[2024-01-24 11:51:11,323] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:11,325] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:11,325] [INFO] DQC Reference Directory: /var/lib/cwl/stg81bad025-4ce8-4cc6-b906-e08ad6850247/dqc_reference
[2024-01-24 11:51:12,757] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:12,757] [INFO] Task started: Prodigal
[2024-01-24 11:51:12,758] [INFO] Running command: gunzip -c /var/lib/cwl/stgb321f28f-def8-4fac-bed0-6f43b39d4e71/GCF_018531465.1_ASM1853146v1_genomic.fna.gz | prodigal -d GCF_018531465.1_ASM1853146v1_genomic.fna/cds.fna -a GCF_018531465.1_ASM1853146v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:41,167] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:41,168] [INFO] Task started: HMMsearch
[2024-01-24 11:51:41,168] [INFO] Running command: hmmsearch --tblout GCF_018531465.1_ASM1853146v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg81bad025-4ce8-4cc6-b906-e08ad6850247/dqc_reference/reference_markers.hmm GCF_018531465.1_ASM1853146v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:41,583] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:41,585] [INFO] Found 6/6 markers.
[2024-01-24 11:51:41,657] [INFO] Query marker FASTA was written to GCF_018531465.1_ASM1853146v1_genomic.fna/markers.fasta
[2024-01-24 11:51:41,658] [INFO] Task started: Blastn
[2024-01-24 11:51:41,658] [INFO] Running command: blastn -query GCF_018531465.1_ASM1853146v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg81bad025-4ce8-4cc6-b906-e08ad6850247/dqc_reference/reference_markers.fasta -out GCF_018531465.1_ASM1853146v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:43,051] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:43,055] [INFO] Selected 12 target genomes.
[2024-01-24 11:51:43,056] [INFO] Target genome list was writen to GCF_018531465.1_ASM1853146v1_genomic.fna/target_genomes.txt
[2024-01-24 11:51:43,069] [INFO] Task started: fastANI
[2024-01-24 11:51:43,069] [INFO] Running command: fastANI --query /var/lib/cwl/stgb321f28f-def8-4fac-bed0-6f43b39d4e71/GCF_018531465.1_ASM1853146v1_genomic.fna.gz --refList GCF_018531465.1_ASM1853146v1_genomic.fna/target_genomes.txt --output GCF_018531465.1_ASM1853146v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:52:09,324] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:09,324] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg81bad025-4ce8-4cc6-b906-e08ad6850247/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:52:09,325] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg81bad025-4ce8-4cc6-b906-e08ad6850247/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:52:09,336] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:52:09,336] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:52:09,337] [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
Sphaerisporangium corydalis	strain=NEAU-YHS15	GCA_025506355.1	1441875	1441875	type	True	83.4711	1845	3330	95	below_threshold
Sphaerisporangium album	strain=CCTCC AA 208026	GCA_003323745.1	509200	509200	type	True	83.1272	1740	3330	95	below_threshold
Sphaerisporangium melleum	strain=JCM 13064	GCA_014646695.1	321316	321316	type	True	83.1004	1681	3330	95	below_threshold
Sphaerisporangium krabiense	strain=NBRC 107571	GCA_016863355.1	763782	763782	type	True	82.8046	1640	3330	95	below_threshold
Sphaerisporangium krabiense	strain=DSM 45790	GCA_014200435.1	763782	763782	type	True	82.7994	1637	3330	95	below_threshold
Sphaerisporangium siamense	strain=DSM 45784	GCA_014205275.1	795645	795645	type	True	82.7453	1639	3330	95	below_threshold
Sphaerisporangium siamense	strain=NBRC 107570	GCA_016863415.1	795645	795645	type	True	82.7151	1625	3330	95	below_threshold
Sphaerisporangium rufum	strain=NBRC 109079	GCA_016863395.1	1381558	1381558	type	True	81.8431	1575	3330	95	below_threshold
Nonomuraea roseoviolacea subsp. carminata	strain=DSM 44170	GCA_024172185.1	160689	103837	type	True	80.5073	1677	3330	95	below_threshold
Nonomuraea rhizosphaerae	strain=CGMCC 4.7431	GCA_019396405.1	2665663	2665663	type	True	79.9556	970	3330	95	below_threshold
Microbispora oryzae	strain=RL4-1S	GCA_017896165.1	2806554	2806554	type	True	79.6871	1240	3330	95	below_threshold
