[2024-01-24 14:22:01,854] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:22:01,855] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:22:01,856] [INFO] DQC Reference Directory: /var/lib/cwl/stg9f94242f-f1c5-40d9-a233-f6222b535acb/dqc_reference
[2024-01-24 14:22:03,134] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:22:03,134] [INFO] Task started: Prodigal
[2024-01-24 14:22:03,135] [INFO] Running command: gunzip -c /var/lib/cwl/stga810c8e4-3233-4a8b-ac94-f4ebee8a92d2/GCF_015751755.1_ASM1575175v1_genomic.fna.gz | prodigal -d GCF_015751755.1_ASM1575175v1_genomic.fna/cds.fna -a GCF_015751755.1_ASM1575175v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:22:28,580] [INFO] Task succeeded: Prodigal
[2024-01-24 14:22:28,580] [INFO] Task started: HMMsearch
[2024-01-24 14:22:28,580] [INFO] Running command: hmmsearch --tblout GCF_015751755.1_ASM1575175v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9f94242f-f1c5-40d9-a233-f6222b535acb/dqc_reference/reference_markers.hmm GCF_015751755.1_ASM1575175v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:22:29,050] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:22:29,051] [INFO] Found 6/6 markers.
[2024-01-24 14:22:29,130] [INFO] Query marker FASTA was written to GCF_015751755.1_ASM1575175v1_genomic.fna/markers.fasta
[2024-01-24 14:22:29,131] [INFO] Task started: Blastn
[2024-01-24 14:22:29,131] [INFO] Running command: blastn -query GCF_015751755.1_ASM1575175v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9f94242f-f1c5-40d9-a233-f6222b535acb/dqc_reference/reference_markers.fasta -out GCF_015751755.1_ASM1575175v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:30,631] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:30,634] [INFO] Selected 30 target genomes.
[2024-01-24 14:22:30,635] [INFO] Target genome list was writen to GCF_015751755.1_ASM1575175v1_genomic.fna/target_genomes.txt
[2024-01-24 14:22:30,645] [INFO] Task started: fastANI
[2024-01-24 14:22:30,645] [INFO] Running command: fastANI --query /var/lib/cwl/stga810c8e4-3233-4a8b-ac94-f4ebee8a92d2/GCF_015751755.1_ASM1575175v1_genomic.fna.gz --refList GCF_015751755.1_ASM1575175v1_genomic.fna/target_genomes.txt --output GCF_015751755.1_ASM1575175v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:23:32,216] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:32,217] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9f94242f-f1c5-40d9-a233-f6222b535acb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:23:32,217] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9f94242f-f1c5-40d9-a233-f6222b535acb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:23:32,238] [INFO] Found 30 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:23:32,238] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:23:32,238] [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 viridis	strain=DSM 43175	GCA_015751755.1	58110	58110	type	True	100.0	2997	2997	95	conclusive
Actinomadura rubrobrunea	strain=NBRC 15275	GCA_001552235.1	115335	115335	type	True	82.2593	1387	2997	95	below_threshold
Actinomadura hibisca	strain=NBRC 15177	GCA_001552635.1	68565	68565	type	True	82.1697	1540	2997	95	below_threshold
Actinomadura mexicana	strain=DSM 44485	GCA_900188105.1	134959	134959	type	True	82.1283	1585	2997	95	below_threshold
Actinomadura macrotermitis	strain=RB68	GCA_009604375.1	2585200	2585200	type	True	82.0086	1531	2997	95	below_threshold
Actinomadura formosensis	strain=NBRC 14204	GCA_001552155.1	60706	60706	type	True	81.8344	1269	2997	95	below_threshold
Actinomadura meyerae	strain=DSM 44715	GCA_900188445.1	240840	240840	type	True	81.8199	1565	2997	95	below_threshold
Actinomadura rubrisoli	strain=H3C3	GCA_004349215.1	2530368	2530368	type	True	81.8072	1419	2997	95	below_threshold
Actinomadura madurae	strain=DSM 43067	GCA_900115095.1	1993	1993	type	True	81.7364	1640	2997	95	below_threshold
Actinomadura geliboluensis	strain=A8036	GCA_005889745.1	882440	882440	type	True	81.7357	1424	2997	95	below_threshold
