[2024-01-24 13:58:10,230] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:58:10,231] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:58:10,232] [INFO] DQC Reference Directory: /var/lib/cwl/stgc1a479e9-2d17-4dc8-abac-b2bd291e23c5/dqc_reference
[2024-01-24 13:58:11,327] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:58:11,328] [INFO] Task started: Prodigal
[2024-01-24 13:58:11,328] [INFO] Running command: gunzip -c /var/lib/cwl/stg4d9a5608-f169-48af-b28b-45b0abf05a77/GCF_008704655.1_ASM870465v1_genomic.fna.gz | prodigal -d GCF_008704655.1_ASM870465v1_genomic.fna/cds.fna -a GCF_008704655.1_ASM870465v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:39,708] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:39,709] [INFO] Task started: HMMsearch
[2024-01-24 13:58:39,709] [INFO] Running command: hmmsearch --tblout GCF_008704655.1_ASM870465v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc1a479e9-2d17-4dc8-abac-b2bd291e23c5/dqc_reference/reference_markers.hmm GCF_008704655.1_ASM870465v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:40,042] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:40,043] [INFO] Found 6/6 markers.
[2024-01-24 13:58:40,106] [INFO] Query marker FASTA was written to GCF_008704655.1_ASM870465v1_genomic.fna/markers.fasta
[2024-01-24 13:58:40,106] [INFO] Task started: Blastn
[2024-01-24 13:58:40,106] [INFO] Running command: blastn -query GCF_008704655.1_ASM870465v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc1a479e9-2d17-4dc8-abac-b2bd291e23c5/dqc_reference/reference_markers.fasta -out GCF_008704655.1_ASM870465v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:41,356] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:41,358] [INFO] Selected 9 target genomes.
[2024-01-24 13:58:41,359] [INFO] Target genome list was writen to GCF_008704655.1_ASM870465v1_genomic.fna/target_genomes.txt
[2024-01-24 13:58:41,362] [INFO] Task started: fastANI
[2024-01-24 13:58:41,362] [INFO] Running command: fastANI --query /var/lib/cwl/stg4d9a5608-f169-48af-b28b-45b0abf05a77/GCF_008704655.1_ASM870465v1_genomic.fna.gz --refList GCF_008704655.1_ASM870465v1_genomic.fna/target_genomes.txt --output GCF_008704655.1_ASM870465v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:59:06,268] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:06,268] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc1a479e9-2d17-4dc8-abac-b2bd291e23c5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:59:06,269] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc1a479e9-2d17-4dc8-abac-b2bd291e23c5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:59:06,275] [INFO] Found 9 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 13:59:06,275] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:59:06,275] [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 rimosus	strain=ATCC 10970	GCA_008704655.1	1927	1927	type	True	100.0	3120	3120	95	conclusive
Streptomyces rimosus subsp. rimosus	strain=R7	GCA_022760195.1	132474	1927	type	True	99.9992	3118	3120	95	conclusive
Streptomyces rimosus subsp. rimosus	strain=ATCC 10970	GCA_000331185.2	132474	1927	type	True	99.9979	3115	3120	95	conclusive
Streptomyces rimosus subsp. rimosus	strain=NRRL ISP-5260	GCA_000717285.1	132474	1927	type	True	99.9706	3049	3120	95	conclusive
Streptomyces albofaciens	strain=ATCC 23873	GCA_008634025.1	66866	66866	type	True	94.1152	2620	3120	95	below_threshold
Streptomyces paromomycinus	strain=NBRC 15454	GCA_003865155.1	92743	92743	type	True	89.7417	2410	3120	95	below_threshold
Streptomyces monomycini	strain=NRRL B-24309	GCA_022271435.1	371720	371720	type	True	89.7258	2346	3120	95	below_threshold
Streptomyces pinistramenti	strain=SF28	GCA_020564935.1	2884812	2884812	type	True	83.9943	1557	3120	95	below_threshold
Streptomyces rapamycinicus	strain=NRRL 5491	GCA_024298965.1	1226757	1226757	type	True	81.0788	1581	3120	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:59:06,277] [INFO] DFAST Taxonomy check result was written to GCF_008704655.1_ASM870465v1_genomic.fna/tc_result.tsv
[2024-01-24 13:59:06,278] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:59:06,278] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:59:06,278] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc1a479e9-2d17-4dc8-abac-b2bd291e23c5/dqc_reference/checkm_data
[2024-01-24 13:59:06,279] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:59:06,362] [INFO] Task started: CheckM
[2024-01-24 13:59:06,362] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008704655.1_ASM870465v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008704655.1_ASM870465v1_genomic.fna/checkm_input GCF_008704655.1_ASM870465v1_genomic.fna/checkm_result
[2024-01-24 14:01:21,137] [INFO] Task succeeded: CheckM
[2024-01-24 14:01:21,138] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:01:21,156] [INFO] ===== Completeness check finished =====
[2024-01-24 14:01:21,156] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:01:21,156] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008704655.1_ASM870465v1_genomic.fna/markers.fasta)
[2024-01-24 14:01:21,157] [INFO] Task started: Blastn
[2024-01-24 14:01:21,157] [INFO] Running command: blastn -query GCF_008704655.1_ASM870465v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc1a479e9-2d17-4dc8-abac-b2bd291e23c5/dqc_reference/reference_markers_gtdb.fasta -out GCF_008704655.1_ASM870465v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:01:23,213] [INFO] Task succeeded: Blastn
[2024-01-24 14:01:23,216] [INFO] Selected 6 target genomes.
[2024-01-24 14:01:23,216] [INFO] Target genome list was writen to GCF_008704655.1_ASM870465v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:01:23,219] [INFO] Task started: fastANI
[2024-01-24 14:01:23,220] [INFO] Running command: fastANI --query /var/lib/cwl/stg4d9a5608-f169-48af-b28b-45b0abf05a77/GCF_008704655.1_ASM870465v1_genomic.fna.gz --refList GCF_008704655.1_ASM870465v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008704655.1_ASM870465v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:01:39,992] [INFO] Task succeeded: fastANI
[2024-01-24 14:01:39,996] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:01:39,997] [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_008704655.1	s__Streptomyces rimosus	100.0	3120	3120	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.17	96.53	0.95	0.89	49	conclusive
GCF_008634025.1	s__Streptomyces albofaciens	94.1318	2618	3120	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000720725.1	s__Streptomyces rimosus_A	93.8999	2588	3120	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001905005.1	s__Streptomyces sp001905005	90.0338	2423	3120	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003865135.1	s__Streptomyces chrestomyceticus	89.8776	2433	3120	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.95	95.89	0.90	0.88	4	-
GCF_000715845.1	s__Streptomyces monomycini	89.8063	2255	3120	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 14:01:39,998] [INFO] GTDB search result was written to GCF_008704655.1_ASM870465v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:01:39,998] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:01:40,000] [INFO] DFAST_QC result json was written to GCF_008704655.1_ASM870465v1_genomic.fna/dqc_result.json
[2024-01-24 14:01:40,000] [INFO] DFAST_QC completed!
[2024-01-24 14:01:40,000] [INFO] Total running time: 0h3m30s