[2024-01-25 20:05:20,527] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:05:20,528] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:05:20,529] [INFO] DQC Reference Directory: /var/lib/cwl/stg4e947389-ef1f-4803-9964-b0dcacacd488/dqc_reference
[2024-01-25 20:05:21,712] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:05:21,712] [INFO] Task started: Prodigal
[2024-01-25 20:05:21,713] [INFO] Running command: gunzip -c /var/lib/cwl/stgdde3d25a-c43b-424b-8a4a-a8acf323a076/GCF_014201115.1_ASM1420111v1_genomic.fna.gz | prodigal -d GCF_014201115.1_ASM1420111v1_genomic.fna/cds.fna -a GCF_014201115.1_ASM1420111v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:05:42,208] [INFO] Task succeeded: Prodigal
[2024-01-25 20:05:42,209] [INFO] Task started: HMMsearch
[2024-01-25 20:05:42,209] [INFO] Running command: hmmsearch --tblout GCF_014201115.1_ASM1420111v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4e947389-ef1f-4803-9964-b0dcacacd488/dqc_reference/reference_markers.hmm GCF_014201115.1_ASM1420111v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:05:42,527] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:05:42,528] [INFO] Found 6/6 markers.
[2024-01-25 20:05:42,583] [INFO] Query marker FASTA was written to GCF_014201115.1_ASM1420111v1_genomic.fna/markers.fasta
[2024-01-25 20:05:42,583] [INFO] Task started: Blastn
[2024-01-25 20:05:42,583] [INFO] Running command: blastn -query GCF_014201115.1_ASM1420111v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4e947389-ef1f-4803-9964-b0dcacacd488/dqc_reference/reference_markers.fasta -out GCF_014201115.1_ASM1420111v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:05:43,761] [INFO] Task succeeded: Blastn
[2024-01-25 20:05:43,764] [INFO] Selected 15 target genomes.
[2024-01-25 20:05:43,764] [INFO] Target genome list was writen to GCF_014201115.1_ASM1420111v1_genomic.fna/target_genomes.txt
[2024-01-25 20:05:43,788] [INFO] Task started: fastANI
[2024-01-25 20:05:43,788] [INFO] Running command: fastANI --query /var/lib/cwl/stgdde3d25a-c43b-424b-8a4a-a8acf323a076/GCF_014201115.1_ASM1420111v1_genomic.fna.gz --refList GCF_014201115.1_ASM1420111v1_genomic.fna/target_genomes.txt --output GCF_014201115.1_ASM1420111v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:06:08,165] [INFO] Task succeeded: fastANI
[2024-01-25 20:06:08,165] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4e947389-ef1f-4803-9964-b0dcacacd488/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:06:08,166] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4e947389-ef1f-4803-9964-b0dcacacd488/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:06:08,176] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 20:06:08,176] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-25 20:06:08,176] [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
Nocardiopsis metallicus	strain=DSM 44598	GCA_014201115.1	179819	179819	type	True	100.0	2591	2591	95	inconclusive
Nocardiopsis exhalans	strain=JCM11759T	GCA_024134545.1	163604	163604	type	True	95.4964	2105	2591	95	inconclusive
Nocardiopsis valliformis	strain=DSM 45023	GCA_000340985.1	239974	239974	type	True	94.8253	1911	2591	95	below_threshold
Nocardiopsis ganjiahuensis	strain=DSM 45031	GCA_000341085.1	239984	239984	type	True	89.3253	1752	2591	95	below_threshold
Nocardiopsis terrae	strain=DSM 45157	GCA_014874035.1	372655	372655	type	True	87.6533	1597	2591	95	below_threshold
Nocardiopsis prasina	strain=DSM 43845	GCA_000341265.1	2015	2015	type	True	87.1891	1453	2591	95	below_threshold
Nocardiopsis listeri	strain=NBRC 13360	GCA_001570765.1	53440	53440	type	True	84.3413	1309	2591	95	below_threshold
Nocardiopsis alkaliphila	strain=YIM 80379	GCA_000341005.1	225762	225762	type	True	83.6278	1195	2591	95	below_threshold
Nocardiopsis sinuspersici	strain=UTMC 00102	GCA_001998325.1	501010	501010	type	True	83.5102	1356	2591	95	below_threshold
Nocardiopsis aegyptia	strain=DSM 44442	GCA_013410755.1	220378	220378	type	True	83.1124	1368	2591	95	below_threshold
Nocardiopsis lucentensis	strain=DSM 44048	GCA_000341125.1	53441	53441	type	True	82.8174	1050	2591	95	below_threshold
Nocardiopsis salina	strain=YIM 90010	GCA_000341025.1	245836	245836	type	True	81.8206	1054	2591	95	below_threshold
Nocardiopsis kunsanensis	strain=DSM 44524	GCA_000340965.1	141693	141693	type	True	81.3466	1028	2591	95	below_threshold
