[2024-01-24 13:24:47,055] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:24:47,057] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:24:47,057] [INFO] DQC Reference Directory: /var/lib/cwl/stg5334e46d-c280-4dab-9fb6-8da6106123ed/dqc_reference
[2024-01-24 13:24:48,457] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:24:48,458] [INFO] Task started: Prodigal
[2024-01-24 13:24:48,459] [INFO] Running command: gunzip -c /var/lib/cwl/stg27a8ad05-db0d-4492-87be-c16f88c925e4/GCF_000968685.2_ASM96868v2_genomic.fna.gz | prodigal -d GCF_000968685.2_ASM96868v2_genomic.fna/cds.fna -a GCF_000968685.2_ASM96868v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:25:18,917] [INFO] Task succeeded: Prodigal
[2024-01-24 13:25:18,918] [INFO] Task started: HMMsearch
[2024-01-24 13:25:18,918] [INFO] Running command: hmmsearch --tblout GCF_000968685.2_ASM96868v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5334e46d-c280-4dab-9fb6-8da6106123ed/dqc_reference/reference_markers.hmm GCF_000968685.2_ASM96868v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:25:19,282] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:25:19,283] [INFO] Found 6/6 markers.
[2024-01-24 13:25:19,348] [INFO] Query marker FASTA was written to GCF_000968685.2_ASM96868v2_genomic.fna/markers.fasta
[2024-01-24 13:25:19,348] [INFO] Task started: Blastn
[2024-01-24 13:25:19,349] [INFO] Running command: blastn -query GCF_000968685.2_ASM96868v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg5334e46d-c280-4dab-9fb6-8da6106123ed/dqc_reference/reference_markers.fasta -out GCF_000968685.2_ASM96868v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:25:20,657] [INFO] Task succeeded: Blastn
[2024-01-24 13:25:20,660] [INFO] Selected 11 target genomes.
[2024-01-24 13:25:20,660] [INFO] Target genome list was writen to GCF_000968685.2_ASM96868v2_genomic.fna/target_genomes.txt
[2024-01-24 13:25:20,674] [INFO] Task started: fastANI
[2024-01-24 13:25:20,674] [INFO] Running command: fastANI --query /var/lib/cwl/stg27a8ad05-db0d-4492-87be-c16f88c925e4/GCF_000968685.2_ASM96868v2_genomic.fna.gz --refList GCF_000968685.2_ASM96868v2_genomic.fna/target_genomes.txt --output GCF_000968685.2_ASM96868v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:25:53,318] [INFO] Task succeeded: fastANI
[2024-01-24 13:25:53,319] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5334e46d-c280-4dab-9fb6-8da6106123ed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:25:53,319] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5334e46d-c280-4dab-9fb6-8da6106123ed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:25:53,329] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:25:53,329] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:25:53,329] [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 iranensis	strain=DSM 41954	GCA_017874715.1	576784	576784	type	True	93.7488	2498	2926	95	below_threshold
Streptomyces rapamycinicus	strain=NRRL 5491	GCA_003675955.1	1226757	1226757	type	True	93.6911	2479	2926	95	below_threshold
Streptomyces rapamycinicus	strain=NRRL 5491	GCA_000418455.1	1226757	1226757	type	True	93.647	2492	2926	95	below_threshold
Streptomyces rapamycinicus	strain=NRRL 5491	GCA_024298965.1	1226757	1226757	type	True	93.645	2479	2926	95	below_threshold
Streptomyces rapamycinicus	strain=DSM 41530	GCA_014205315.1	1226757	1226757	type	True	93.6248	2493	2926	95	below_threshold
Streptomyces javensis	strain=DSM 41764	GCA_016103505.1	114698	114698	type	True	93.3401	1906	2926	95	below_threshold
Streptomyces sabulosicollis	strain=PRKS01-29	GCA_016103465.1	2715963	2715963	type	True	93.0661	2033	2926	95	below_threshold
Streptomyces albireticuli	strain=NRRL B1670	GCA_021228125.1	1940	1940	type	True	81.2916	1307	2926	95	below_threshold
Streptomyces rimosus subsp. rimosus	strain=R7	GCA_022760195.1	132474	1927	type	True	81.1186	1437	2926	95	below_threshold
Streptomyces paromomycinus	strain=NBRC 15454	GCA_003865155.1	92743	92743	type	True	80.944	1442	2926	95	below_threshold
