[2024-01-24 13:41:10,155] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:41:10,157] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:41:10,157] [INFO] DQC Reference Directory: /var/lib/cwl/stg40c7e494-f182-4e5c-b425-34473fe7425c/dqc_reference
[2024-01-24 13:41:11,411] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:41:11,412] [INFO] Task started: Prodigal
[2024-01-24 13:41:11,412] [INFO] Running command: gunzip -c /var/lib/cwl/stg12eefce1-2f41-429f-be32-cdde02e07c1d/GCF_008923365.1_ASM892336v1_genomic.fna.gz | prodigal -d GCF_008923365.1_ASM892336v1_genomic.fna/cds.fna -a GCF_008923365.1_ASM892336v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:36,734] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:36,735] [INFO] Task started: HMMsearch
[2024-01-24 13:41:36,735] [INFO] Running command: hmmsearch --tblout GCF_008923365.1_ASM892336v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg40c7e494-f182-4e5c-b425-34473fe7425c/dqc_reference/reference_markers.hmm GCF_008923365.1_ASM892336v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:37,135] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:37,137] [INFO] Found 6/6 markers.
[2024-01-24 13:41:37,219] [INFO] Query marker FASTA was written to GCF_008923365.1_ASM892336v1_genomic.fna/markers.fasta
[2024-01-24 13:41:37,220] [INFO] Task started: Blastn
[2024-01-24 13:41:37,220] [INFO] Running command: blastn -query GCF_008923365.1_ASM892336v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg40c7e494-f182-4e5c-b425-34473fe7425c/dqc_reference/reference_markers.fasta -out GCF_008923365.1_ASM892336v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:38,617] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:38,621] [INFO] Selected 14 target genomes.
[2024-01-24 13:41:38,621] [INFO] Target genome list was writen to GCF_008923365.1_ASM892336v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:38,752] [INFO] Task started: fastANI
[2024-01-24 13:41:38,753] [INFO] Running command: fastANI --query /var/lib/cwl/stg12eefce1-2f41-429f-be32-cdde02e07c1d/GCF_008923365.1_ASM892336v1_genomic.fna.gz --refList GCF_008923365.1_ASM892336v1_genomic.fna/target_genomes.txt --output GCF_008923365.1_ASM892336v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:42:18,802] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:18,803] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg40c7e494-f182-4e5c-b425-34473fe7425c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:42:18,803] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg40c7e494-f182-4e5c-b425-34473fe7425c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:42:18,814] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:42:18,814] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:42:18,815] [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
Actinomadura montaniterrae	strain=CYP1-1B	GCA_008923365.1	1803903	1803903	type	True	100.0	3287	3310	95	conclusive
Actinomadura physcomitrii	strain=LD22	GCA_008923205.2	2650748	2650748	type	True	93.2762	2309	3310	95	below_threshold
Actinomadura nitritigenes	strain=L46	GCA_017573545.1	134602	134602	type	True	92.8901	2543	3310	95	below_threshold
Actinomadura violacea	strain=LCR2-06	GCA_017573465.1	2819934	2819934	type	True	92.2197	2526	3310	95	below_threshold
Actinomadura latina	strain=ATCC BAA-277	GCA_012396395.1	163603	163603	type	True	85.1094	1731	3310	95	below_threshold
Actinomadura darangshiensis	strain=DSM 45941	GCA_004349235.1	705336	705336	type	True	85.1043	1892	3310	95	below_threshold
Actinomadura geliboluensis	strain=A8036	GCA_005889745.1	882440	882440	type	True	85.0865	1646	3310	95	below_threshold
Actinomadura bangladeshensis	strain=DSM 45347	GCA_004348335.1	453573	453573	type	True	85.0456	1665	3310	95	below_threshold
Actinomadura latina	strain=NBRC 106108	GCA_001552195.1	163603	163603	type	True	85.019	1750	3310	95	below_threshold
Actinomadura citrea	strain=DSM 43461	GCA_013409045.1	46158	46158	type	True	84.736	1950	3310	95	below_threshold
Actinomadura graeca	strain=32-07	GCA_019175365.1	2750812	2750812	type	True	83.8686	1654	3310	95	below_threshold
Actinomadura spongiicola	strain=LHW52907	GCA_003432485.1	2303421	2303421	type	True	82.9222	1516	3310	95	below_threshold
Actinomadura parmotrematis	strain=PM05-2	GCA_019458805.1	2864039	2864039	type	True	81.9737	1699	3310	95	below_threshold
