[2024-01-24 13:26:26,334] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:26:26,336] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:26:26,336] [INFO] DQC Reference Directory: /var/lib/cwl/stgfdce8b8b-eb62-4a68-a2f4-a7ea57428826/dqc_reference
[2024-01-24 13:26:27,528] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:26:27,528] [INFO] Task started: Prodigal
[2024-01-24 13:26:27,529] [INFO] Running command: gunzip -c /var/lib/cwl/stgab4ae274-a27f-487d-8d6d-2f0279e57da7/GCF_008923185.1_ASM892318v1_genomic.fna.gz | prodigal -d GCF_008923185.1_ASM892318v1_genomic.fna/cds.fna -a GCF_008923185.1_ASM892318v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:26:58,348] [INFO] Task succeeded: Prodigal
[2024-01-24 13:26:58,348] [INFO] Task started: HMMsearch
[2024-01-24 13:26:58,348] [INFO] Running command: hmmsearch --tblout GCF_008923185.1_ASM892318v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfdce8b8b-eb62-4a68-a2f4-a7ea57428826/dqc_reference/reference_markers.hmm GCF_008923185.1_ASM892318v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:26:58,796] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:26:58,797] [INFO] Found 6/6 markers.
[2024-01-24 13:26:58,893] [INFO] Query marker FASTA was written to GCF_008923185.1_ASM892318v1_genomic.fna/markers.fasta
[2024-01-24 13:26:58,894] [INFO] Task started: Blastn
[2024-01-24 13:26:58,894] [INFO] Running command: blastn -query GCF_008923185.1_ASM892318v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfdce8b8b-eb62-4a68-a2f4-a7ea57428826/dqc_reference/reference_markers.fasta -out GCF_008923185.1_ASM892318v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:27:00,279] [INFO] Task succeeded: Blastn
[2024-01-24 13:27:00,284] [INFO] Selected 24 target genomes.
[2024-01-24 13:27:00,285] [INFO] Target genome list was writen to GCF_008923185.1_ASM892318v1_genomic.fna/target_genomes.txt
[2024-01-24 13:27:00,651] [INFO] Task started: fastANI
[2024-01-24 13:27:00,652] [INFO] Running command: fastANI --query /var/lib/cwl/stgab4ae274-a27f-487d-8d6d-2f0279e57da7/GCF_008923185.1_ASM892318v1_genomic.fna.gz --refList GCF_008923185.1_ASM892318v1_genomic.fna/target_genomes.txt --output GCF_008923185.1_ASM892318v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:27:53,757] [INFO] Task succeeded: fastANI
[2024-01-24 13:27:53,758] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfdce8b8b-eb62-4a68-a2f4-a7ea57428826/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:27:53,758] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfdce8b8b-eb62-4a68-a2f4-a7ea57428826/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:27:53,787] [INFO] Found 24 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:27:53,788] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:27:53,788] [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 rudentiformis	strain=HMC1	GCA_008923185.1	359158	359158	type	True	100.0	3540	3542	95	conclusive
Actinomadura barringtoniae	strain=GKU 128	GCA_017573505.1	1427535	1427535	type	True	82.687	1946	3542	95	below_threshold
Actinomadura macrotermitis	strain=RB68	GCA_009604375.1	2585200	2585200	type	True	81.4037	1555	3542	95	below_threshold
Actinomadura hibisca	strain=NBRC 15177	GCA_001552635.1	68565	68565	type	True	81.3904	1578	3542	95	below_threshold
Actinomadura viridis	strain=DSM 43175	GCA_015751755.1	58110	58110	type	True	81.3462	1591	3542	95	below_threshold
Actinomadura kijaniata	strain=NBRC 14229	GCA_001552175.1	46161	46161	type	True	81.3284	1673	3542	95	below_threshold
Actinomadura rubrisoli	strain=H3C3	GCA_004349215.1	2530368	2530368	type	True	81.2697	1467	3542	95	below_threshold
Actinomadura namibiensis	strain=DSM 44197	GCA_014138665.1	182080	182080	type	True	81.2535	1719	3542	95	below_threshold
Actinomadura madurae	strain=DSM 43067	GCA_900115095.1	1993	1993	type	True	81.1318	1629	3542	95	below_threshold
Actinomadura meyerae	strain=DSM 44715	GCA_900188445.1	240840	240840	type	True	81.0139	1539	3542	95	below_threshold
Actinomadura darangshiensis	strain=DSM 45941	GCA_004349235.1	705336	705336	type	True	81.0132	1454	3542	95	below_threshold
Actinomadura violacea	strain=LCR2-06	GCA_017573465.1	2819934	2819934	type	True	80.9144	1660	3542	95	below_threshold
Actinomadura nitritigenes	strain=L46	GCA_017573545.1	134602	134602	type	True	80.908	1670	3542	95	below_threshold
Actinomadura macra	strain=NBRC 14102	GCA_001552215.1	46164	46164	type	True	80.8281	1401	3542	95	below_threshold
Actinomadura roseirufa		GCA_900659635.1	2094049	2094049	type	True	80.7928	1305	3542	95	below_threshold
Actinomadura litoris	strain=NEAU-AAG5	GCA_009733595.1	2678616	2678616	type	True	80.7927	1477	3542	95	below_threshold
Actinomadura graeca	strain=32-07	GCA_019175365.1	2750812	2750812	type	True	80.7394	1450	3542	95	below_threshold
Actinomadura soli	strain=14C53	GCA_005889715.1	2508997	2508997	type	True	80.6953	1344	3542	95	below_threshold
Actinomadura parmotrematis	strain=PM05-2	GCA_019458805.1	2864039	2864039	type	True	80.6305	1409	3542	95	below_threshold
Actinomadura rupiterrae	strain=DSM 45251	GCA_024172125.1	559627	559627	type	True	80.3338	1440	3542	95	below_threshold
Actinomadura spongiicola	strain=LHW52907	GCA_003432485.1	2303421	2303421	type	True	80.2865	1281	3542	95	below_threshold
Actinomadura syzygii	strain=GKU157	GCA_008085905.1	1427538	1427538	type	True	80.2714	1484	3542	95	below_threshold
Actinomadura rayongensis	strain=DSM 102126	GCA_009831215.1	1429076	1429076	type	True	79.8784	1136	3542	95	below_threshold
Actinomadura atramentaria	strain=SF2197	GCA_000381885.1	1990	1990	type	True	79.7948	1200	3542	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:27:53,790] [INFO] DFAST Taxonomy check result was written to GCF_008923185.1_ASM892318v1_genomic.fna/tc_result.tsv
