[2024-01-24 13:19:25,681] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:19:25,682] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:19:25,683] [INFO] DQC Reference Directory: /var/lib/cwl/stgd23c1635-24d0-495e-838e-6e23df05a554/dqc_reference
[2024-01-24 13:19:26,877] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:19:26,877] [INFO] Task started: Prodigal
[2024-01-24 13:19:26,878] [INFO] Running command: gunzip -c /var/lib/cwl/stgb184c678-4669-4428-b534-252e3a47d6a3/GCF_008085895.1_ASM808589v1_genomic.fna.gz | prodigal -d GCF_008085895.1_ASM808589v1_genomic.fna/cds.fna -a GCF_008085895.1_ASM808589v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:19:51,619] [INFO] Task succeeded: Prodigal
[2024-01-24 13:19:51,620] [INFO] Task started: HMMsearch
[2024-01-24 13:19:51,620] [INFO] Running command: hmmsearch --tblout GCF_008085895.1_ASM808589v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd23c1635-24d0-495e-838e-6e23df05a554/dqc_reference/reference_markers.hmm GCF_008085895.1_ASM808589v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:19:52,032] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:19:52,033] [INFO] Found 6/6 markers.
[2024-01-24 13:19:52,109] [INFO] Query marker FASTA was written to GCF_008085895.1_ASM808589v1_genomic.fna/markers.fasta
[2024-01-24 13:19:52,109] [INFO] Task started: Blastn
[2024-01-24 13:19:52,110] [INFO] Running command: blastn -query GCF_008085895.1_ASM808589v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd23c1635-24d0-495e-838e-6e23df05a554/dqc_reference/reference_markers.fasta -out GCF_008085895.1_ASM808589v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:53,428] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:53,432] [INFO] Selected 14 target genomes.
[2024-01-24 13:19:53,433] [INFO] Target genome list was writen to GCF_008085895.1_ASM808589v1_genomic.fna/target_genomes.txt
[2024-01-24 13:19:53,460] [INFO] Task started: fastANI
[2024-01-24 13:19:53,460] [INFO] Running command: fastANI --query /var/lib/cwl/stgb184c678-4669-4428-b534-252e3a47d6a3/GCF_008085895.1_ASM808589v1_genomic.fna.gz --refList GCF_008085895.1_ASM808589v1_genomic.fna/target_genomes.txt --output GCF_008085895.1_ASM808589v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:20:34,130] [INFO] Task succeeded: fastANI
[2024-01-24 13:20:34,130] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd23c1635-24d0-495e-838e-6e23df05a554/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:20:34,131] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd23c1635-24d0-495e-838e-6e23df05a554/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:20:34,147] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:20:34,147] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:20:34,147] [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 chibensis	strain=JCM 14158	GCA_008085895.1	392828	392828	type	True	100.0	3125	3126	95	conclusive
Actinomadura chibensis	strain=NBRC 106107	GCA_001552135.1	392828	392828	type	True	99.9814	3053	3126	95	conclusive
Actinomadura decatromicini	strain=CYP1-5	GCA_008121305.1	2604572	2604572	type	True	94.5589	2618	3126	95	below_threshold
Actinomadura syzygii	strain=GKU157	GCA_008085905.1	1427538	1427538	type	True	94.3301	2603	3126	95	below_threshold
Actinomadura soli	strain=14C53	GCA_005889715.1	2508997	2508997	type	True	86.4485	1860	3126	95	below_threshold
Actinomadura latina	strain=ATCC BAA-277	GCA_012396395.1	163603	163603	type	True	85.6082	1748	3126	95	below_threshold
Actinomadura meyerae	strain=DSM 44715	GCA_900188445.1	240840	240840	type	True	85.3652	1840	3126	95	below_threshold
Actinomadura mexicana	strain=DSM 44485	GCA_900188105.1	134959	134959	type	True	85.2593	1809	3126	95	below_threshold
Actinomadura madurae	strain=DSM 43067	GCA_900115095.1	1993	1993	type	True	85.2228	1925	3126	95	below_threshold
Actinomadura spongiicola	strain=LHW52907	GCA_003432485.1	2303421	2303421	type	True	85.0236	1746	3126	95	below_threshold
Actinomadura violacea	strain=LCR2-06	GCA_017573465.1	2819934	2819934	type	True	83.9311	1961	3126	95	below_threshold
Actinomadura graeca	strain=32-07	GCA_019175365.1	2750812	2750812	type	True	83.8208	1829	3126	95	below_threshold
Actinomadura parmotrematis	strain=PM05-2	GCA_019458805.1	2864039	2864039	type	True	80.9555	1554	3126	95	below_threshold
Actinomadura rupiterrae	strain=DSM 45251	GCA_024172125.1	559627	559627	type	True	80.9443	1610	3126	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:20:34,149] [INFO] DFAST Taxonomy check result was written to GCF_008085895.1_ASM808589v1_genomic.fna/tc_result.tsv
