[2024-01-24 14:19:01,329] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:01,331] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:01,331] [INFO] DQC Reference Directory: /var/lib/cwl/stg77aa17cf-b196-4d83-bd61-d63f0cd3318a/dqc_reference
[2024-01-24 14:19:02,577] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:02,578] [INFO] Task started: Prodigal
[2024-01-24 14:19:02,578] [INFO] Running command: gunzip -c /var/lib/cwl/stg8dcb829d-4898-480e-9811-b4a3982f73ec/GCF_008704855.1_ASM870485v1_genomic.fna.gz | prodigal -d GCF_008704855.1_ASM870485v1_genomic.fna/cds.fna -a GCF_008704855.1_ASM870485v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:19:28,805] [INFO] Task succeeded: Prodigal
[2024-01-24 14:19:28,805] [INFO] Task started: HMMsearch
[2024-01-24 14:19:28,806] [INFO] Running command: hmmsearch --tblout GCF_008704855.1_ASM870485v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg77aa17cf-b196-4d83-bd61-d63f0cd3318a/dqc_reference/reference_markers.hmm GCF_008704855.1_ASM870485v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:19:29,254] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:19:29,255] [INFO] Found 6/6 markers.
[2024-01-24 14:19:29,340] [INFO] Query marker FASTA was written to GCF_008704855.1_ASM870485v1_genomic.fna/markers.fasta
[2024-01-24 14:19:29,341] [INFO] Task started: Blastn
[2024-01-24 14:19:29,341] [INFO] Running command: blastn -query GCF_008704855.1_ASM870485v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg77aa17cf-b196-4d83-bd61-d63f0cd3318a/dqc_reference/reference_markers.fasta -out GCF_008704855.1_ASM870485v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:19:30,777] [INFO] Task succeeded: Blastn
[2024-01-24 14:19:30,789] [INFO] Selected 14 target genomes.
[2024-01-24 14:19:30,789] [INFO] Target genome list was writen to GCF_008704855.1_ASM870485v1_genomic.fna/target_genomes.txt
[2024-01-24 14:19:30,807] [INFO] Task started: fastANI
[2024-01-24 14:19:30,808] [INFO] Running command: fastANI --query /var/lib/cwl/stg8dcb829d-4898-480e-9811-b4a3982f73ec/GCF_008704855.1_ASM870485v1_genomic.fna.gz --refList GCF_008704855.1_ASM870485v1_genomic.fna/target_genomes.txt --output GCF_008704855.1_ASM870485v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:20:07,081] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:07,081] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg77aa17cf-b196-4d83-bd61-d63f0cd3318a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:20:07,082] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg77aa17cf-b196-4d83-bd61-d63f0cd3318a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:20:07,094] [INFO] Found 14 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 14:20:07,094] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 14:20:07,095] [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 platensis	strain=ATCC 23948	GCA_008704855.1	58346	58346	type	True	100.0	2830	2833	95	inconclusive
Streptomyces platensis	strain=DSM 40041	GCA_002119195.1	58346	58346	type	True	99.9661	2723	2833	95	inconclusive
Streptomyces glebosus	strain=NBRC 13786	GCA_009811575.1	249580	249580	type	True	97.6485	2474	2833	95	inconclusive
Streptomyces glebosus	strain=JCM 4954	GCA_014656235.1	249580	249580	type	True	97.6132	2443	2833	95	inconclusive
Streptomyces lydicamycinicus	strain=NBRC 110027	GCA_000829715.2	1546107	1546107	type	True	95.2165	2401	2833	95	inconclusive
Streptomyces libani subsp. libani	strain=NBRC 13452	GCA_009811595.1	68044	68043	type	True	92.813	2334	2833	95	below_threshold
Streptomyces libani subsp. libani	strain=JCM 4322	GCA_014649275.1	68044	68043	type	True	92.7631	2324	2833	95	below_threshold
Streptomyces caniferus	strain=NBRC 15389	GCA_009811555.1	285557	285557	type	True	89.8557	2163	2833	95	below_threshold
Streptomyces sioyaensis	strain=DSM 40032	GCA_004122735.1	67364	67364	type	True	89.2668	1876	2833	95	below_threshold
Streptomyces pinistramenti	strain=SF28	GCA_020564935.1	2884812	2884812	type	True	85.4134	1586	2833	95	below_threshold
Streptomyces benahoarensis	strain=MZ03-37	GCA_007280575.1	2595054	2595054	type	True	84.4545	1283	2833	95	below_threshold
Streptomyces paromomycinus	strain=NBRC 15454	GCA_003865155.1	92743	92743	type	True	83.7561	1626	2833	95	below_threshold
