[2024-01-24 11:21:07,407] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:21:07,409] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:21:07,409] [INFO] DQC Reference Directory: /var/lib/cwl/stg7d5ab456-2f0a-4b0b-b067-c8efc88e69de/dqc_reference
[2024-01-24 11:21:11,960] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:21:11,961] [INFO] Task started: Prodigal
[2024-01-24 11:21:11,961] [INFO] Running command: gunzip -c /var/lib/cwl/stgb4febdf0-fad8-4409-ab85-de1f7ba64f8d/GCF_016862655.1_ASM1686265v1_genomic.fna.gz | prodigal -d GCF_016862655.1_ASM1686265v1_genomic.fna/cds.fna -a GCF_016862655.1_ASM1686265v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:21:37,287] [INFO] Task succeeded: Prodigal
[2024-01-24 11:21:37,288] [INFO] Task started: HMMsearch
[2024-01-24 11:21:37,288] [INFO] Running command: hmmsearch --tblout GCF_016862655.1_ASM1686265v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7d5ab456-2f0a-4b0b-b067-c8efc88e69de/dqc_reference/reference_markers.hmm GCF_016862655.1_ASM1686265v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:21:37,663] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:21:37,665] [INFO] Found 6/6 markers.
[2024-01-24 11:21:37,728] [INFO] Query marker FASTA was written to GCF_016862655.1_ASM1686265v1_genomic.fna/markers.fasta
[2024-01-24 11:21:37,729] [INFO] Task started: Blastn
[2024-01-24 11:21:37,729] [INFO] Running command: blastn -query GCF_016862655.1_ASM1686265v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7d5ab456-2f0a-4b0b-b067-c8efc88e69de/dqc_reference/reference_markers.fasta -out GCF_016862655.1_ASM1686265v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:21:39,003] [INFO] Task succeeded: Blastn
[2024-01-24 11:21:39,007] [INFO] Selected 11 target genomes.
[2024-01-24 11:21:39,007] [INFO] Target genome list was writen to GCF_016862655.1_ASM1686265v1_genomic.fna/target_genomes.txt
[2024-01-24 11:21:39,013] [INFO] Task started: fastANI
[2024-01-24 11:21:39,013] [INFO] Running command: fastANI --query /var/lib/cwl/stgb4febdf0-fad8-4409-ab85-de1f7ba64f8d/GCF_016862655.1_ASM1686265v1_genomic.fna.gz --refList GCF_016862655.1_ASM1686265v1_genomic.fna/target_genomes.txt --output GCF_016862655.1_ASM1686265v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:22:06,089] [INFO] Task succeeded: fastANI
[2024-01-24 11:22:06,090] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7d5ab456-2f0a-4b0b-b067-c8efc88e69de/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:22:06,090] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7d5ab456-2f0a-4b0b-b067-c8efc88e69de/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:22:06,099] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:22:06,100] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:22:06,100] [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 methionotrophica	strain=NBRC 14553	GCA_016862655.1	121620	121620	type	True	100.0	2755	2758	95	conclusive
Catellatospora methionotrophica	strain=IMSNU 22006	GCA_011297335.1	121620	121620	type	True	99.992	2741	2758	95	conclusive
Catellatospora citrea	strain=NBRC 14495	GCA_016862615.1	53366	53366	type	True	90.8004	2109	2758	95	below_threshold
Catellatospora paridis	strain=NEAU-CL2	GCA_009720365.1	1617086	1617086	type	True	90.7466	2124	2758	95	below_threshold
Catellatospora chokoriensis	strain=2-25(1)	GCA_011297315.1	310353	310353	type	True	90.6562	2053	2758	95	below_threshold
Catellatospora vulcania	strain=NEAU-JM1	GCA_009720385.1	1460450	1460450	type	True	90.3149	2249	2758	95	below_threshold
Catellatospora sichuanensis	strain=H14505	GCA_007483665.1	1969805	1969805	type	True	90.2155	2130	2758	95	below_threshold
Phytohabitans suffuscus	strain=NBRC 105367	GCA_011764565.1	624315	624315	type	True	78.1936	1182	2758	95	below_threshold
Actinoplanes ianthinogenes	strain=JCM 3249	GCA_014648375.1	122358	122358	type	True	77.7248	1131	2758	95	below_threshold
Actinoplanes ianthinogenes	strain=NBRC 13996	GCA_018324205.1	122358	122358	type	True	77.6899	1129	2758	95	below_threshold
