[2024-01-24 14:47:06,333] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:47:06,335] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:47:06,335] [INFO] DQC Reference Directory: /var/lib/cwl/stgfece3112-a5a2-4349-adb4-a868292ee74d/dqc_reference
[2024-01-24 14:47:07,591] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:47:07,592] [INFO] Task started: Prodigal
[2024-01-24 14:47:07,593] [INFO] Running command: gunzip -c /var/lib/cwl/stgcc7c72cf-7b23-4907-99bd-8cee6f92fdc7/GCF_014648695.1_ASM1464869v1_genomic.fna.gz | prodigal -d GCF_014648695.1_ASM1464869v1_genomic.fna/cds.fna -a GCF_014648695.1_ASM1464869v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:47:33,077] [INFO] Task succeeded: Prodigal
[2024-01-24 14:47:33,077] [INFO] Task started: HMMsearch
[2024-01-24 14:47:33,078] [INFO] Running command: hmmsearch --tblout GCF_014648695.1_ASM1464869v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfece3112-a5a2-4349-adb4-a868292ee74d/dqc_reference/reference_markers.hmm GCF_014648695.1_ASM1464869v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:47:33,528] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:47:33,529] [INFO] Found 6/6 markers.
[2024-01-24 14:47:33,609] [INFO] Query marker FASTA was written to GCF_014648695.1_ASM1464869v1_genomic.fna/markers.fasta
[2024-01-24 14:47:33,609] [INFO] Task started: Blastn
[2024-01-24 14:47:33,610] [INFO] Running command: blastn -query GCF_014648695.1_ASM1464869v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfece3112-a5a2-4349-adb4-a868292ee74d/dqc_reference/reference_markers.fasta -out GCF_014648695.1_ASM1464869v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:47:35,074] [INFO] Task succeeded: Blastn
[2024-01-24 14:47:35,077] [INFO] Selected 20 target genomes.
[2024-01-24 14:47:35,078] [INFO] Target genome list was writen to GCF_014648695.1_ASM1464869v1_genomic.fna/target_genomes.txt
[2024-01-24 14:47:35,086] [INFO] Task started: fastANI
[2024-01-24 14:47:35,087] [INFO] Running command: fastANI --query /var/lib/cwl/stgcc7c72cf-7b23-4907-99bd-8cee6f92fdc7/GCF_014648695.1_ASM1464869v1_genomic.fna.gz --refList GCF_014648695.1_ASM1464869v1_genomic.fna/target_genomes.txt --output GCF_014648695.1_ASM1464869v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:48:17,263] [INFO] Task succeeded: fastANI
[2024-01-24 14:48:17,264] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfece3112-a5a2-4349-adb4-a868292ee74d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:48:17,265] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfece3112-a5a2-4349-adb4-a868292ee74d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:48:17,286] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:48:17,287] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:48:17,287] [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 albospinus	strain=JCM 3399	GCA_014648695.1	285515	285515	type	True	100.0	2992	2998	95	conclusive
Streptomyces albulus	strain=JCM 4718	GCA_014650635.1	68570	68570	suspected-type	True	87.8033	2077	2998	95	below_threshold
Streptomyces angustmyceticus	strain=NRRL B-2347	GCA_002154415.1	285578	285578	type	True	86.7699	1353	2998	95	below_threshold
Streptomyces angustmyceticus	strain=NBRC 3934	GCA_009176265.1	285578	285578	type	True	86.6141	1761	2998	95	below_threshold
Streptomyces angustmyceticus	strain=JCM 4053	GCA_019933235.1	285578	285578	type	True	86.6132	1750	2998	95	below_threshold
Streptomyces lydicamycinicus	strain=NBRC 110027	GCA_000829715.2	1546107	1546107	type	True	86.5985	1806	2998	95	below_threshold
Streptomyces sioyaensis	strain=DSM 40032	GCA_004122735.1	67364	67364	type	True	86.4871	1654	2998	95	below_threshold
Streptomyces platensis	strain=DSM 40041	GCA_002119195.1	58346	58346	type	True	86.4688	1759	2998	95	below_threshold
Streptomyces platensis	strain=ATCC 23948	GCA_008704855.1	58346	58346	type	True	86.4501	1793	2998	95	below_threshold
Streptomyces glebosus	strain=NBRC 13786	GCA_009811575.1	249580	249580	type	True	86.4151	1821	2998	95	below_threshold
Streptomyces kronopolitis	strain=CGMCC 4.7323	GCA_014646275.1	1612435	1612435	type	True	86.3482	1687	2998	95	below_threshold
Streptomyces tubercidicus	strain=NBRC 13090	GCA_009811635.1	47759	47759	type	True	86.2422	1735	2998	95	below_threshold
Streptomyces kasugaensis	strain=BCRC 12349	GCA_002261115.1	1946	1946	type	True	85.8001	1717	2998	95	below_threshold
Streptomyces pinistramenti	strain=SF28	GCA_020564935.1	2884812	2884812	type	True	85.1339	1589	2998	95	below_threshold
Streptomyces benahoarensis	strain=MZ03-37	GCA_007280575.1	2595054	2595054	type	True	84.3779	1244	2998	95	below_threshold
Streptomyces rimosus subsp. rimosus	strain=R7	GCA_022760195.1	132474	1927	type	True	83.7288	1610	2998	95	below_threshold
Streptomyces monomycini	strain=NRRL B-24309	GCA_000715845.1	371720	371720	type	True	83.6327	1551	2998	95	below_threshold
Streptomyces chrestomyceticus	strain=NBRC 13444	GCA_003865135.1	68185	68185	type	True	83.5818	1603	2998	95	below_threshold