Streptomyces monomycini	strain=NRRL B-24309	GCA_022271435.1	371720	371720	type	True	80.885	1404	2926	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:25:53,330] [INFO] DFAST Taxonomy check result was written to GCF_000968685.2_ASM96868v2_genomic.fna/tc_result.tsv
[2024-01-24 13:25:53,331] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:25:53,331] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:25:53,331] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5334e46d-c280-4dab-9fb6-8da6106123ed/dqc_reference/checkm_data
[2024-01-24 13:25:53,333] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:25:53,415] [INFO] Task started: CheckM
[2024-01-24 13:25:53,415] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000968685.2_ASM96868v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000968685.2_ASM96868v2_genomic.fna/checkm_input GCF_000968685.2_ASM96868v2_genomic.fna/checkm_result
[2024-01-24 13:27:33,087] [INFO] Task succeeded: CheckM
[2024-01-24 13:27:33,088] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:27:33,117] [INFO] ===== Completeness check finished =====
[2024-01-24 13:27:33,118] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:27:33,118] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000968685.2_ASM96868v2_genomic.fna/markers.fasta)
[2024-01-24 13:27:33,118] [INFO] Task started: Blastn
[2024-01-24 13:27:33,119] [INFO] Running command: blastn -query GCF_000968685.2_ASM96868v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg5334e46d-c280-4dab-9fb6-8da6106123ed/dqc_reference/reference_markers_gtdb.fasta -out GCF_000968685.2_ASM96868v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:27:35,287] [INFO] Task succeeded: Blastn
[2024-01-24 13:27:35,290] [INFO] Selected 7 target genomes.
[2024-01-24 13:27:35,290] [INFO] Target genome list was writen to GCF_000968685.2_ASM96868v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:27:35,319] [INFO] Task started: fastANI
[2024-01-24 13:27:35,319] [INFO] Running command: fastANI --query /var/lib/cwl/stg27a8ad05-db0d-4492-87be-c16f88c925e4/GCF_000968685.2_ASM96868v2_genomic.fna.gz --refList GCF_000968685.2_ASM96868v2_genomic.fna/target_genomes_gtdb.txt --output GCF_000968685.2_ASM96868v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:28:01,373] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:01,385] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:28:01,385] [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_000968685.2	s__Streptomyces antioxidans	100.0	2921	2926	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_017874715.1	s__Streptomyces iranensis	93.7576	2497	2926	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.67	99.98	99.98	1.00	1.00	2	-
GCF_016741935.1	s__Streptomyces sp016741935	93.7352	2447	2926	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0488	N/A	N/A	N/A	N/A	1	-
GCF_018138715.1	s__Streptomyces asiaticus	93.7113	2382	2926	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.17	95.36	0.90	0.81	10	-
GCF_003675955.1	s__Streptomyces rapamycinicus	93.6996	2478	2926	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.67	99.95	99.91	0.99	0.99	3	-
GCA_005405945.1	s__Streptomyces violaceusniger	93.4661	2363	2926	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.67	97.67	0.85	0.85	2	-
GCF_001553455.1	s__Streptomyces hygroscopicus	90.0011	1888	2926	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.24	98.00	0.92	0.90	7	-
--------------------------------------------------------------------------------
[2024-01-24 13:28:01,390] [INFO] GTDB search result was written to GCF_000968685.2_ASM96868v2_genomic.fna/result_gtdb.tsv
[2024-01-24 13:28:01,390] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:28:01,394] [INFO] DFAST_QC result json was written to GCF_000968685.2_ASM96868v2_genomic.fna/dqc_result.json
[2024-01-24 13:28:01,395] [INFO] DFAST_QC completed!
[2024-01-24 13:28:01,395] [INFO] Total running time: 0h3m14s