[2024-01-24 14:07:15,340] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:07:15,342] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:07:15,342] [INFO] DQC Reference Directory: /var/lib/cwl/stge09ae44a-46ea-477d-9bcb-45c4bf10b569/dqc_reference
[2024-01-24 14:07:16,739] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:07:16,740] [INFO] Task started: Prodigal
[2024-01-24 14:07:16,741] [INFO] Running command: gunzip -c /var/lib/cwl/stg654ee5e9-233c-40e2-ab29-d98177433117/GCF_000024025.1_ASM2402v1_genomic.fna.gz | prodigal -d GCF_000024025.1_ASM2402v1_genomic.fna/cds.fna -a GCF_000024025.1_ASM2402v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:07:47,368] [INFO] Task succeeded: Prodigal
[2024-01-24 14:07:47,368] [INFO] Task started: HMMsearch
[2024-01-24 14:07:47,368] [INFO] Running command: hmmsearch --tblout GCF_000024025.1_ASM2402v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge09ae44a-46ea-477d-9bcb-45c4bf10b569/dqc_reference/reference_markers.hmm GCF_000024025.1_ASM2402v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:07:47,826] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:07:47,828] [INFO] Found 6/6 markers.
[2024-01-24 14:07:47,926] [INFO] Query marker FASTA was written to GCF_000024025.1_ASM2402v1_genomic.fna/markers.fasta
[2024-01-24 14:07:47,927] [INFO] Task started: Blastn
[2024-01-24 14:07:47,927] [INFO] Running command: blastn -query GCF_000024025.1_ASM2402v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge09ae44a-46ea-477d-9bcb-45c4bf10b569/dqc_reference/reference_markers.fasta -out GCF_000024025.1_ASM2402v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:49,402] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:49,405] [INFO] Selected 20 target genomes.
[2024-01-24 14:07:49,406] [INFO] Target genome list was writen to GCF_000024025.1_ASM2402v1_genomic.fna/target_genomes.txt
[2024-01-24 14:07:49,414] [INFO] Task started: fastANI
[2024-01-24 14:07:49,414] [INFO] Running command: fastANI --query /var/lib/cwl/stg654ee5e9-233c-40e2-ab29-d98177433117/GCF_000024025.1_ASM2402v1_genomic.fna.gz --refList GCF_000024025.1_ASM2402v1_genomic.fna/target_genomes.txt --output GCF_000024025.1_ASM2402v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:08:27,458] [INFO] Task succeeded: fastANI
[2024-01-24 14:08:27,459] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge09ae44a-46ea-477d-9bcb-45c4bf10b569/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:08:27,459] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge09ae44a-46ea-477d-9bcb-45c4bf10b569/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:08:27,474] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:08:27,474] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:08:27,474] [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
Catenulispora acidiphila	strain=DSM 44928	GCA_000024025.1	304895	304895	type	True	100.0	3489	3489	95	conclusive
Catenulispora rubra	strain=DSM 44948	GCA_015356825.1	280293	280293	type	True	87.3601	2247	3489	95	below_threshold
Catenulispora pinistramenti	strain=NL8	GCA_018274385.1	2705254	2705254	type	True	86.6455	2112	3489	95	below_threshold
Catenulispora pinisilvae	strain=NH11	GCA_015356865.1	2705253	2705253	type	True	86.5355	2158	3489	95	below_threshold
Actinospica durhamensis	strain=CSCA 57	GCA_018139695.1	1508375	1508375	type	True	77.8762	963	3489	95	below_threshold
Streptomyces parmotrematis	strain=Ptm05	GCA_019890615.1	2873249	2873249	type	True	77.259	782	3489	95	below_threshold
Streptomyces rubrisoli	strain=DSM 42083	GCA_024436055.1	1387313	1387313	type	True	77.1703	675	3489	95	below_threshold
Kitasatospora setae	strain=KM-6054	GCA_000269985.1	2066	2066	type	True	77.0391	1032	3489	95	below_threshold
Streptomyces griseocarneus	strain=JCM 4580	GCA_014655595.1	51201	51201	type	True	77.0083	726	3489	95	below_threshold
Streptomyces spinosus	strain=SBTS01	GCA_020400655.1	2872623	2872623	type	True	76.8939	831	3489	95	below_threshold
Streptomyces barringtoniae	strain=JA03	GCA_020819595.1	2892029	2892029	type	True	76.8711	807	3489	95	below_threshold
Allostreptomyces psammosilenae	strain=DSM 42178	GCA_013407765.1	1892865	1892865	type	True	76.8561	771	3489	95	below_threshold
Streptomyces albireticuli	strain=NRRL B1670	GCA_021228125.1	1940	1940	type	True	76.73	754	3489	95	below_threshold
Embleya hyalina	strain=NBRC 13850	GCA_003967355.1	516124	516124	type	True	76.6656	923	3489	95	below_threshold
Micromonospora ureilytica	strain=DSM 101692	GCA_015751765.1	709868	709868	type	True	76.3615	626	3489	95	below_threshold
Actinokineospora enzanensis	strain=DSM 44649	GCA_000374445.1	155975	155975	type	True	76.2308	633	3489	95	below_threshold
Micromonospora rifamycinica	strain=DSM 44983	GCA_900090265.1	291594	291594	type	True	76.2174	699	3489	95	below_threshold