Streptomyces rimosus subsp. rimosus	strain=R7	GCA_022760195.1	132474	1927	type	True	83.6216	1683	2833	95	below_threshold
Streptomyces monomycini	strain=NRRL B-24309	GCA_022271435.1	371720	371720	type	True	83.5748	1607	2833	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:20:07,096] [INFO] DFAST Taxonomy check result was written to GCF_008704855.1_ASM870485v1_genomic.fna/tc_result.tsv
[2024-01-24 14:20:07,097] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:20:07,097] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:20:07,097] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg77aa17cf-b196-4d83-bd61-d63f0cd3318a/dqc_reference/checkm_data
[2024-01-24 14:20:07,098] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:20:07,184] [INFO] Task started: CheckM
[2024-01-24 14:20:07,184] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008704855.1_ASM870485v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008704855.1_ASM870485v1_genomic.fna/checkm_input GCF_008704855.1_ASM870485v1_genomic.fna/checkm_result
[2024-01-24 14:21:51,977] [INFO] Task succeeded: CheckM
[2024-01-24 14:21:51,979] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:21:52,005] [INFO] ===== Completeness check finished =====
[2024-01-24 14:21:52,005] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:21:52,006] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008704855.1_ASM870485v1_genomic.fna/markers.fasta)
[2024-01-24 14:21:52,006] [INFO] Task started: Blastn
[2024-01-24 14:21:52,006] [INFO] Running command: blastn -query GCF_008704855.1_ASM870485v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg77aa17cf-b196-4d83-bd61-d63f0cd3318a/dqc_reference/reference_markers_gtdb.fasta -out GCF_008704855.1_ASM870485v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:21:54,119] [INFO] Task succeeded: Blastn
[2024-01-24 14:21:54,123] [INFO] Selected 9 target genomes.
[2024-01-24 14:21:54,123] [INFO] Target genome list was writen to GCF_008704855.1_ASM870485v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:21:54,160] [INFO] Task started: fastANI
[2024-01-24 14:21:54,160] [INFO] Running command: fastANI --query /var/lib/cwl/stg8dcb829d-4898-480e-9811-b4a3982f73ec/GCF_008704855.1_ASM870485v1_genomic.fna.gz --refList GCF_008704855.1_ASM870485v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008704855.1_ASM870485v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:22:16,456] [INFO] Task succeeded: fastANI
[2024-01-24 14:22:16,465] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:22:16,465] [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_008704855.1	s__Streptomyces platensis	100.0	2831	2833	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.55	95.21	0.91	0.87	7	conclusive
GCF_009811595.1	s__Streptomyces libani	92.7943	2336	2833	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.04	96.45	0.91	0.86	12	-
GCF_009811635.1	s__Streptomyces tubercidicus	92.299	2126	2833	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001270575.1	s__Streptomyces decoyicus	90.015	2061	2833	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.25	96.25	0.87	0.87	2	-
GCF_009811555.1	s__Streptomyces caniferus	89.8626	2162	2833	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900187385.1	s__Streptomyces sp900187385	89.6051	2081	2833	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.81	99.51	0.98	0.96	9	-
GCF_004125265.1	s__Streptomyces lydicus_C	89.4933	2001	2833	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004122735.1	s__Streptomyces sioyaensis	89.2627	1876	2833	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.26	95.36	0.89	0.84	9	-
GCF_014646275.1	s__Streptomyces kronopolitis	88.7282	1929	2833	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 14:22:16,467] [INFO] GTDB search result was written to GCF_008704855.1_ASM870485v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:22:16,468] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:22:16,471] [INFO] DFAST_QC result json was written to GCF_008704855.1_ASM870485v1_genomic.fna/dqc_result.json
[2024-01-24 14:22:16,471] [INFO] DFAST_QC completed!
[2024-01-24 14:22:16,471] [INFO] Total running time: 0h3m15s