2143	3108	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:48:56,574] [INFO] DFAST Taxonomy check result was written to GCF_003610235.1_ASM361023v1_genomic.fna/tc_result.tsv
[2024-01-25 19:48:56,575] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:48:56,575] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:48:56,575] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfb93336f-c8f8-4c3b-88ea-b8adcedb3754/dqc_reference/checkm_data
[2024-01-25 19:48:56,576] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:48:56,657] [INFO] Task started: CheckM
[2024-01-25 19:48:56,657] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003610235.1_ASM361023v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003610235.1_ASM361023v1_genomic.fna/checkm_input GCF_003610235.1_ASM361023v1_genomic.fna/checkm_result
[2024-01-25 19:51:07,627] [INFO] Task succeeded: CheckM
[2024-01-25 19:51:07,631] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:51:07,654] [INFO] ===== Completeness check finished =====
[2024-01-25 19:51:07,654] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:51:07,655] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003610235.1_ASM361023v1_genomic.fna/markers.fasta)
[2024-01-25 19:51:07,655] [INFO] Task started: Blastn
[2024-01-25 19:51:07,655] [INFO] Running command: blastn -query GCF_003610235.1_ASM361023v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfb93336f-c8f8-4c3b-88ea-b8adcedb3754/dqc_reference/reference_markers_gtdb.fasta -out GCF_003610235.1_ASM361023v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:51:09,667] [INFO] Task succeeded: Blastn
[2024-01-25 19:51:09,669] [INFO] Selected 7 target genomes.
[2024-01-25 19:51:09,670] [INFO] Target genome list was writen to GCF_003610235.1_ASM361023v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:51:09,679] [INFO] Task started: fastANI
[2024-01-25 19:51:09,679] [INFO] Running command: fastANI --query /var/lib/cwl/stg76c923b9-b69d-4093-9059-a26ffca692e1/GCF_003610235.1_ASM361023v1_genomic.fna.gz --refList GCF_003610235.1_ASM361023v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003610235.1_ASM361023v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:51:30,139] [INFO] Task succeeded: fastANI
[2024-01-25 19:51:30,145] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:51:30,146] [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
GCA_003610235.1	s__Catellatospora citrea	100.0	3108	3108	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Catellatospora	95.0	97.34	95.99	0.88	0.83	4	conclusive
GCF_009720365.1	s__Catellatospora paridis	94.6489	2558	3108	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	92.1517	2359	3108	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	91.4429	2312	3108	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	91.0895	2276	3108	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	90.5465	2138	3108	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Catellatospora	95.0	99.99	99.99	0.99	0.99	2	-
GCF_016862575.1	s__Catellatospora bangladeshensis	86.7759	2031	3108	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Catellatospora	95.0	95.24	95.24	0.85	0.85	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:51:30,147] [INFO] GTDB search result was written to GCF_003610235.1_ASM361023v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:51:30,147] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:51:30,150] [INFO] DFAST_QC result json was written to GCF_003610235.1_ASM361023v1_genomic.fna/dqc_result.json
[2024-01-25 19:51:30,150] [INFO] DFAST_QC completed!
[2024-01-25 19:51:30,150] [INFO] Total running time: 0h3m24s