Micromonospora rifamycinica	strain=AM105	GCA_001542325.1	291594	291594	type	True	76.1542	656	3489	95	below_threshold
Pilimelia anulata	strain=JCM 3090	GCA_014647895.1	53371	53371	type	True	76.0846	646	3489	95	below_threshold
Brevibacterium atlanticum	strain=WO024	GCA_011617245.1	2697563	2697563	type	True	75.7722	200	3489	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:08:27,476] [INFO] DFAST Taxonomy check result was written to GCF_000024025.1_ASM2402v1_genomic.fna/tc_result.tsv
[2024-01-24 14:08:27,477] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:08:27,477] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:08:27,477] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge09ae44a-46ea-477d-9bcb-45c4bf10b569/dqc_reference/checkm_data
[2024-01-24 14:08:27,478] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:08:27,575] [INFO] Task started: CheckM
[2024-01-24 14:08:27,575] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000024025.1_ASM2402v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000024025.1_ASM2402v1_genomic.fna/checkm_input GCF_000024025.1_ASM2402v1_genomic.fna/checkm_result
[2024-01-24 14:10:10,004] [INFO] Task succeeded: CheckM
[2024-01-24 14:10:10,005] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:10:10,033] [INFO] ===== Completeness check finished =====
[2024-01-24 14:10:10,033] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:10:10,034] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000024025.1_ASM2402v1_genomic.fna/markers.fasta)
[2024-01-24 14:10:10,034] [INFO] Task started: Blastn
[2024-01-24 14:10:10,034] [INFO] Running command: blastn -query GCF_000024025.1_ASM2402v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge09ae44a-46ea-477d-9bcb-45c4bf10b569/dqc_reference/reference_markers_gtdb.fasta -out GCF_000024025.1_ASM2402v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:10:12,216] [INFO] Task succeeded: Blastn
[2024-01-24 14:10:12,220] [INFO] Selected 10 target genomes.
[2024-01-24 14:10:12,220] [INFO] Target genome list was writen to GCF_000024025.1_ASM2402v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:10:12,229] [INFO] Task started: fastANI
[2024-01-24 14:10:12,230] [INFO] Running command: fastANI --query /var/lib/cwl/stg654ee5e9-233c-40e2-ab29-d98177433117/GCF_000024025.1_ASM2402v1_genomic.fna.gz --refList GCF_000024025.1_ASM2402v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000024025.1_ASM2402v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:10:33,713] [INFO] Task succeeded: fastANI
[2024-01-24 14:10:33,725] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:10:33,726] [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_000024025.1	s__Catenulispora acidiphila	100.0	3489	3489	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Catenulisporaceae;g__Catenulispora	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_015356825.1	s__Catenulispora rubra	87.4039	2239	3489	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Catenulisporaceae;g__Catenulispora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018274385.1	s__Catenulispora sp018274385	86.6207	2117	3489	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Catenulisporaceae;g__Catenulispora	95.0	99.51	99.51	0.94	0.94	2	-
GCF_015356865.1	s__Catenulispora pinisilvae	86.5266	2159	3489	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Catenulisporaceae;g__Catenulispora	95.0	99.32	99.32	0.94	0.94	2	-
GCA_013361685.1	s__Catenulispora sp013361685	83.6153	1608	3489	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Catenulisporaceae;g__Catenulispora	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013362315.1	s__Catenulispora sp013362315	83.1451	1358	3489	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Catenulisporaceae;g__Catenulispora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014655595.1	s__Streptomyces griseocarneus	76.9795	732	3489	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001758225.1	s__Terracoccus sp001758225	76.2035	349	3489	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Terracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014647895.1	s__Pilimelia anulata	76.0673	654	3489	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Pilimelia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011617245.1	s__Brevibacterium sp011617245	75.8412	201	3489	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:10:33,728] [INFO] GTDB search result was written to GCF_000024025.1_ASM2402v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:10:33,729] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:10:33,732] [INFO] DFAST_QC result json was written to GCF_000024025.1_ASM2402v1_genomic.fna/dqc_result.json
[2024-01-24 14:10:33,733] [INFO] DFAST_QC completed!
[2024-01-24 14:10:33,733] [INFO] Total running time: 0h3m18s