Nonomuraea typhae	strain=p1410	GCA_009760925.1	2603600	2603600	type	True	79.174	1445	3330	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:52:09,338] [INFO] DFAST Taxonomy check result was written to GCF_018531465.1_ASM1853146v1_genomic.fna/tc_result.tsv
[2024-01-24 11:52:09,339] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:52:09,339] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:52:09,339] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg81bad025-4ce8-4cc6-b906-e08ad6850247/dqc_reference/checkm_data
[2024-01-24 11:52:09,340] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:52:09,426] [INFO] Task started: CheckM
[2024-01-24 11:52:09,426] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018531465.1_ASM1853146v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018531465.1_ASM1853146v1_genomic.fna/checkm_input GCF_018531465.1_ASM1853146v1_genomic.fna/checkm_result
[2024-01-24 11:53:35,938] [INFO] Task succeeded: CheckM
[2024-01-24 11:53:35,939] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:53:35,966] [INFO] ===== Completeness check finished =====
[2024-01-24 11:53:35,966] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:53:35,966] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018531465.1_ASM1853146v1_genomic.fna/markers.fasta)
[2024-01-24 11:53:35,967] [INFO] Task started: Blastn
[2024-01-24 11:53:35,967] [INFO] Running command: blastn -query GCF_018531465.1_ASM1853146v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg81bad025-4ce8-4cc6-b906-e08ad6850247/dqc_reference/reference_markers_gtdb.fasta -out GCF_018531465.1_ASM1853146v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:53:38,046] [INFO] Task succeeded: Blastn
[2024-01-24 11:53:38,050] [INFO] Selected 7 target genomes.
[2024-01-24 11:53:38,050] [INFO] Target genome list was writen to GCF_018531465.1_ASM1853146v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:53:38,055] [INFO] Task started: fastANI
[2024-01-24 11:53:38,055] [INFO] Running command: fastANI --query /var/lib/cwl/stgb321f28f-def8-4fac-bed0-6f43b39d4e71/GCF_018531465.1_ASM1853146v1_genomic.fna.gz --refList GCF_018531465.1_ASM1853146v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018531465.1_ASM1853146v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:53:54,014] [INFO] Task succeeded: fastANI
[2024-01-24 11:53:54,021] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:53:54,022] [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_018531465.1	s__Sphaerisporangium sp018531465	100.0	3311	3330	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Sphaerisporangium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003323745.1	s__Sphaerisporangium album	83.115	1742	3330	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Sphaerisporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014646695.1	s__Sphaerisporangium melleum	83.0743	1687	3330	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Sphaerisporangium	95.0	99.98	99.98	0.99	0.99	2	-
GCF_014200435.1	s__Sphaerisporangium krabiense	82.7797	1640	3330	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Sphaerisporangium	95.0	100.00	100.00	0.99	0.99	2	-
GCF_014205275.1	s__Sphaerisporangium siamense	82.7503	1640	3330	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Sphaerisporangium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016863395.1	s__Sphaerisporangium rufum	81.8726	1568	3330	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Sphaerisporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014161445.1	s__Microbispora sp014161445	80.1386	1440	3330	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	98.71	98.71	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:53:54,023] [INFO] GTDB search result was written to GCF_018531465.1_ASM1853146v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:53:54,024] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:53:54,027] [INFO] DFAST_QC result json was written to GCF_018531465.1_ASM1853146v1_genomic.fna/dqc_result.json
[2024-01-24 11:53:54,027] [INFO] DFAST_QC completed!
[2024-01-24 11:53:54,027] [INFO] Total running time: 0h2m43s