Actinomadura physcomitrii	strain=LD22	GCA_008923205.2	2650748	2650748	type	True	81.7008	1583	2997	95	below_threshold
Actinomadura montaniterrae	strain=CYP1-1B	GCA_008923365.1	1803903	1803903	type	True	81.6831	1575	2997	95	below_threshold
Actinomadura litoris	strain=NEAU-AAG5	GCA_009733595.1	2678616	2678616	type	True	81.6171	1482	2997	95	below_threshold
Actinomadura nitritigenes	strain=L46	GCA_017573545.1	134602	134602	type	True	81.5954	1687	2997	95	below_threshold
Actinomadura darangshiensis	strain=DSM 45941	GCA_004349235.1	705336	705336	type	True	81.5788	1477	2997	95	below_threshold
Actinomadura roseirufa		GCA_900659635.1	2094049	2094049	type	True	81.5711	1366	2997	95	below_threshold
Actinomadura graeca	strain=32-07	GCA_019175365.1	2750812	2750812	type	True	81.517	1467	2997	95	below_threshold
Actinomadura violacea	strain=LCR2-06	GCA_017573465.1	2819934	2819934	type	True	81.511	1698	2997	95	below_threshold
Actinomadura parmotrematis	strain=PM05-2	GCA_019458805.1	2864039	2864039	type	True	81.1449	1454	2997	95	below_threshold
Actinomadura decatromicini	strain=CYP1-5	GCA_008121305.1	2604572	2604572	type	True	81.1123	1490	2997	95	below_threshold
Actinomadura spongiicola	strain=LHW52907	GCA_003432485.1	2303421	2303421	type	True	80.8864	1278	2997	95	below_threshold
Thermomonospora catenispora	strain=3-22-3	GCA_006363815.1	2493090	2493090	type	True	80.7756	1131	2997	95	below_threshold
Actinomadura rupiterrae	strain=DSM 45251	GCA_024172125.1	559627	559627	type	True	80.7152	1425	2997	95	below_threshold
Actinoallomurus spadix	strain=KCTC 9252	GCA_024055725.1	79912	79912	type	True	78.6099	1072	2997	95	below_threshold
Actinoallomurus bryophytorum	strain=DSM 102200	GCA_006716425.1	1490222	1490222	type	True	78.4787	1074	2997	95	below_threshold
Actinacidiphila paucisporea	strain=CGMCC 4.2025	GCA_900142575.1	310782	310782	type	True	76.5791	816	2997	95	below_threshold
Actinacidiphila epipremni	strain=PRB2-1	GCA_012034175.1	2053013	2053013	type	True	76.5304	901	2997	95	below_threshold
Streptomyces griseoruber	strain=NRRL B-1818	GCA_001418585.1	1943	1943	type	True	76.4521	754	2997	95	below_threshold
Sanguibacter suarezii	strain=NBRC 16159	GCA_001552735.1	60921	60921	type	True	76.0934	325	2997	95	below_threshold
Cellulomonas telluris	strain=CPCC 204705	GCA_004886325.1	2306636	2306636	type	True	75.7358	489	2997	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:23:32,240] [INFO] DFAST Taxonomy check result was written to GCF_015751755.1_ASM1575175v1_genomic.fna/tc_result.tsv
[2024-01-24 14:23:32,241] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:23:32,241] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:23:32,241] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9f94242f-f1c5-40d9-a233-f6222b535acb/dqc_reference/checkm_data
[2024-01-24 14:23:32,242] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:23:32,318] [INFO] Task started: CheckM
[2024-01-24 14:23:32,318] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_015751755.1_ASM1575175v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_015751755.1_ASM1575175v1_genomic.fna/checkm_input GCF_015751755.1_ASM1575175v1_genomic.fna/checkm_result
[2024-01-24 14:25:47,707] [INFO] Task succeeded: CheckM
[2024-01-24 14:25:47,708] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:25:47,730] [INFO] ===== Completeness check finished =====
[2024-01-24 14:25:47,730] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:25:47,730] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_015751755.1_ASM1575175v1_genomic.fna/markers.fasta)
[2024-01-24 14:25:47,731] [INFO] Task started: Blastn
[2024-01-24 14:25:47,731] [INFO] Running command: blastn -query GCF_015751755.1_ASM1575175v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9f94242f-f1c5-40d9-a233-f6222b535acb/dqc_reference/reference_markers_gtdb.fasta -out GCF_015751755.1_ASM1575175v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:25:49,860] [INFO] Task succeeded: Blastn
[2024-01-24 14:25:49,864] [INFO] Selected 27 target genomes.
