[2024-01-24 13:23:11,016] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:23:11,018] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:23:11,018] [INFO] DQC Reference Directory: /var/lib/cwl/stg17d8e212-2f76-4776-a8b0-c20c4bdd79d9/dqc_reference
[2024-01-24 13:23:12,253] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:23:12,254] [INFO] Task started: Prodigal
[2024-01-24 13:23:12,254] [INFO] Running command: gunzip -c /var/lib/cwl/stg0765714b-9fb2-40ab-857d-6b58a46e8c01/GCF_001552635.1_ASM155263v1_genomic.fna.gz | prodigal -d GCF_001552635.1_ASM155263v1_genomic.fna/cds.fna -a GCF_001552635.1_ASM155263v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:23:35,684] [INFO] Task succeeded: Prodigal
[2024-01-24 13:23:35,685] [INFO] Task started: HMMsearch
[2024-01-24 13:23:35,685] [INFO] Running command: hmmsearch --tblout GCF_001552635.1_ASM155263v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg17d8e212-2f76-4776-a8b0-c20c4bdd79d9/dqc_reference/reference_markers.hmm GCF_001552635.1_ASM155263v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:23:35,999] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:23:36,000] [INFO] Found 6/6 markers.
[2024-01-24 13:23:36,063] [INFO] Query marker FASTA was written to GCF_001552635.1_ASM155263v1_genomic.fna/markers.fasta
[2024-01-24 13:23:36,064] [INFO] Task started: Blastn
[2024-01-24 13:23:36,064] [INFO] Running command: blastn -query GCF_001552635.1_ASM155263v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg17d8e212-2f76-4776-a8b0-c20c4bdd79d9/dqc_reference/reference_markers.fasta -out GCF_001552635.1_ASM155263v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:37,327] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:37,330] [INFO] Selected 17 target genomes.
[2024-01-24 13:23:37,331] [INFO] Target genome list was writen to GCF_001552635.1_ASM155263v1_genomic.fna/target_genomes.txt
[2024-01-24 13:23:37,347] [INFO] Task started: fastANI
[2024-01-24 13:23:37,347] [INFO] Running command: fastANI --query /var/lib/cwl/stg0765714b-9fb2-40ab-857d-6b58a46e8c01/GCF_001552635.1_ASM155263v1_genomic.fna.gz --refList GCF_001552635.1_ASM155263v1_genomic.fna/target_genomes.txt --output GCF_001552635.1_ASM155263v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:24:17,253] [INFO] Task succeeded: fastANI
[2024-01-24 13:24:17,253] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg17d8e212-2f76-4776-a8b0-c20c4bdd79d9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:24:17,254] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg17d8e212-2f76-4776-a8b0-c20c4bdd79d9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:24:17,267] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:24:17,267] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:24:17,267] [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 hibisca	strain=NBRC 15177	GCA_001552635.1	68565	68565	type	True	100.0	2908	2922	95	conclusive
Actinomadura kijaniata	strain=NBRC 14229	GCA_001552175.1	46161	46161	type	True	84.4256	1832	2922	95	below_threshold
Actinomadura namibiensis	strain=DSM 44197	GCA_014138665.1	182080	182080	type	True	84.319	1911	2922	95	below_threshold
Actinomadura macrotermitis	strain=RB68	GCA_009604375.1	2585200	2585200	type	True	84.1975	1740	2922	95	below_threshold
Actinomadura parmotrematis	strain=PM05-2	GCA_019458805.1	2864039	2864039	type	True	83.1882	1644	2922	95	below_threshold
Actinomadura rubrisoli	strain=H3C3	GCA_004349215.1	2530368	2530368	type	True	82.1664	1457	2922	95	below_threshold
Actinomadura rubrobrunea	strain=NBRC 15275	GCA_001552235.1	115335	115335	type	True	82.1045	1321	2922	95	below_threshold
Actinomadura coerulea	strain=JCM 3320	GCA_014648535.1	46159	46159	type	True	82.0995	1532	2922	95	below_threshold
Actinomadura montaniterrae	strain=CYP1-1B	GCA_008923365.1	1803903	1803903	type	True	82.0819	1619	2922	95	below_threshold
Actinomadura coerulea	strain=DSM 43675	GCA_014208105.1	46159	46159	type	True	82.033	1558	2922	95	below_threshold
Actinomadura violacea	strain=LCR2-06	GCA_017573465.1	2819934	2819934	type	True	82.0046	1744	2922	95	below_threshold
Actinomadura madurae	strain=DSM 43067	GCA_900115095.1	1993	1993	type	True	81.7776	1562	2922	95	below_threshold
Actinomadura roseirufa		GCA_900659635.1	2094049	2094049	type	True	81.7682	1354	2922	95	below_threshold
Actinomadura rupiterrae	strain=DSM 45251	GCA_024172125.1	559627	559627	type	True	81.7009	1589	2922	95	below_threshold
Actinomadura graeca	strain=32-07	GCA_019175365.1	2750812	2750812	type	True	81.6586	1466	2922	95	below_threshold
