[2024-01-24 11:26:36,084] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:36,086] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:36,086] [INFO] DQC Reference Directory: /var/lib/cwl/stg9ad3ac39-946e-48ed-b0de-9364534ffedc/dqc_reference
[2024-01-24 11:26:37,324] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:37,325] [INFO] Task started: Prodigal
[2024-01-24 11:26:37,325] [INFO] Running command: gunzip -c /var/lib/cwl/stgdb03322a-2017-46cf-a8ef-144787ad7412/GCF_902825375.1_D1_genomic.fna.gz | prodigal -d GCF_902825375.1_D1_genomic.fna/cds.fna -a GCF_902825375.1_D1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:53,537] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:53,538] [INFO] Task started: HMMsearch
[2024-01-24 11:26:53,538] [INFO] Running command: hmmsearch --tblout GCF_902825375.1_D1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9ad3ac39-946e-48ed-b0de-9364534ffedc/dqc_reference/reference_markers.hmm GCF_902825375.1_D1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:53,887] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:53,889] [INFO] Found 6/6 markers.
[2024-01-24 11:26:53,941] [INFO] Query marker FASTA was written to GCF_902825375.1_D1_genomic.fna/markers.fasta
[2024-01-24 11:26:53,942] [INFO] Task started: Blastn
[2024-01-24 11:26:53,942] [INFO] Running command: blastn -query GCF_902825375.1_D1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9ad3ac39-946e-48ed-b0de-9364534ffedc/dqc_reference/reference_markers.fasta -out GCF_902825375.1_D1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:55,229] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:55,232] [INFO] Selected 18 target genomes.
[2024-01-24 11:26:55,233] [INFO] Target genome list was writen to GCF_902825375.1_D1_genomic.fna/target_genomes.txt
[2024-01-24 11:26:55,242] [INFO] Task started: fastANI
[2024-01-24 11:26:55,242] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb03322a-2017-46cf-a8ef-144787ad7412/GCF_902825375.1_D1_genomic.fna.gz --refList GCF_902825375.1_D1_genomic.fna/target_genomes.txt --output GCF_902825375.1_D1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:27:20,167] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:20,168] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9ad3ac39-946e-48ed-b0de-9364534ffedc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:27:20,168] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9ad3ac39-946e-48ed-b0de-9364534ffedc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:27:20,188] [INFO] Found 18 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 11:27:20,188] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:27:20,188] [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 dassonvillei subsp. crassaminis	strain=D1	GCA_902825375.1	2580523	2014	type	True	100.0	1851	1877	95	conclusive
Nocardiopsis dassonvillei	strain=NCTC10488	GCA_900638215.1	2014	2014	type	True	97.8364	1691	1877	95	conclusive
Nocardiopsis dassonvillei	strain=ATCC 23218	GCA_012396345.1	2014	2014	type	True	97.8306	1650	1877	95	conclusive
Nocardiopsis dassonvillei subsp. dassonvillei	strain=DSM 43111	GCA_000092985.1	568208	2014	type	True	97.7731	1693	1877	95	conclusive
Nocardiopsis alborubida	strain=ATCC 23612	GCA_012396365.1	146802	146802	type	True	94.3195	1586	1877	95	below_threshold
Nocardiopsis alborubida	strain=NBRC 13392	GCA_001552695.1	146802	146802	type	True	94.3021	1551	1877	95	below_threshold
Nocardiopsis deserti	strain=H13	GCA_008638355.1	2605988	2605988	type	True	94.2086	1600	1877	95	below_threshold
Nocardiopsis sinuspersici	strain=UTMC 00102	GCA_001998325.1	501010	501010	type	True	88.4023	1345	1877	95	below_threshold
Nocardiopsis quinghaiensis	strain=YIM 28A4	GCA_008638365.1	464995	464995	type	True	88.2105	1270	1877	95	below_threshold
Nocardiopsis exhalans	strain=JCM11759T	GCA_024134545.1	163604	163604	type	True	83.7495	1174	1877	95	below_threshold
Nocardiopsis kunsanensis	strain=DSM 44524	GCA_000340965.1	141693	141693	type	True	81.8215	912	1877	95	below_threshold
Thermobifida cellulosilytica	strain=TB100	GCA_001517975.1	144786	144786	type	True	80.0608	668	1877	95	below_threshold
Streptomonospora litoralis	strain=M2	GCA_004323735.1	2498135	2498135	type	True	79.8359	774	1877	95	below_threshold
Thermobifida alba	strain=DSM 43795	GCA_023208015.1	53522	53522	type	True	79.7286	738	1877	95	below_threshold
Streptomyces verrucosisporus	strain=CPB1-1	GCA_017114865.1	1695161	1695161	type	True	77.198	526	1877	95	below_threshold
Actinomadura atramentaria	strain=SF2197	GCA_000381885.1	1990	1990	type	True	76.7421	558	1877	95	below_threshold
Streptomyces diacarni	strain=LHW51701	GCA_003323715.1	2800381	2800381	type	True	76.7011	481	1877	95	below_threshold
Sporichthya polymorpha	strain=DSM 43042	GCA_000384115.1	35751	35751	type	True	76.4736	328	1877	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:27:20,190] [INFO] DFAST Taxonomy check result was written to GCF_902825375.1_D1_genomic.fna/tc_result.tsv
