[2024-01-24 13:55:20,018] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:55:20,020] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:55:20,020] [INFO] DQC Reference Directory: /var/lib/cwl/stg664b2c8c-e2af-459e-8ef5-2985455f4df9/dqc_reference
[2024-01-24 13:55:21,489] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:55:21,490] [INFO] Task started: Prodigal
[2024-01-24 13:55:21,490] [INFO] Running command: gunzip -c /var/lib/cwl/stg2d13c80c-181c-40d1-abbe-ecf75f667227/GCF_009733595.1_ASM973359v1_genomic.fna.gz | prodigal -d GCF_009733595.1_ASM973359v1_genomic.fna/cds.fna -a GCF_009733595.1_ASM973359v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:55:49,095] [INFO] Task succeeded: Prodigal
[2024-01-24 13:55:49,095] [INFO] Task started: HMMsearch
[2024-01-24 13:55:49,095] [INFO] Running command: hmmsearch --tblout GCF_009733595.1_ASM973359v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg664b2c8c-e2af-459e-8ef5-2985455f4df9/dqc_reference/reference_markers.hmm GCF_009733595.1_ASM973359v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:55:49,545] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:55:49,546] [INFO] Found 6/6 markers.
[2024-01-24 13:55:49,617] [INFO] Query marker FASTA was written to GCF_009733595.1_ASM973359v1_genomic.fna/markers.fasta
[2024-01-24 13:55:49,618] [INFO] Task started: Blastn
[2024-01-24 13:55:49,618] [INFO] Running command: blastn -query GCF_009733595.1_ASM973359v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg664b2c8c-e2af-459e-8ef5-2985455f4df9/dqc_reference/reference_markers.fasta -out GCF_009733595.1_ASM973359v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:55:51,070] [INFO] Task succeeded: Blastn
[2024-01-24 13:55:51,073] [INFO] Selected 16 target genomes.
[2024-01-24 13:55:51,074] [INFO] Target genome list was writen to GCF_009733595.1_ASM973359v1_genomic.fna/target_genomes.txt
[2024-01-24 13:55:51,095] [INFO] Task started: fastANI
[2024-01-24 13:55:51,096] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d13c80c-181c-40d1-abbe-ecf75f667227/GCF_009733595.1_ASM973359v1_genomic.fna.gz --refList GCF_009733595.1_ASM973359v1_genomic.fna/target_genomes.txt --output GCF_009733595.1_ASM973359v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:56:34,443] [INFO] Task succeeded: fastANI
[2024-01-24 13:56:34,444] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg664b2c8c-e2af-459e-8ef5-2985455f4df9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:56:34,445] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg664b2c8c-e2af-459e-8ef5-2985455f4df9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:56:34,461] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:56:34,461] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:56:34,461] [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 litoris	strain=NEAU-AAG5	GCA_009733595.1	2678616	2678616	type	True	100.0	3031	3033	95	conclusive
Actinomadura graeca	strain=32-07	GCA_019175365.1	2750812	2750812	type	True	86.3328	1959	3033	95	below_threshold
Actinomadura macra	strain=NBRC 14102	GCA_001552215.1	46164	46164	type	True	85.9483	1969	3033	95	below_threshold
Actinomadura rubrisoli	strain=H3C3	GCA_004349215.1	2530368	2530368	type	True	85.213	1776	3033	95	below_threshold
Actinomadura roseirufa		GCA_900659635.1	2094049	2094049	type	True	84.6133	1692	3033	95	below_threshold
Actinomadura montaniterrae	strain=CYP1-1B	GCA_008923365.1	1803903	1803903	type	True	83.9294	1742	3033	95	below_threshold
Actinomadura meyerae	strain=DSM 44715	GCA_900188445.1	240840	240840	type	True	83.9114	1666	3033	95	below_threshold
Actinomadura violacea	strain=LCR2-06	GCA_017573465.1	2819934	2819934	type	True	83.8534	1859	3033	95	below_threshold
Actinomadura darangshiensis	strain=DSM 45941	GCA_004349235.1	705336	705336	type	True	83.7125	1618	3033	95	below_threshold
Actinomadura nitritigenes	strain=L46	GCA_017573545.1	134602	134602	type	True	83.7041	1845	3033	95	below_threshold
Actinomadura madurae	strain=DSM 43067	GCA_900115095.1	1993	1993	type	True	83.6539	1753	3033	95	below_threshold
Actinomadura geliboluensis	strain=A8036	GCA_005889745.1	882440	882440	type	True	83.6161	1499	3033	95	below_threshold
Actinomadura spongiicola	strain=LHW52907	GCA_003432485.1	2303421	2303421	type	True	83.1505	1611	3033	95	below_threshold
Actinomadura rifamycini	strain=DSM 43936	GCA_000425065.1	31962	31962	type	True	82.7106	1597	3033	95	below_threshold
Actinomadura parmotrematis	strain=PM05-2	GCA_019458805.1	2864039	2864039	type	True	81.4335	1505	3033	95	below_threshold
