[2024-01-25 18:56:50,567] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:56:50,568] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:56:50,569] [INFO] DQC Reference Directory: /var/lib/cwl/stg00ec392a-794c-4ec2-b358-684dbcacfbc9/dqc_reference
[2024-01-25 18:56:51,734] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:56:51,734] [INFO] Task started: Prodigal
[2024-01-25 18:56:51,735] [INFO] Running command: gunzip -c /var/lib/cwl/stg0a9b30ce-8e44-4d0f-ac01-788ac4792c42/GCF_016925535.1_ASM1692553v1_genomic.fna.gz | prodigal -d GCF_016925535.1_ASM1692553v1_genomic.fna/cds.fna -a GCF_016925535.1_ASM1692553v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:57:03,139] [INFO] Task succeeded: Prodigal
[2024-01-25 18:57:03,139] [INFO] Task started: HMMsearch
[2024-01-25 18:57:03,139] [INFO] Running command: hmmsearch --tblout GCF_016925535.1_ASM1692553v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg00ec392a-794c-4ec2-b358-684dbcacfbc9/dqc_reference/reference_markers.hmm GCF_016925535.1_ASM1692553v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:57:03,395] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:57:03,396] [INFO] Found 6/6 markers.
[2024-01-25 18:57:03,426] [INFO] Query marker FASTA was written to GCF_016925535.1_ASM1692553v1_genomic.fna/markers.fasta
[2024-01-25 18:57:03,427] [INFO] Task started: Blastn
[2024-01-25 18:57:03,427] [INFO] Running command: blastn -query GCF_016925535.1_ASM1692553v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg00ec392a-794c-4ec2-b358-684dbcacfbc9/dqc_reference/reference_markers.fasta -out GCF_016925535.1_ASM1692553v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:57:04,233] [INFO] Task succeeded: Blastn
[2024-01-25 18:57:04,236] [INFO] Selected 18 target genomes.
[2024-01-25 18:57:04,236] [INFO] Target genome list was writen to GCF_016925535.1_ASM1692553v1_genomic.fna/target_genomes.txt
[2024-01-25 18:57:04,247] [INFO] Task started: fastANI
[2024-01-25 18:57:04,247] [INFO] Running command: fastANI --query /var/lib/cwl/stg0a9b30ce-8e44-4d0f-ac01-788ac4792c42/GCF_016925535.1_ASM1692553v1_genomic.fna.gz --refList GCF_016925535.1_ASM1692553v1_genomic.fna/target_genomes.txt --output GCF_016925535.1_ASM1692553v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:57:20,319] [INFO] Task succeeded: fastANI
[2024-01-25 18:57:20,320] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg00ec392a-794c-4ec2-b358-684dbcacfbc9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:57:20,320] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg00ec392a-794c-4ec2-b358-684dbcacfbc9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:57:20,330] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:57:20,330] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:57:20,330] [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
Natronoglycomyces albus	strain=DSM 106290	GCA_016925535.1	2811108	2811108	type	True	100.0	1335	1335	95	conclusive
Glycomyces salinus	strain=YIM 93776	GCA_016428645.1	980294	980294	type	True	77.464	222	1335	95	below_threshold
Glycomyces buryatensis	strain=18	GCA_004912275.1	2570927	2570927	type	True	77.4277	198	1335	95	below_threshold
Glycomyces xiaoerkulensis	strain=TRM 41368	GCA_002798405.1	2038139	2038139	type	True	77.3537	211	1335	95	below_threshold
Glycomyces tenuis	strain=NRRL B-16895	GCA_000715885.1	58116	58116	type	True	77.3413	233	1335	95	below_threshold
Glycomyces arizonensis	strain=DSM 44726	GCA_000482705.1	256035	256035	type	True	77.2369	234	1335	95	below_threshold
Glycomyces dulcitolivorans	strain=SJ-25	GCA_003265355.1	2200759	2200759	type	True	77.1952	195	1335	95	below_threshold
Glycomyces tenuis	strain=DSM 44171	GCA_000427885.1	58116	58116	type	True	77.1523	222	1335	95	below_threshold
Glycomyces albidus	strain=NEAU-7082	GCA_009451885.1	2656774	2656774	type	True	76.829	210	1335	95	below_threshold
Stackebrandtia albiflava	strain=DSM 45044	GCA_007994225.1	406432	406432	type	True	76.7264	157	1335	95	below_threshold
Saccharopolyspora subtropica	strain=CGMCC 4.7206	GCA_014646075.1	1530170	1530170	type	True	75.796	77	1335	95	below_threshold
Nocardia stercoris	strain=NEAU-LL90	GCA_003696265.1	2483361	2483361	type	True	75.7036	75	1335	95	below_threshold
Nocardia lijiangensis	strain=NBRC 108240	GCA_001613045.1	299618	299618	type	True	75.6558	86	1335	95	below_threshold
Actinophytocola xinjiangensis	strain=CGMCC 4.4663	GCA_001921215.1	485602	485602	type	True	75.5919	95	1335	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:57:20,332] [INFO] DFAST Taxonomy check result was written to GCF_016925535.1_ASM1692553v1_genomic.fna/tc_result.tsv
