[2024-01-25 17:55:05,681] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:55:05,683] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:55:05,683] [INFO] DQC Reference Directory: /var/lib/cwl/stg23cb911e-34b1-4a2a-888a-0d4019894e8c/dqc_reference
[2024-01-25 17:55:06,778] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:55:06,779] [INFO] Task started: Prodigal
[2024-01-25 17:55:06,779] [INFO] Running command: gunzip -c /var/lib/cwl/stgaa47477a-c230-4a7f-bd13-2e3885575f2f/GCF_016863295.1_ASM1686329v1_genomic.fna.gz | prodigal -d GCF_016863295.1_ASM1686329v1_genomic.fna/cds.fna -a GCF_016863295.1_ASM1686329v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:55:29,185] [INFO] Task succeeded: Prodigal
[2024-01-25 17:55:29,186] [INFO] Task started: HMMsearch
[2024-01-25 17:55:29,186] [INFO] Running command: hmmsearch --tblout GCF_016863295.1_ASM1686329v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg23cb911e-34b1-4a2a-888a-0d4019894e8c/dqc_reference/reference_markers.hmm GCF_016863295.1_ASM1686329v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:55:29,508] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:55:29,510] [INFO] Found 6/6 markers.
[2024-01-25 17:55:29,578] [INFO] Query marker FASTA was written to GCF_016863295.1_ASM1686329v1_genomic.fna/markers.fasta
[2024-01-25 17:55:29,578] [INFO] Task started: Blastn
[2024-01-25 17:55:29,578] [INFO] Running command: blastn -query GCF_016863295.1_ASM1686329v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg23cb911e-34b1-4a2a-888a-0d4019894e8c/dqc_reference/reference_markers.fasta -out GCF_016863295.1_ASM1686329v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:55:30,792] [INFO] Task succeeded: Blastn
[2024-01-25 17:55:30,796] [INFO] Selected 10 target genomes.
[2024-01-25 17:55:30,797] [INFO] Target genome list was writen to GCF_016863295.1_ASM1686329v1_genomic.fna/target_genomes.txt
[2024-01-25 17:55:30,804] [INFO] Task started: fastANI
[2024-01-25 17:55:30,804] [INFO] Running command: fastANI --query /var/lib/cwl/stgaa47477a-c230-4a7f-bd13-2e3885575f2f/GCF_016863295.1_ASM1686329v1_genomic.fna.gz --refList GCF_016863295.1_ASM1686329v1_genomic.fna/target_genomes.txt --output GCF_016863295.1_ASM1686329v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:55:53,374] [INFO] Task succeeded: fastANI
[2024-01-25 17:55:53,374] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg23cb911e-34b1-4a2a-888a-0d4019894e8c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:55:53,375] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg23cb911e-34b1-4a2a-888a-0d4019894e8c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:55:53,382] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:55:53,382] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:55:53,382] [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
Planotetraspora phitsanulokensis	strain=NBRC 104273	GCA_016863295.1	575192	575192	type	True	100.0	3009	3013	95	conclusive
Planotetraspora kaengkrachanensis	strain=NBRC 104272	GCA_016862895.1	575193	575193	type	True	92.8857	2468	3013	95	below_threshold
Planotetraspora mira	strain=NBRC 15435	GCA_016863275.1	58121	58121	type	True	90.7596	2411	3013	95	below_threshold
Planotetraspora silvatica	strain=NBRC 100141	GCA_016863315.1	234614	234614	type	True	90.6359	2333	3013	95	below_threshold
Planotetraspora thailandica	strain=NBRC 104271	GCA_016863335.1	487172	487172	type	True	85.8417	2098	3013	95	below_threshold
Microbispora oryzae	strain=RL4-1S	GCA_017896165.1	2806554	2806554	type	True	81.7306	1295	3013	95	below_threshold
Sphaerimonospora thailandensis	strain=NBRC 107569	GCA_016863115.1	795644	795644	type	True	81.4008	1029	3013	95	below_threshold
Sphaerisporangium corydalis	strain=NEAU-YHS15	GCA_025506355.1	1441875	1441875	type	True	79.8976	1328	3013	95	below_threshold
Nonomuraea rhizosphaerae	strain=CGMCC 4.7431	GCA_019396405.1	2665663	2665663	type	True	79.364	836	3013	95	below_threshold