Actinomadura rupiterrae	strain=DSM 45251	GCA_024172125.1	559627	559627	type	True	81.4678	1656	3310	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:42:18,816] [INFO] DFAST Taxonomy check result was written to GCF_008923365.1_ASM892336v1_genomic.fna/tc_result.tsv
[2024-01-24 13:42:18,817] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:42:18,817] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:42:18,817] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg40c7e494-f182-4e5c-b425-34473fe7425c/dqc_reference/checkm_data
[2024-01-24 13:42:18,818] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:42:18,911] [INFO] Task started: CheckM
[2024-01-24 13:42:18,912] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008923365.1_ASM892336v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008923365.1_ASM892336v1_genomic.fna/checkm_input GCF_008923365.1_ASM892336v1_genomic.fna/checkm_result
[2024-01-24 13:44:11,613] [INFO] Task succeeded: CheckM
[2024-01-24 13:44:11,615] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 12.50%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:44:11,644] [INFO] ===== Completeness check finished =====
[2024-01-24 13:44:11,645] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:44:11,645] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008923365.1_ASM892336v1_genomic.fna/markers.fasta)
[2024-01-24 13:44:11,646] [INFO] Task started: Blastn
[2024-01-24 13:44:11,646] [INFO] Running command: blastn -query GCF_008923365.1_ASM892336v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg40c7e494-f182-4e5c-b425-34473fe7425c/dqc_reference/reference_markers_gtdb.fasta -out GCF_008923365.1_ASM892336v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:44:13,794] [INFO] Task succeeded: Blastn
[2024-01-24 13:44:13,799] [INFO] Selected 11 target genomes.
[2024-01-24 13:44:13,799] [INFO] Target genome list was writen to GCF_008923365.1_ASM892336v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:44:13,899] [INFO] Task started: fastANI
[2024-01-24 13:44:13,900] [INFO] Running command: fastANI --query /var/lib/cwl/stg12eefce1-2f41-429f-be32-cdde02e07c1d/GCF_008923365.1_ASM892336v1_genomic.fna.gz --refList GCF_008923365.1_ASM892336v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008923365.1_ASM892336v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:44:46,234] [INFO] Task succeeded: fastANI
[2024-01-24 13:44:46,246] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:44:46,246] [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_008923365.1	s__Spirillospora montaniterrae	100.0	3285	3310	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_008923205.2	s__Spirillospora physcomitrii	93.2674	2311	3310	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017573545.1	s__Spirillospora nitritigenes	92.8852	2545	3310	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	95.12	95.12	0.83	0.83	2	-
GCF_013211575.1	s__Spirillospora verrucosospora	92.3251	2533	3310	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	95.82	95.82	0.89	0.89	2	-
GCF_004349235.1	s__Spirillospora darangshiensis	85.1464	1886	3310	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013372625.1	s__Spirillospora sp013372625	85.132	1554	3310	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005889745.1	s__Spirillospora geliboluensis	85.0369	1653	3310	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004348335.1	s__Spirillospora bangladeshensis	84.9917	1674	3310	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008327685.1	s__Spirillospora sp008327685	84.7956	1954	3310	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013409045.1	s__Spirillospora citrea	84.6995	1958	3310	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004348535.1	s__Spirillospora sp004348535	84.0097	1497	3310	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:44:46,248] [INFO] GTDB search result was written to GCF_008923365.1_ASM892336v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:44:46,249] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:44:46,252] [INFO] DFAST_QC result json was written to GCF_008923365.1_ASM892336v1_genomic.fna/dqc_result.json
[2024-01-24 13:44:46,252] [INFO] DFAST_QC completed!
[2024-01-24 13:44:46,253] [INFO] Total running time: 0h3m36s