[2024-01-24 11:27:20,191] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:27:20,191] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:27:20,191] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9ad3ac39-946e-48ed-b0de-9364534ffedc/dqc_reference/checkm_data
[2024-01-24 11:27:20,192] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:27:20,255] [INFO] Task started: CheckM
[2024-01-24 11:27:20,255] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_902825375.1_D1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_902825375.1_D1_genomic.fna/checkm_input GCF_902825375.1_D1_genomic.fna/checkm_result
[2024-01-24 11:28:09,051] [INFO] Task succeeded: CheckM
[2024-01-24 11:28:09,052] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:28:09,075] [INFO] ===== Completeness check finished =====
[2024-01-24 11:28:09,076] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:28:09,076] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_902825375.1_D1_genomic.fna/markers.fasta)
[2024-01-24 11:28:09,077] [INFO] Task started: Blastn
[2024-01-24 11:28:09,077] [INFO] Running command: blastn -query GCF_902825375.1_D1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9ad3ac39-946e-48ed-b0de-9364534ffedc/dqc_reference/reference_markers_gtdb.fasta -out GCF_902825375.1_D1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:28:11,108] [INFO] Task succeeded: Blastn
[2024-01-24 11:28:11,112] [INFO] Selected 18 target genomes.
[2024-01-24 11:28:11,112] [INFO] Target genome list was writen to GCF_902825375.1_D1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:28:11,142] [INFO] Task started: fastANI
[2024-01-24 11:28:11,142] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb03322a-2017-46cf-a8ef-144787ad7412/GCF_902825375.1_D1_genomic.fna.gz --refList GCF_902825375.1_D1_genomic.fna/target_genomes_gtdb.txt --output GCF_902825375.1_D1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:28:35,646] [INFO] Task succeeded: fastANI
[2024-01-24 11:28:35,663] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:28:35,663] [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_000092985.1	s__Nocardiopsis dassonvillei	97.7868	1692	1877	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	97.80	95.11	0.93	0.87	11	conclusive
GCF_012396365.1	s__Nocardiopsis alborubida	94.3321	1585	1877	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	96.95	95.06	0.88	0.80	4	-
GCA_002529455.1	s__Nocardiopsis fusca	92.9445	1507	1877	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000341065.1	s__Nocardiopsis halotolerans	89.1082	1301	1877	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001905145.1	s__Nocardiopsis sp001905145	88.5183	1346	1877	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008638415.1	s__Nocardiopsis sinuspersici	88.3865	1342	1877	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	99.63	98.89	0.96	0.91	4	-
GCF_008638365.1	s__Nocardiopsis quinghaiensis	88.2334	1267	1877	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009830945.1	s__Nocardiopsis sp009830945	87.6027	1273	1877	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	99.72	99.66	0.93	0.93	3	-
GCF_003386285.1	s__Nocardiopsis sp003386285	84.0654	1086	1877	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003634495.1	s__Nocardiopsis sp003634495	83.8418	1257	1877	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001517975.1	s__Thermobifida cellulosilytica	80.0239	672	1877	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Thermobifida	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017114865.1	s__Streptomyces verrucosisporus	77.1884	528	1877	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.1585	N/A	N/A	N/A	N/A	1	-
GCA_002128465.1	s__Streptomyces pharetrae	76.7401	509	1877	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003323715.1	s__Streptomyces diacarni	76.7071	481	1877	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000720255.1	s__Streptomyces griseus_I	76.695	490	1877	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000384115.1	s__Sporichthya polymorpha	76.4851	326	1877	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Sporichthyales;f__Sporichthyaceae;g__Sporichthya	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000331005.1	s__Streptomyces turgidiscabies	76.4554	428	1877	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.81	99.67	0.92	0.88	3	-
GCF_001668615.1	s__Mycobacterium sp001668615	75.9641	157	1877	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:28:35,664] [INFO] GTDB search result was written to GCF_902825375.1_D1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:28:35,665] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:28:35,669] [INFO] DFAST_QC result json was written to GCF_902825375.1_D1_genomic.fna/dqc_result.json
[2024-01-24 11:28:35,669] [INFO] DFAST_QC completed!
[2024-01-24 11:28:35,669] [INFO] Total running time: 0h1m60s