Cryptosporangium phraense	strain=A-T 5661	GCA_006912135.1	2593070	2593070	type	True	76.3755	799	2758	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:22:06,102] [INFO] DFAST Taxonomy check result was written to GCF_016862655.1_ASM1686265v1_genomic.fna/tc_result.tsv
[2024-01-24 11:22:06,102] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:22:06,102] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:22:06,103] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7d5ab456-2f0a-4b0b-b067-c8efc88e69de/dqc_reference/checkm_data
[2024-01-24 11:22:06,104] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:22:06,181] [INFO] Task started: CheckM
[2024-01-24 11:22:06,181] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016862655.1_ASM1686265v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016862655.1_ASM1686265v1_genomic.fna/checkm_input GCF_016862655.1_ASM1686265v1_genomic.fna/checkm_result
[2024-01-24 11:23:26,804] [INFO] Task succeeded: CheckM
[2024-01-24 11:23:26,805] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:23:26,826] [INFO] ===== Completeness check finished =====
[2024-01-24 11:23:26,826] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:23:26,827] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016862655.1_ASM1686265v1_genomic.fna/markers.fasta)
[2024-01-24 11:23:26,827] [INFO] Task started: Blastn
[2024-01-24 11:23:26,827] [INFO] Running command: blastn -query GCF_016862655.1_ASM1686265v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7d5ab456-2f0a-4b0b-b067-c8efc88e69de/dqc_reference/reference_markers_gtdb.fasta -out GCF_016862655.1_ASM1686265v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:23:28,753] [INFO] Task succeeded: Blastn
[2024-01-24 11:23:28,756] [INFO] Selected 11 target genomes.
[2024-01-24 11:23:28,757] [INFO] Target genome list was writen to GCF_016862655.1_ASM1686265v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:23:28,765] [INFO] Task started: fastANI
[2024-01-24 11:23:28,765] [INFO] Running command: fastANI --query /var/lib/cwl/stgb4febdf0-fad8-4409-ab85-de1f7ba64f8d/GCF_016862655.1_ASM1686265v1_genomic.fna.gz --refList GCF_016862655.1_ASM1686265v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016862655.1_ASM1686265v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:23:55,737] [INFO] Task succeeded: fastANI
[2024-01-24 11:23:55,748] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:23:55,748] [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_011297335.1	s__Catellatospora methionotrophica	99.992	2741	2758	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Catellatospora	95.0	99.99	99.99	0.99	0.99	2	conclusive
GCF_009720365.1	s__Catellatospora paridis	90.7399	2125	2758	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	90.7345	2126	2758	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	90.3365	2246	2758	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	90.2064	2132	2758	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	90.1388	2131	2758	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	86.3939	1922	2758	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Catellatospora	95.0	95.24	95.24	0.85	0.85	2	-
GCF_011764565.1	s__Phytohabitans suffuscus	78.2128	1175	2758	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Phytohabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000389965.1	s__Actinoplanes sp000389965	77.8862	985	2758	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018324205.1	s__Actinoplanes ianthinogenes	77.6742	1132	2758	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	99.99	99.99	0.99	0.99	2	-
GCF_006912135.1	s__Cryptosporangium phraense	76.3971	790	2758	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Cryptosporangiaceae;g__Cryptosporangium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:23:55,749] [INFO] GTDB search result was written to GCF_016862655.1_ASM1686265v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:23:55,750] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:23:55,753] [INFO] DFAST_QC result json was written to GCF_016862655.1_ASM1686265v1_genomic.fna/dqc_result.json
[2024-01-24 11:23:55,753] [INFO] DFAST_QC completed!
[2024-01-24 11:23:55,753] [INFO] Total running time: 0h2m48s