Thermobifida alba	strain=DSM 43795	GCA_023208015.1	53522	53522	type	True	79.595	727	2591	95	below_threshold
Streptomonospora litoralis	strain=M2	GCA_004323735.1	2498135	2498135	type	True	79.2209	815	2591	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:06:08,177] [INFO] DFAST Taxonomy check result was written to GCF_014201115.1_ASM1420111v1_genomic.fna/tc_result.tsv
[2024-01-25 20:06:08,178] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:06:08,178] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:06:08,178] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4e947389-ef1f-4803-9964-b0dcacacd488/dqc_reference/checkm_data
[2024-01-25 20:06:08,179] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:06:08,252] [INFO] Task started: CheckM
[2024-01-25 20:06:08,252] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014201115.1_ASM1420111v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014201115.1_ASM1420111v1_genomic.fna/checkm_input GCF_014201115.1_ASM1420111v1_genomic.fna/checkm_result
[2024-01-25 20:07:25,846] [INFO] Task succeeded: CheckM
[2024-01-25 20:07:25,850] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:07:25,882] [INFO] ===== Completeness check finished =====
[2024-01-25 20:07:25,882] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:07:25,883] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014201115.1_ASM1420111v1_genomic.fna/markers.fasta)
[2024-01-25 20:07:25,883] [INFO] Task started: Blastn
[2024-01-25 20:07:25,883] [INFO] Running command: blastn -query GCF_014201115.1_ASM1420111v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4e947389-ef1f-4803-9964-b0dcacacd488/dqc_reference/reference_markers_gtdb.fasta -out GCF_014201115.1_ASM1420111v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:07:27,856] [INFO] Task succeeded: Blastn
[2024-01-25 20:07:27,859] [INFO] Selected 11 target genomes.
[2024-01-25 20:07:27,859] [INFO] Target genome list was writen to GCF_014201115.1_ASM1420111v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:07:27,867] [INFO] Task started: fastANI
[2024-01-25 20:07:27,867] [INFO] Running command: fastANI --query /var/lib/cwl/stgdde3d25a-c43b-424b-8a4a-a8acf323a076/GCF_014201115.1_ASM1420111v1_genomic.fna.gz --refList GCF_014201115.1_ASM1420111v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014201115.1_ASM1420111v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:07:47,353] [INFO] Task succeeded: fastANI
[2024-01-25 20:07:47,361] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:07:47,361] [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_014201115.1	s__Nocardiopsis metallicus	100.0	2590	2591	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000340985.1	s__Nocardiopsis valliformis	94.8438	1909	2591	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000341085.1	s__Nocardiopsis ganjiahuensis	89.3263	1752	2591	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014651695.1	s__Nocardiopsis terrae	87.6004	1574	2591	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000341265.1	s__Nocardiopsis prasina	87.1912	1452	2591	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	96.74	95.74	0.91	0.87	4	-
GCA_018388625.1	s__Nocardiopsis sp018388625	86.965	1555	2591	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900143625.1	s__Nocardiopsis sp900143625	84.4662	1490	2591	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001570765.1	s__Nocardiopsis listeri	84.3641	1306	2591	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001279585.1	s__Nocardiopsis sp001279585	83.0713	1317	2591	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000341125.1	s__Nocardiopsis lucentensis	82.8092	1051	2591	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000341025.1	s__Nocardiopsis salina	81.8142	1055	2591	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:07:47,362] [INFO] GTDB search result was written to GCF_014201115.1_ASM1420111v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:07:47,363] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:07:47,366] [INFO] DFAST_QC result json was written to GCF_014201115.1_ASM1420111v1_genomic.fna/dqc_result.json
[2024-01-25 20:07:47,366] [INFO] DFAST_QC completed!
[2024-01-25 20:07:47,366] [INFO] Total running time: 0h2m27s