[2024-01-24 14:25:49,864] [INFO] Target genome list was writen to GCF_015751755.1_ASM1575175v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:25:49,913] [INFO] Task started: fastANI
[2024-01-24 14:25:49,914] [INFO] Running command: fastANI --query /var/lib/cwl/stga810c8e4-3233-4a8b-ac94-f4ebee8a92d2/GCF_015751755.1_ASM1575175v1_genomic.fna.gz --refList GCF_015751755.1_ASM1575175v1_genomic.fna/target_genomes_gtdb.txt --output GCF_015751755.1_ASM1575175v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:26:42,974] [INFO] Task succeeded: fastANI
[2024-01-24 14:26:42,994] [INFO] Found 27 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:26:42,995] [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_015751755.1	s__Spirillospora viridis	100.0	2997	2997	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_003001795.1	s__Actinomadura_B viridilutea	82.2151	1432	2997	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_001552635.1	s__Spirillospora hibisca	82.1155	1551	2997	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	82.0466	1683	2997	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	82.0457	1523	2997	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001552155.1	s__Spirillospora formosensis	81.8559	1264	2997	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	99.99	99.99	0.99	0.99	2	-
GCF_005889745.1	s__Spirillospora geliboluensis	81.8056	1406	2997	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	81.7903	1568	2997	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	81.756	1426	2997	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	81.7429	1312	2997	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	81.7414	1638	2997	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	99.34	99.27	0.95	0.95	3	-
GCF_900659615.1	s__Spirillospora fibrosa	81.7322	1604	2997	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	81.712	1581	2997	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	81.5851	1690	2997	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	95.12	95.12	0.83	0.83	2	-
GCF_013211575.1	s__Spirillospora verrucosospora	81.5838	1714	2997	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	95.82	95.82	0.89	0.89	2	-
GCF_008923185.1	s__Spirillospora rudentiformis	81.5706	1544	2997	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	81.5681	1367	2997	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	81.5623	1479	2997	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	81.5308	1499	2997	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	99.22	99.22	0.97	0.97	2	-
GCF_000718255.1	s__Spirillospora albida	81.4149	1265	2997	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003589885.1	s__Thermomonospora amylolytica	81.3513	1328	2997	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Thermomonospora	95.0	98.39	98.39	0.92	0.92	2	-
GCF_006363815.1	s__Thermomonospora catenispora	80.8928	1110	2997	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Thermomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003289645.1	s__Actinomadura_D craniellae	80.6569	1258	2997	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Actinomadura_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012034175.1	s__Streptomyces sp012034175	76.5116	910	2997	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015390235.1	s__Quadrisphaera sp015390235	76.1514	524	2997	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Quadrisphaeraceae;g__Quadrisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001552735.1	s__Sanguibacter suarezii	76.0744	329	2997	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Sanguibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004886325.1	s__Cellulomonas telluris	75.7407	485	2997	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:26:42,996] [INFO] GTDB search result was written to GCF_015751755.1_ASM1575175v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:26:42,997] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:26:43,002] [INFO] DFAST_QC result json was written to GCF_015751755.1_ASM1575175v1_genomic.fna/dqc_result.json
[2024-01-24 14:26:43,002] [INFO] DFAST_QC completed!
[2024-01-24 14:26:43,002] [INFO] Total running time: 0h4m41s