[2024-01-24 13:18:33,559] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:18:33,564] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:18:33,564] [INFO] DQC Reference Directory: /var/lib/cwl/stg66a9d69c-18b7-4cff-9931-de15adf510ff/dqc_reference
[2024-01-24 13:18:34,939] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:18:34,942] [INFO] Task started: Prodigal
[2024-01-24 13:18:34,942] [INFO] Running command: gunzip -c /var/lib/cwl/stge8a8a4fe-f5d1-43e9-8652-f72339b3656b/GCF_007856155.1_ASM785615v1_genomic.fna.gz | prodigal -d GCF_007856155.1_ASM785615v1_genomic.fna/cds.fna -a GCF_007856155.1_ASM785615v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:19:01,820] [INFO] Task succeeded: Prodigal
[2024-01-24 13:19:01,820] [INFO] Task started: HMMsearch
[2024-01-24 13:19:01,821] [INFO] Running command: hmmsearch --tblout GCF_007856155.1_ASM785615v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg66a9d69c-18b7-4cff-9931-de15adf510ff/dqc_reference/reference_markers.hmm GCF_007856155.1_ASM785615v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:19:02,231] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:19:02,232] [INFO] Found 6/6 markers.
[2024-01-24 13:19:02,310] [INFO] Query marker FASTA was written to GCF_007856155.1_ASM785615v1_genomic.fna/markers.fasta
[2024-01-24 13:19:02,310] [INFO] Task started: Blastn
[2024-01-24 13:19:02,311] [INFO] Running command: blastn -query GCF_007856155.1_ASM785615v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg66a9d69c-18b7-4cff-9931-de15adf510ff/dqc_reference/reference_markers.fasta -out GCF_007856155.1_ASM785615v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:03,697] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:03,701] [INFO] Selected 28 target genomes.
[2024-01-24 13:19:03,702] [INFO] Target genome list was writen to GCF_007856155.1_ASM785615v1_genomic.fna/target_genomes.txt
[2024-01-24 13:19:03,733] [INFO] Task started: fastANI
[2024-01-24 13:19:03,734] [INFO] Running command: fastANI --query /var/lib/cwl/stge8a8a4fe-f5d1-43e9-8652-f72339b3656b/GCF_007856155.1_ASM785615v1_genomic.fna.gz --refList GCF_007856155.1_ASM785615v1_genomic.fna/target_genomes.txt --output GCF_007856155.1_ASM785615v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:19:53,321] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:53,322] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg66a9d69c-18b7-4cff-9931-de15adf510ff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:19:53,323] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg66a9d69c-18b7-4cff-9931-de15adf510ff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:19:53,345] [INFO] Found 28 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:19:53,345] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:19:53,346] [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
Streptomyces qinzhouensis	strain=SSL-25	GCA_007856155.1	2599401	2599401	type	True	100.0	2694	2715	95	conclusive
Streptomyces inusitatus	strain=JCM 4988	GCA_014651115.1	68221	68221	type	True	82.8004	1514	2715	95	below_threshold
Streptomyces clavuligerus	strain=ATCC 27064	GCA_015912925.1	1901	1901	type	True	82.7497	1159	2715	95	below_threshold
Streptomyces clavuligerus	strain=ATCC 27064	GCA_000154925.1	1901	1901	suspected-type	True	82.7214	1159	2715	95	below_threshold
Streptomyces clavuligerus	strain=ATCC 27064	GCA_000163875.1	1901	1901	suspected-type	True	82.5533	1539	2715	95	below_threshold
Streptomyces purpureus	strain=JCM 3172	GCA_014648195.1	1951	1951	type	True	81.9114	1269	2715	95	below_threshold
Streptomyces formicae	strain=1H-GS9	GCA_022647665.1	1616117	1616117	type	True	81.7365	1307	2715	95	below_threshold
Streptomyces zhihengii	strain=YIM T102	GCA_016919245.1	1818004	1818004	type	True	81.5946	1455	2715	95	below_threshold
Streptomyces fradiae	strain=NRRL B-1195	GCA_002154445.1	1906	1906	suspected-type	True	81.5174	762	2715	95	below_threshold
Streptomyces lichenis	strain=LCR6-01	GCA_023218175.1	2306967	2306967	type	True	81.508	1268	2715	95	below_threshold
Streptomyces genisteinicus	strain=CRPJ-33	GCA_014489615.1	2768068	2768068	type	True	81.48	1379	2715	95	below_threshold
Streptomyces roseicoloratus	strain=TRM44457	GCA_004117935.1	2508722	2508722	type	True	81.4758	1211	2715	95	below_threshold
Streptomyces melanogenes	strain=JCM 4398	GCA_014649795.1	67326	67326	type	True	81.3065	1281	2715	95	below_threshold
Streptomyces somaliensis	strain=DSM 40738	GCA_024349285.1	78355	78355	type	True	81.256	1006	2715	95	below_threshold
Streptomyces sudanensis	strain=SD 504	GCA_023614315.1	436397	436397	type	True	81.21	1028	2715	95	below_threshold
Streptomyces filamentosus	strain=JCM 4122	GCA_014654895.1	67294	67294	type	True	81.1646	1343	2715	95	below_threshold
Streptomyces roseolus	strain=JCM 4411	GCA_014649855.1	67358	67358	type	True	81.1362	1268	2715	95	below_threshold
Streptomyces fradiae	strain=DSM 40063	GCA_002119225.1	1906	1906	suspected-type	True	81.1001	1103	2715	95	below_threshold
Streptomyces fradiae	strain=ATCC 10745	GCA_008704425.1	1906	1906	suspected-type	True	81.0533	1188	2715	95	below_threshold
Streptomyces fradiae	strain=ATCC 10745	GCA_009834665.1	1906	1906	suspected-type	True	80.9723	1182	2715	95	below_threshold
Streptomyces atriruber	strain=NRRL B-24165	GCA_001418325.1	545121	545121	type	True	80.4427	1121	2715	95	below_threshold
Streptomyces spinoverrucosus	strain=NBRC 14228	GCA_006539505.1	284043	284043	type	True	80.3468	1167	2715	95	below_threshold
Streptomyces spectabilis	strain=ATCC 27465	GCA_008704795.1	68270	68270	type	True	80.3176	1332	2715	95	below_threshold