Actinomadura rifamycini	strain=DSM 43936	GCA_000425065.1	31962	31962	type	True	81.2798	1516	2922	95	below_threshold
Actinomadura spongiicola	strain=LHW52907	GCA_003432485.1	2303421	2303421	type	True	80.8678	1235	2922	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:24:17,269] [INFO] DFAST Taxonomy check result was written to GCF_001552635.1_ASM155263v1_genomic.fna/tc_result.tsv
[2024-01-24 13:24:17,269] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:24:17,269] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:24:17,270] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg17d8e212-2f76-4776-a8b0-c20c4bdd79d9/dqc_reference/checkm_data
[2024-01-24 13:24:17,271] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:24:17,347] [INFO] Task started: CheckM
[2024-01-24 13:24:17,347] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001552635.1_ASM155263v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001552635.1_ASM155263v1_genomic.fna/checkm_input GCF_001552635.1_ASM155263v1_genomic.fna/checkm_result
[2024-01-24 13:25:32,386] [INFO] Task succeeded: CheckM
[2024-01-24 13:25:32,387] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 23.15%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2024-01-24 13:25:32,408] [INFO] ===== Completeness check finished =====
[2024-01-24 13:25:32,409] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:25:32,409] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001552635.1_ASM155263v1_genomic.fna/markers.fasta)
[2024-01-24 13:25:32,409] [INFO] Task started: Blastn
[2024-01-24 13:25:32,409] [INFO] Running command: blastn -query GCF_001552635.1_ASM155263v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg17d8e212-2f76-4776-a8b0-c20c4bdd79d9/dqc_reference/reference_markers_gtdb.fasta -out GCF_001552635.1_ASM155263v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:25:34,468] [INFO] Task succeeded: Blastn
[2024-01-24 13:25:34,471] [INFO] Selected 14 target genomes.
[2024-01-24 13:25:34,472] [INFO] Target genome list was writen to GCF_001552635.1_ASM155263v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:25:34,495] [INFO] Task started: fastANI
[2024-01-24 13:25:34,495] [INFO] Running command: fastANI --query /var/lib/cwl/stg0765714b-9fb2-40ab-857d-6b58a46e8c01/GCF_001552635.1_ASM155263v1_genomic.fna.gz --refList GCF_001552635.1_ASM155263v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001552635.1_ASM155263v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:26:09,333] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:09,345] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:26:09,345] [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_001552635.1	s__Spirillospora hibisca	100.0	2908	2922	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_001552175.1	s__Spirillospora kijaniata	84.39	1840	2922	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	97.32	97.32	0.88	0.88	2	-
GCF_009604375.1	s__Spirillospora macrotermitis	84.2082	1739	2922	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	82.7671	1780	2922	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	82.2157	1449	2922	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	82.2156	1695	2922	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	95.82	95.82	0.89	0.89	2	-
GCF_008923365.1	s__Spirillospora montaniterrae	82.0639	1623	2922	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003001795.1	s__Actinomadura_B viridilutea	82.0522	1391	2922	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_017573545.1	s__Spirillospora nitritigenes	82.0343	1716	2922	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	95.12	95.12	0.83	0.83	2	-
GCF_014208105.1	s__Spirillospora coerulea	82.0133	1562	2922	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900659615.1	s__Spirillospora fibrosa	81.9847	1596	2922	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	81.7992	1348	2922	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	81.7762	1564	2922	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	99.34	99.27	0.95	0.95	3	-
GCF_000425065.1	s__Spirillospora rifamycini	81.3164	1509	2922	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	99.13	99.13	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:26:09,347] [INFO] GTDB search result was written to GCF_001552635.1_ASM155263v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:26:09,347] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:26:09,351] [INFO] DFAST_QC result json was written to GCF_001552635.1_ASM155263v1_genomic.fna/dqc_result.json
[2024-01-24 13:26:09,351] [INFO] DFAST_QC completed!
[2024-01-24 13:26:09,351] [INFO] Total running time: 0h2m58s