[2024-01-25 18:57:20,334] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:57:20,335] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:57:20,336] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg00ec392a-794c-4ec2-b358-684dbcacfbc9/dqc_reference/checkm_data
[2024-01-25 18:57:20,339] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:57:20,383] [INFO] Task started: CheckM
[2024-01-25 18:57:20,383] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016925535.1_ASM1692553v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016925535.1_ASM1692553v1_genomic.fna/checkm_input GCF_016925535.1_ASM1692553v1_genomic.fna/checkm_result
[2024-01-25 18:57:55,620] [INFO] Task succeeded: CheckM
[2024-01-25 18:57:55,621] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:57:55,641] [INFO] ===== Completeness check finished =====
[2024-01-25 18:57:55,642] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:57:55,642] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016925535.1_ASM1692553v1_genomic.fna/markers.fasta)
[2024-01-25 18:57:55,642] [INFO] Task started: Blastn
[2024-01-25 18:57:55,642] [INFO] Running command: blastn -query GCF_016925535.1_ASM1692553v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg00ec392a-794c-4ec2-b358-684dbcacfbc9/dqc_reference/reference_markers_gtdb.fasta -out GCF_016925535.1_ASM1692553v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:57:56,828] [INFO] Task succeeded: Blastn
[2024-01-25 18:57:56,832] [INFO] Selected 18 target genomes.
[2024-01-25 18:57:56,832] [INFO] Target genome list was writen to GCF_016925535.1_ASM1692553v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:57:56,848] [INFO] Task started: fastANI
[2024-01-25 18:57:56,848] [INFO] Running command: fastANI --query /var/lib/cwl/stg0a9b30ce-8e44-4d0f-ac01-788ac4792c42/GCF_016925535.1_ASM1692553v1_genomic.fna.gz --refList GCF_016925535.1_ASM1692553v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016925535.1_ASM1692553v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:58:14,419] [INFO] Task succeeded: fastANI
[2024-01-25 18:58:14,428] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:58:14,428] [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_016925535.1	s__Natronoglycomyces albus	100.0	1335	1335	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Natronoglycomyces	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_016428645.1	s__Glycomyces sp016428645	77.464	222	1335	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Glycomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004912275.1	s__Glycomyces buryatensis	77.4151	199	1335	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Glycomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002798405.1	s__Glycomyces xiaoerkulensis	77.3392	210	1335	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Glycomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000482705.1	s__Glycomyces arizonensis	77.2601	232	1335	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Glycomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003265355.1	s__Glycomyces dulcitolivorans	77.1807	196	1335	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Glycomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000427885.1	s__Glycomyces tenuis	77.1523	222	1335	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Glycomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003933745.1	s__Glycomyces terrestris	77.1328	207	1335	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Glycomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009451885.1	s__Glycomyces albidus	76.8173	211	1335	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Glycomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007994225.1	s__Stackebrandtia albiflava	76.6382	157	1335	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Stackebrandtia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011947195.1	s__Planosporangium thailandense	76.104	99	1335	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Planosporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004362315.1	s__Mycobacterium sp004362315	75.894	53	1335	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.02	98.99	0.96	0.96	6	-
GCF_003696265.1	s__Nocardia stercoris	75.7036	75	1335	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001613045.1	s__Nocardia lijiangensis	75.6414	87	1335	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:58:14,432] [INFO] GTDB search result was written to GCF_016925535.1_ASM1692553v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:58:14,432] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:58:14,435] [INFO] DFAST_QC result json was written to GCF_016925535.1_ASM1692553v1_genomic.fna/dqc_result.json
[2024-01-25 18:58:14,435] [INFO] DFAST_QC completed!
[2024-01-25 18:58:14,435] [INFO] Total running time: 0h1m24s