Actinomadura rupiterrae	strain=DSM 45251	GCA_024172125.1	559627	559627	type	True	81.0216	1561	3033	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:56:34,463] [INFO] DFAST Taxonomy check result was written to GCF_009733595.1_ASM973359v1_genomic.fna/tc_result.tsv
[2024-01-24 13:56:34,463] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:56:34,464] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:56:34,464] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg664b2c8c-e2af-459e-8ef5-2985455f4df9/dqc_reference/checkm_data
[2024-01-24 13:56:34,465] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:56:34,546] [INFO] Task started: CheckM
[2024-01-24 13:56:34,546] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009733595.1_ASM973359v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009733595.1_ASM973359v1_genomic.fna/checkm_input GCF_009733595.1_ASM973359v1_genomic.fna/checkm_result
[2024-01-24 13:58:02,476] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:02,478] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 16.67%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:02,505] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:02,506] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:02,506] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009733595.1_ASM973359v1_genomic.fna/markers.fasta)
[2024-01-24 13:58:02,507] [INFO] Task started: Blastn
[2024-01-24 13:58:02,507] [INFO] Running command: blastn -query GCF_009733595.1_ASM973359v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg664b2c8c-e2af-459e-8ef5-2985455f4df9/dqc_reference/reference_markers_gtdb.fasta -out GCF_009733595.1_ASM973359v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:04,834] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:04,838] [INFO] Selected 17 target genomes.
[2024-01-24 13:58:04,839] [INFO] Target genome list was writen to GCF_009733595.1_ASM973359v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:04,851] [INFO] Task started: fastANI
[2024-01-24 13:58:04,852] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d13c80c-181c-40d1-abbe-ecf75f667227/GCF_009733595.1_ASM973359v1_genomic.fna.gz --refList GCF_009733595.1_ASM973359v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009733595.1_ASM973359v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:58:49,860] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:49,874] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:58:49,874] [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_009733595.1	s__Spirillospora litoris	100.0	3031	3033	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	99.22	99.22	0.97	0.97	2	conclusive
GCF_001552215.1	s__Spirillospora macra	85.939	1971	3033	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004349215.1	s__Spirillospora rubrisoli	85.2076	1778	3033	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	84.644	1685	3033	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	84.5065	1745	3033	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013372625.1	s__Spirillospora sp013372625	84.0051	1389	3033	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013211575.1	s__Spirillospora verrucosospora	83.9476	1845	3033	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	95.82	95.82	0.89	0.89	2	-
GCF_900188445.1	s__Spirillospora meyerae	83.94	1659	3033	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008923365.1	s__Spirillospora montaniterrae	83.9042	1746	3033	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	83.8631	1737	3033	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	83.79	1760	3033	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004349235.1	s__Spirillospora darangshiensis	83.743	1613	3033	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017573545.1	s__Spirillospora nitritigenes	83.7006	1846	3033	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	95.12	95.12	0.83	0.83	2	-
GCF_006547145.1	s__Spirillospora sp006547145	83.6661	1729	3033	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	83.6176	1759	3033	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	99.34	99.27	0.95	0.95	3	-
GCF_005889745.1	s__Spirillospora geliboluensis	83.5683	1507	3033	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	83.391	1286	3033	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 13:58:49,876] [INFO] GTDB search result was written to GCF_009733595.1_ASM973359v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:58:49,876] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:58:49,880] [INFO] DFAST_QC result json was written to GCF_009733595.1_ASM973359v1_genomic.fna/dqc_result.json
[2024-01-24 13:58:49,880] [INFO] DFAST_QC completed!
[2024-01-24 13:58:49,880] [INFO] Total running time: 0h3m30s