Streptomyces paromomycinus	strain=NBRC 15454	GCA_003865155.1	92743	92743	type	True	83.5635	1616	2998	95	below_threshold
Streptomyces monomycini	strain=NRRL B-24309	GCA_022271435.1	371720	371720	type	True	83.5494	1590	2998	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:48:17,289] [INFO] DFAST Taxonomy check result was written to GCF_014648695.1_ASM1464869v1_genomic.fna/tc_result.tsv
[2024-01-24 14:48:17,289] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:48:17,290] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:48:17,290] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfece3112-a5a2-4349-adb4-a868292ee74d/dqc_reference/checkm_data
[2024-01-24 14:48:17,291] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:48:17,377] [INFO] Task started: CheckM
[2024-01-24 14:48:17,377] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014648695.1_ASM1464869v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014648695.1_ASM1464869v1_genomic.fna/checkm_input GCF_014648695.1_ASM1464869v1_genomic.fna/checkm_result
[2024-01-24 14:50:16,238] [INFO] Task succeeded: CheckM
[2024-01-24 14:50:16,239] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 15.62%
Strain heterogeneity: 33.33%
--------------------------------------------------------------------------------
[2024-01-24 14:50:16,269] [INFO] ===== Completeness check finished =====
[2024-01-24 14:50:16,269] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:50:16,270] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014648695.1_ASM1464869v1_genomic.fna/markers.fasta)
[2024-01-24 14:50:16,270] [INFO] Task started: Blastn
[2024-01-24 14:50:16,270] [INFO] Running command: blastn -query GCF_014648695.1_ASM1464869v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfece3112-a5a2-4349-adb4-a868292ee74d/dqc_reference/reference_markers_gtdb.fasta -out GCF_014648695.1_ASM1464869v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:50:18,640] [INFO] Task succeeded: Blastn
[2024-01-24 14:50:18,644] [INFO] Selected 13 target genomes.
[2024-01-24 14:50:18,644] [INFO] Target genome list was writen to GCF_014648695.1_ASM1464869v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:50:18,656] [INFO] Task started: fastANI
[2024-01-24 14:50:18,656] [INFO] Running command: fastANI --query /var/lib/cwl/stgcc7c72cf-7b23-4907-99bd-8cee6f92fdc7/GCF_014648695.1_ASM1464869v1_genomic.fna.gz --refList GCF_014648695.1_ASM1464869v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014648695.1_ASM1464869v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:50:51,454] [INFO] Task succeeded: fastANI
[2024-01-24 14:50:51,472] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:50:51,472] [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_014648695.1	s__Streptomyces albospinus	100.0	2992	2998	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_009834125.1	s__Streptomyces sp009834125	93.3908	2358	2998	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000805335.1	s__Streptomyces sp000805335	92.9806	2080	2998	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002803155.1	s__Streptomyces sp002803155	88.1386	2095	2998	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001704275.1	s__Streptomyces noursei	87.9898	2061	2998	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.5028	97.67	97.67	0.83	0.83	2	-
GCF_016917755.1	s__Streptomyces yunnanensis	87.8834	2096	2998	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.5028	97.38	97.21	0.85	0.85	4	-
GCF_000373585.1	s__Streptomyces sp000373585	87.634	1948	2998	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009176265.1	s__Streptomyces angustmyceticus	86.6076	1761	2998	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.96	99.96	1.00	1.00	2	-
GCF_009811635.1	s__Streptomyces tubercidicus	86.2087	1742	2998	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002082195.1	s__Streptomyces gilvosporeus	86.0211	1862	2998	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0251	N/A	N/A	N/A	N/A	1	-
GCA_000720995.1	s__Streptomyces celluloflavus	85.9279	1675	2998	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.24	98.62	0.95	0.89	4	-
GCF_000935125.1	s__Streptomyces natalensis	85.8927	1854	2998	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0251	N/A	N/A	N/A	N/A	1	-
GCF_003865135.1	s__Streptomyces chrestomyceticus	83.5799	1603	2998	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.95	95.89	0.90	0.88	4	-
--------------------------------------------------------------------------------
[2024-01-24 14:50:51,474] [INFO] GTDB search result was written to GCF_014648695.1_ASM1464869v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:50:51,474] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:50:51,481] [INFO] DFAST_QC result json was written to GCF_014648695.1_ASM1464869v1_genomic.fna/dqc_result.json
[2024-01-24 14:50:51,481] [INFO] DFAST_QC completed!
[2024-01-24 14:50:51,481] [INFO] Total running time: 0h3m45s