[2024-01-24 13:45:57,933] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:45:57,935] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:45:57,935] [INFO] DQC Reference Directory: /var/lib/cwl/stg5232fd7e-58b1-43c4-8d50-25eb6e93ea07/dqc_reference
[2024-01-24 13:45:59,221] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:45:59,222] [INFO] Task started: Prodigal
[2024-01-24 13:45:59,222] [INFO] Running command: gunzip -c /var/lib/cwl/stg040197fc-6deb-4a64-9bc6-d25c733fa6c4/GCF_008085905.1_ASM808590v1_genomic.fna.gz | prodigal -d GCF_008085905.1_ASM808590v1_genomic.fna/cds.fna -a GCF_008085905.1_ASM808590v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:28,853] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:28,854] [INFO] Task started: HMMsearch
[2024-01-24 13:46:28,854] [INFO] Running command: hmmsearch --tblout GCF_008085905.1_ASM808590v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5232fd7e-58b1-43c4-8d50-25eb6e93ea07/dqc_reference/reference_markers.hmm GCF_008085905.1_ASM808590v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:29,270] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:29,272] [INFO] Found 6/6 markers.
[2024-01-24 13:46:29,347] [INFO] Query marker FASTA was written to GCF_008085905.1_ASM808590v1_genomic.fna/markers.fasta
[2024-01-24 13:46:29,347] [INFO] Task started: Blastn
[2024-01-24 13:46:29,348] [INFO] Running command: blastn -query GCF_008085905.1_ASM808590v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5232fd7e-58b1-43c4-8d50-25eb6e93ea07/dqc_reference/reference_markers.fasta -out GCF_008085905.1_ASM808590v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:30,733] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:30,737] [INFO] Selected 17 target genomes.
[2024-01-24 13:46:30,737] [INFO] Target genome list was writen to GCF_008085905.1_ASM808590v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:30,741] [INFO] Task started: fastANI
[2024-01-24 13:46:30,742] [INFO] Running command: fastANI --query /var/lib/cwl/stg040197fc-6deb-4a64-9bc6-d25c733fa6c4/GCF_008085905.1_ASM808590v1_genomic.fna.gz --refList GCF_008085905.1_ASM808590v1_genomic.fna/target_genomes.txt --output GCF_008085905.1_ASM808590v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:47:16,421] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:16,422] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5232fd7e-58b1-43c4-8d50-25eb6e93ea07/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:47:16,423] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5232fd7e-58b1-43c4-8d50-25eb6e93ea07/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:47:16,453] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:47:16,453] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:47:16,453] [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
Actinomadura syzygii	strain=GKU157	GCA_008085905.1	1427538	1427538	type	True	100.0	3221	3222	95	inconclusive
Actinomadura decatromicini	strain=CYP1-5	GCA_008121305.1	2604572	2604572	type	True	95.8768	2769	3222	95	inconclusive
Actinomadura chibensis	strain=NBRC 106107	GCA_001552135.1	392828	392828	type	True	94.3308	2555	3222	95	below_threshold
Actinomadura chibensis	strain=JCM 14158	GCA_008085895.1	392828	392828	type	True	94.2999	2600	3222	95	below_threshold
Actinomadura soli	strain=14C53	GCA_005889715.1	2508997	2508997	type	True	86.4564	1853	3222	95	below_threshold
Actinomadura latina	strain=ATCC BAA-277	GCA_012396395.1	163603	163603	type	True	85.4907	1724	3222	95	below_threshold
Actinomadura madurae	strain=DSM 43067	GCA_900115095.1	1993	1993	type	True	84.9791	1894	3222	95	below_threshold
Actinomadura spongiicola	strain=LHW52907	GCA_003432485.1	2303421	2303421	type	True	84.8111	1743	3222	95	below_threshold
Actinomadura hallensis	strain=DSM 45043	GCA_006716765.1	337895	337895	type	True	84.4705	1591	3222	95	below_threshold
Actinomadura physcomitrii	strain=LD22	GCA_008923205.2	2650748	2650748	type	True	83.7755	1757	3222	95	below_threshold
Actinomadura montaniterrae	strain=CYP1-1B	GCA_008923365.1	1803903	1803903	type	True	83.7344	1793	3222	95	below_threshold
Actinomadura violacea	strain=LCR2-06	GCA_017573465.1	2819934	2819934	type	True	83.7198	1893	3222	95	below_threshold
Actinomadura graeca	strain=32-07	GCA_019175365.1	2750812	2750812	type	True	83.5164	1823	3222	95	below_threshold
Actinomadura roseirufa		GCA_900659635.1	2094049	2094049	type	True	83.257	1557	3222	95	below_threshold
Actinomadura parmotrematis	strain=PM05-2	GCA_019458805.1	2864039	2864039	type	True	80.9707	1521	3222	95	below_threshold
Actinomadura rupiterrae	strain=DSM 45251	GCA_024172125.1	559627	559627	type	True	80.7933	1570	3222	95	below_threshold