[2024-01-24 13:20:34,149] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:20:34,149] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:20:34,150] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd23c1635-24d0-495e-838e-6e23df05a554/dqc_reference/checkm_data
[2024-01-24 13:20:34,151] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:20:34,232] [INFO] Task started: CheckM
[2024-01-24 13:20:34,232] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008085895.1_ASM808589v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008085895.1_ASM808589v1_genomic.fna/checkm_input GCF_008085895.1_ASM808589v1_genomic.fna/checkm_result
[2024-01-24 13:21:54,138] [INFO] Task succeeded: CheckM
[2024-01-24 13:21:54,139] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:21:54,168] [INFO] ===== Completeness check finished =====
[2024-01-24 13:21:54,168] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:21:54,169] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008085895.1_ASM808589v1_genomic.fna/markers.fasta)
[2024-01-24 13:21:54,169] [INFO] Task started: Blastn
[2024-01-24 13:21:54,169] [INFO] Running command: blastn -query GCF_008085895.1_ASM808589v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd23c1635-24d0-495e-838e-6e23df05a554/dqc_reference/reference_markers_gtdb.fasta -out GCF_008085895.1_ASM808589v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:21:56,260] [INFO] Task succeeded: Blastn
[2024-01-24 13:21:56,263] [INFO] Selected 16 target genomes.
[2024-01-24 13:21:56,263] [INFO] Target genome list was writen to GCF_008085895.1_ASM808589v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:21:56,283] [INFO] Task started: fastANI
[2024-01-24 13:21:56,284] [INFO] Running command: fastANI --query /var/lib/cwl/stgb184c678-4669-4428-b534-252e3a47d6a3/GCF_008085895.1_ASM808589v1_genomic.fna.gz --refList GCF_008085895.1_ASM808589v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008085895.1_ASM808589v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:22:46,516] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:46,531] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:22:46,531] [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_001552135.1	s__Spirillospora chibensis	99.9814	3053	3126	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_008085905.1	s__Spirillospora syzygii	94.3476	2600	3126	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	95.88	95.88	0.90	0.90	2	-
GCF_004348535.1	s__Spirillospora sp004348535	86.5585	1762	3126	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	85.6456	1770	3126	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	99.98	99.98	0.98	0.98	2	-
GCF_004348335.1	s__Spirillospora bangladeshensis	85.5635	1630	3126	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013364275.1	s__Spirillospora sp013364275	85.4555	1960	3126	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008327685.1	s__Spirillospora sp008327685	85.3721	1928	3126	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188445.1	s__Spirillospora meyerae	85.2948	1853	3126	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188105.1	s__Spirillospora mexicana	85.2397	1812	3126	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	85.234	1678	3126	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	85.2302	1923	3126	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	99.34	99.27	0.95	0.95	3	-
GCF_003432485.1	s__Spirillospora sp003432485	85.053	1741	3126	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648675.1	s__Spirillospora livida	84.951	1727	3126	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	98.54	97.09	0.95	0.91	3	-
GCF_006547145.1	s__Spirillospora sp006547145	84.9469	1929	3126	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	84.7576	1448	3126	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900659615.1	s__Spirillospora fibrosa	83.3285	1767	3126	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 13:22:46,533] [INFO] GTDB search result was written to GCF_008085895.1_ASM808589v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:22:46,533] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:22:46,537] [INFO] DFAST_QC result json was written to GCF_008085895.1_ASM808589v1_genomic.fna/dqc_result.json
[2024-01-24 13:22:46,538] [INFO] DFAST_QC completed!
[2024-01-24 13:22:46,538] [INFO] Total running time: 0h3m21s