Nonomuraea aurantiaca	strain=NEAU-L178	GCA_020215705.1	2878562	2878562	type	True	79.3341	1211	3013	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:55:53,383] [INFO] DFAST Taxonomy check result was written to GCF_016863295.1_ASM1686329v1_genomic.fna/tc_result.tsv
[2024-01-25 17:55:53,384] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:55:53,384] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:55:53,384] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg23cb911e-34b1-4a2a-888a-0d4019894e8c/dqc_reference/checkm_data
[2024-01-25 17:55:53,385] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:55:53,464] [INFO] Task started: CheckM
[2024-01-25 17:55:53,465] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016863295.1_ASM1686329v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016863295.1_ASM1686329v1_genomic.fna/checkm_input GCF_016863295.1_ASM1686329v1_genomic.fna/checkm_result
[2024-01-25 17:57:03,769] [INFO] Task succeeded: CheckM
[2024-01-25 17:57:03,770] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.85%
Strain heterogeneity: 75.00%
--------------------------------------------------------------------------------
[2024-01-25 17:57:03,803] [INFO] ===== Completeness check finished =====
[2024-01-25 17:57:03,803] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:57:03,804] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016863295.1_ASM1686329v1_genomic.fna/markers.fasta)
[2024-01-25 17:57:03,804] [INFO] Task started: Blastn
[2024-01-25 17:57:03,804] [INFO] Running command: blastn -query GCF_016863295.1_ASM1686329v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg23cb911e-34b1-4a2a-888a-0d4019894e8c/dqc_reference/reference_markers_gtdb.fasta -out GCF_016863295.1_ASM1686329v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:57:05,834] [INFO] Task succeeded: Blastn
[2024-01-25 17:57:05,837] [INFO] Selected 5 target genomes.
[2024-01-25 17:57:05,837] [INFO] Target genome list was writen to GCF_016863295.1_ASM1686329v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:57:05,842] [INFO] Task started: fastANI
[2024-01-25 17:57:05,842] [INFO] Running command: fastANI --query /var/lib/cwl/stgaa47477a-c230-4a7f-bd13-2e3885575f2f/GCF_016863295.1_ASM1686329v1_genomic.fna.gz --refList GCF_016863295.1_ASM1686329v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016863295.1_ASM1686329v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:57:18,748] [INFO] Task succeeded: fastANI
[2024-01-25 17:57:18,752] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:57:18,752] [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_016863295.1	s__Planotetraspora phitsanulokensis	100.0	3009	3013	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planotetraspora	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_016862895.1	s__Planotetraspora kaengkrachanensis	92.8904	2467	3013	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planotetraspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016863275.1	s__Planotetraspora mira	90.7603	2411	3013	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planotetraspora	95.2969	N/A	N/A	N/A	N/A	1	-
GCF_016863315.1	s__Planotetraspora silvatica	90.6391	2332	3013	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planotetraspora	95.2969	N/A	N/A	N/A	N/A	1	-
GCF_016863335.1	s__Planotetraspora thailandica	85.8581	2094	3013	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planotetraspora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:57:18,753] [INFO] GTDB search result was written to GCF_016863295.1_ASM1686329v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:57:18,754] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:57:18,756] [INFO] DFAST_QC result json was written to GCF_016863295.1_ASM1686329v1_genomic.fna/dqc_result.json
[2024-01-25 17:57:18,756] [INFO] DFAST_QC completed!
[2024-01-25 17:57:18,756] [INFO] Total running time: 0h2m13s