Actinomadura barringtoniae	strain=GKU 128	GCA_017573505.1	1427535	1427535	type	True	80.6246	1619	3222	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:47:16,458] [INFO] DFAST Taxonomy check result was written to GCF_008085905.1_ASM808590v1_genomic.fna/tc_result.tsv
[2024-01-24 13:47:16,458] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:47:16,459] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:47:16,459] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5232fd7e-58b1-43c4-8d50-25eb6e93ea07/dqc_reference/checkm_data
[2024-01-24 13:47:16,460] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:47:16,548] [INFO] Task started: CheckM
[2024-01-24 13:47:16,548] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008085905.1_ASM808590v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008085905.1_ASM808590v1_genomic.fna/checkm_input GCF_008085905.1_ASM808590v1_genomic.fna/checkm_result
[2024-01-24 13:48:47,533] [INFO] Task succeeded: CheckM
[2024-01-24 13:48:47,534] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:48:47,561] [INFO] ===== Completeness check finished =====
[2024-01-24 13:48:47,562] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:48:47,562] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008085905.1_ASM808590v1_genomic.fna/markers.fasta)
[2024-01-24 13:48:47,563] [INFO] Task started: Blastn
[2024-01-24 13:48:47,563] [INFO] Running command: blastn -query GCF_008085905.1_ASM808590v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5232fd7e-58b1-43c4-8d50-25eb6e93ea07/dqc_reference/reference_markers_gtdb.fasta -out GCF_008085905.1_ASM808590v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:48:49,712] [INFO] Task succeeded: Blastn
[2024-01-24 13:48:49,716] [INFO] Selected 17 target genomes.
[2024-01-24 13:48:49,717] [INFO] Target genome list was writen to GCF_008085905.1_ASM808590v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:48:49,775] [INFO] Task started: fastANI
[2024-01-24 13:48:49,775] [INFO] Running command: fastANI --query /var/lib/cwl/stg040197fc-6deb-4a64-9bc6-d25c733fa6c4/GCF_008085905.1_ASM808590v1_genomic.fna.gz --refList GCF_008085905.1_ASM808590v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008085905.1_ASM808590v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:49:32,647] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:32,673] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:49:32,673] [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_008085905.1	s__Spirillospora syzygii	100.0	3221	3222	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	95.88	95.88	0.90	0.90	2	conclusive
GCF_001552135.1	s__Spirillospora chibensis	94.3221	2556	3222	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	100.00	100.00	1.00	1.00	2	-
GCF_005889715.1	s__Spirillospora sp005889715	86.4315	1856	3222	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004348535.1	s__Spirillospora sp004348535	86.3222	1733	3222	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004348735.1	s__Spirillospora sp004348735	86.2956	1931	3222	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001552195.1	s__Spirillospora latina	85.4432	1768	3222	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	99.98	99.98	0.98	0.98	2	-
GCF_900188445.1	s__Spirillospora meyerae	85.0648	1841	3222	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115095.1	s__Spirillospora madurae	84.9697	1897	3222	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	99.34	99.27	0.95	0.95	3	-
GCF_008327685.1	s__Spirillospora sp008327685	84.9547	1914	3222	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013409365.1	s__Spirillospora luteofluorescens	84.9252	1934	3222	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006547145.1	s__Spirillospora sp006547145	84.8649	1896	3222	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005889745.1	s__Spirillospora geliboluensis	84.8532	1673	3222	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004348665.1	s__Spirillospora sp004348665	84.8444	1412	3222	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004349245.1	s__Spirillospora sp004349245	84.6279	1588	3222	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008923205.2	s__Spirillospora physcomitrii	83.7825	1756	3222	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900659635.1	s__Spirillospora roseirufa	83.2595	1557	3222	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000718255.1	s__Spirillospora albida	82.9801	1398	3222	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:49:32,675] [INFO] GTDB search result was written to GCF_008085905.1_ASM808590v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:49:32,675] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:49:32,682] [INFO] DFAST_QC result json was written to GCF_008085905.1_ASM808590v1_genomic.fna/dqc_result.json
[2024-01-24 13:49:32,683] [INFO] DFAST_QC completed!
[2024-01-24 13:49:32,683] [INFO] Total running time: 0h3m35s