Streptomyces spinoverrucosus	strain=JCM 5077	GCA_014651195.1	284043	284043	type	True	80.312	1201	2715	95	below_threshold
Streptomyces spectabilis	strain=KCTC9218	GCA_022698305.1	68270	68270	type	True	80.2824	1329	2715	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	80.2423	1131	2715	95	below_threshold
Streptomyces spectabilis	strain=JCM 4308	GCA_014649235.1	68270	68270	type	True	80.2195	1323	2715	95	below_threshold
Streptomyces panaciradicis	strain=NBRC 109811	GCA_023516615.1	1470261	1470261	type	True	80.1051	1168	2715	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:19:53,347] [INFO] DFAST Taxonomy check result was written to GCF_007856155.1_ASM785615v1_genomic.fna/tc_result.tsv
[2024-01-24 13:19:53,348] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:19:53,348] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:19:53,348] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg66a9d69c-18b7-4cff-9931-de15adf510ff/dqc_reference/checkm_data
[2024-01-24 13:19:53,349] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:19:53,437] [INFO] Task started: CheckM
[2024-01-24 13:19:53,438] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007856155.1_ASM785615v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007856155.1_ASM785615v1_genomic.fna/checkm_input GCF_007856155.1_ASM785615v1_genomic.fna/checkm_result
[2024-01-24 13:21:31,882] [INFO] Task succeeded: CheckM
[2024-01-24 13:21:31,884] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:21:31,915] [INFO] ===== Completeness check finished =====
[2024-01-24 13:21:31,915] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:21:31,915] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007856155.1_ASM785615v1_genomic.fna/markers.fasta)
[2024-01-24 13:21:31,916] [INFO] Task started: Blastn
[2024-01-24 13:21:31,916] [INFO] Running command: blastn -query GCF_007856155.1_ASM785615v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg66a9d69c-18b7-4cff-9931-de15adf510ff/dqc_reference/reference_markers_gtdb.fasta -out GCF_007856155.1_ASM785615v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:21:33,920] [INFO] Task succeeded: Blastn
[2024-01-24 13:21:33,924] [INFO] Selected 19 target genomes.
[2024-01-24 13:21:33,924] [INFO] Target genome list was writen to GCF_007856155.1_ASM785615v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:21:33,998] [INFO] Task started: fastANI
[2024-01-24 13:21:33,998] [INFO] Running command: fastANI --query /var/lib/cwl/stge8a8a4fe-f5d1-43e9-8652-f72339b3656b/GCF_007856155.1_ASM785615v1_genomic.fna.gz --refList GCF_007856155.1_ASM785615v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007856155.1_ASM785615v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:22:10,630] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:10,646] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:22:10,647] [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_007856155.1	s__Streptomyces qinzhouensis	100.0	2691	2715	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003932715.1	s__Streptomyces tsukubensis	91.4659	2231	2715	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	99.99	1.00	1.00	5	-
GCF_009600885.1	s__Streptomyces jumonjinensis_A	82.9622	1444	2715	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.98	97.98	0.89	0.89	2	-
GCF_014651115.1	s__Streptomyces inusitatus	82.772	1519	2715	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000377145.1	s__Streptomyces sp000377145	81.9575	1273	2715	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648195.1	s__Streptomyces purpureus	81.8753	1275	2715	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.54	99.54	0.95	0.95	2	-
GCF_001278075.1	s__Streptomyces pristinaespiralis	81.6824	1311	2715	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.86	99.72	0.99	0.98	3	-
GCF_016919245.1	s__Streptomyces zhihengii	81.6121	1458	2715	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001646665.1	s__Streptomyces albulus_A	81.4665	1273	2715	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004117935.1	s__Streptomyces roseicoloratus	81.4542	1215	2715	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001653515.1	s__Streptomyces sp001653515	81.381	1143	2715	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014649795.1	s__Streptomyces melanogenes	81.2891	1284	2715	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.19	95.19	0.83	0.83	2	-
GCF_014654895.1	s__Streptomyces filamentosus	81.1815	1342	2715	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.28	96.27	0.93	0.92	4	-
GCF_014649855.1	s__Streptomyces roseolus	81.1676	1262	2715	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008704425.1	s__Streptomyces fradiae	81.06	1190	2715	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.82	99.37	0.98	0.97	5	-
GCF_000761215.1	s__Streptomyces glaucescens	80.6083	1204	2715	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001418325.1	s__Streptomyces atriruber	80.4573	1118	2715	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008642335.1	s__Streptomyces venezuelae_F	80.4485	1222	2715	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018069565.1	s__Streptomyces sp018069565	80.3802	1173	2715	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:22:10,649] [INFO] GTDB search result was written to GCF_007856155.1_ASM785615v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:22:10,649] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:22:10,655] [INFO] DFAST_QC result json was written to GCF_007856155.1_ASM785615v1_genomic.fna/dqc_result.json
[2024-01-24 13:22:10,655] [INFO] DFAST_QC completed!
[2024-01-24 13:22:10,655] [INFO] Total running time: 0h3m37s