[2024-01-24 13:27:53,790] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:27:53,790] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:27:53,791] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfdce8b8b-eb62-4a68-a2f4-a7ea57428826/dqc_reference/checkm_data
[2024-01-24 13:27:53,792] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:27:53,885] [INFO] Task started: CheckM
[2024-01-24 13:27:53,885] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008923185.1_ASM892318v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008923185.1_ASM892318v1_genomic.fna/checkm_input GCF_008923185.1_ASM892318v1_genomic.fna/checkm_result
[2024-01-24 13:29:34,396] [INFO] Task succeeded: CheckM
[2024-01-24 13:29:34,397] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 10.19%
Strain heterogeneity: 71.43%
--------------------------------------------------------------------------------
[2024-01-24 13:29:34,425] [INFO] ===== Completeness check finished =====
[2024-01-24 13:29:34,425] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:29:34,426] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008923185.1_ASM892318v1_genomic.fna/markers.fasta)
[2024-01-24 13:29:34,426] [INFO] Task started: Blastn
[2024-01-24 13:29:34,426] [INFO] Running command: blastn -query GCF_008923185.1_ASM892318v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfdce8b8b-eb62-4a68-a2f4-a7ea57428826/dqc_reference/reference_markers_gtdb.fasta -out GCF_008923185.1_ASM892318v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:29:36,616] [INFO] Task succeeded: Blastn
[2024-01-24 13:29:36,623] [INFO] Selected 25 target genomes.
[2024-01-24 13:29:36,624] [INFO] Target genome list was writen to GCF_008923185.1_ASM892318v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:29:36,916] [INFO] Task started: fastANI
[2024-01-24 13:29:36,917] [INFO] Running command: fastANI --query /var/lib/cwl/stgab4ae274-a27f-487d-8d6d-2f0279e57da7/GCF_008923185.1_ASM892318v1_genomic.fna.gz --refList GCF_008923185.1_ASM892318v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008923185.1_ASM892318v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:30:29,505] [INFO] Task succeeded: fastANI
[2024-01-24 13:30:29,526] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:30:29,527] [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_008923185.1	s__Spirillospora rudentiformis	100.0	3540	3542	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_017573505.1	s__Spirillospora barringtoniae	82.6808	1949	3542	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009793335.1	s__Spirillospora sp009793335	81.5308	1717	3542	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001552635.1	s__Spirillospora hibisca	81.4036	1574	3542	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009604375.1	s__Spirillospora macrotermitis	81.3986	1555	3542	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015751755.1	s__Spirillospora viridis	81.3284	1595	3542	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001552175.1	s__Spirillospora kijaniata	81.3046	1679	3542	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	97.32	97.32	0.88	0.88	2	-
GCF_013372625.1	s__Spirillospora sp013372625	81.2925	1269	3542	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	81.2848	1463	3542	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	81.2399	1189	3542	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	81.1766	1624	3542	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	81.1453	1624	3542	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	99.34	99.27	0.95	0.95	3	-
GCF_013211575.1	s__Spirillospora verrucosospora	81.1276	1641	3542	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	95.82	95.82	0.89	0.89	2	-
GCA_003001795.1	s__Actinomadura_B viridilutea	81.1025	1352	3542	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Actinomadura_B	95.0	100.00	100.00	0.99	0.99	2	-
GCF_900188445.1	s__Spirillospora meyerae	81.0541	1527	3542	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	80.9444	1661	3542	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	95.12	95.12	0.83	0.83	2	-
GCF_008923365.1	s__Spirillospora montaniterrae	80.9196	1587	3542	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001552215.1	s__Spirillospora macra	80.8435	1395	3542	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	80.8298	1297	3542	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009733595.1	s__Spirillospora litoris	80.7816	1480	3542	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	99.22	99.22	0.97	0.97	2	-
GCF_005889715.1	s__Spirillospora sp005889715	80.6677	1351	3542	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	80.631	1332	3542	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008085905.1	s__Spirillospora syzygii	80.3348	1468	3542	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	95.88	95.88	0.90	0.90	2	-
GCF_000518265.1	s__Spirillospora oligospora	80.2393	1443	3542	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009831215.1	s__Spirillospora rayongensis	79.9036	1128	3542	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 13:30:29,529] [INFO] GTDB search result was written to GCF_008923185.1_ASM892318v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:30:29,529] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:30:29,536] [INFO] DFAST_QC result json was written to GCF_008923185.1_ASM892318v1_genomic.fna/dqc_result.json
[2024-01-24 13:30:29,536] [INFO] DFAST_QC completed!
[2024-01-24 13:30:29,536] [INFO] Total running time: 0h4m3s