[2024-01-25 19:50:35,396] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:50:35,398] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:50:35,398] [INFO] DQC Reference Directory: /var/lib/cwl/stg53bd812b-130c-48a3-b652-d47a3340b07e/dqc_reference
[2024-01-25 19:50:36,555] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:50:36,555] [INFO] Task started: Prodigal
[2024-01-25 19:50:36,556] [INFO] Running command: gunzip -c /var/lib/cwl/stga2403048-70a9-4f3d-8b8f-db3553c5a571/GCF_016863055.1_ASM1686305v1_genomic.fna.gz | prodigal -d GCF_016863055.1_ASM1686305v1_genomic.fna/cds.fna -a GCF_016863055.1_ASM1686305v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:50:57,816] [INFO] Task succeeded: Prodigal
[2024-01-25 19:50:57,817] [INFO] Task started: HMMsearch
[2024-01-25 19:50:57,817] [INFO] Running command: hmmsearch --tblout GCF_016863055.1_ASM1686305v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg53bd812b-130c-48a3-b652-d47a3340b07e/dqc_reference/reference_markers.hmm GCF_016863055.1_ASM1686305v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:50:58,147] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:50:58,148] [INFO] Found 6/6 markers.
[2024-01-25 19:50:58,213] [INFO] Query marker FASTA was written to GCF_016863055.1_ASM1686305v1_genomic.fna/markers.fasta
[2024-01-25 19:50:58,213] [INFO] Task started: Blastn
[2024-01-25 19:50:58,213] [INFO] Running command: blastn -query GCF_016863055.1_ASM1686305v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg53bd812b-130c-48a3-b652-d47a3340b07e/dqc_reference/reference_markers.fasta -out GCF_016863055.1_ASM1686305v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:50:59,476] [INFO] Task succeeded: Blastn
[2024-01-25 19:50:59,478] [INFO] Selected 12 target genomes.
[2024-01-25 19:50:59,478] [INFO] Target genome list was writen to GCF_016863055.1_ASM1686305v1_genomic.fna/target_genomes.txt
[2024-01-25 19:50:59,484] [INFO] Task started: fastANI
[2024-01-25 19:50:59,484] [INFO] Running command: fastANI --query /var/lib/cwl/stga2403048-70a9-4f3d-8b8f-db3553c5a571/GCF_016863055.1_ASM1686305v1_genomic.fna.gz --refList GCF_016863055.1_ASM1686305v1_genomic.fna/target_genomes.txt --output GCF_016863055.1_ASM1686305v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:51:25,575] [INFO] Task succeeded: fastANI
[2024-01-25 19:51:25,575] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg53bd812b-130c-48a3-b652-d47a3340b07e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:51:25,575] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg53bd812b-130c-48a3-b652-d47a3340b07e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:51:25,584] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:51:25,584] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:51:25,584] [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
Microbispora rosea subsp. rosea	strain=NBRC 14044	GCA_016863055.1	58118	58117	type	True	100.0	2876	2883	95	conclusive
Microbispora rosea	strain=ATCC 12950	GCA_900156315.1	58117	58117	type	True	99.9901	2875	2883	95	conclusive
Microbispora hainanensis	strain=DSM 45428	GCA_006874475.1	568844	568844	type	True	93.6716	2347	2883	95	below_threshold
Microbispora catharanthi	strain=CR1-09	GCA_006334915.2	1712871	1712871	type	True	93.429	2360	2883	95	below_threshold
Microbispora camponoti	strain=2C-HV3	GCA_014712745.1	1677852	1677852	type	True	93.0061	2266	2883	95	below_threshold
Microbispora siamensis	strain=NBRC 104113	GCA_016863095.1	564413	564413	type	True	92.8165	2243	2883	95	below_threshold
Microbispora sitophila	strain=NEAU-D428	GCA_014892245.1	2771537	2771537	type	True	92.7832	2312	2883	95	below_threshold
Microbispora oryzae	strain=RL4-1S	GCA_017896165.1	2806554	2806554	type	True	83.2675	1551	2883	95	below_threshold
Sphaerimonospora thailandensis	strain=NBRC 107569	GCA_016863115.1	795644	795644	type	True	82.2975	1159	2883	95	below_threshold
Sphaerisporangium corydalis	strain=NEAU-YHS15	GCA_025506355.1	1441875	1441875	type	True	80.0869	1328	2883	95	below_threshold
Nonomuraea roseoviolacea subsp. carminata	strain=DSM 44170	GCA_024172185.1	160689	103837	type	True	79.8777	1373	2883	95	below_threshold
Nonomuraea rhizosphaerae	strain=CGMCC 4.7431	GCA_019396405.1	2665663	2665663	type	True	79.8394	864	2883	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:51:25,585] [INFO] DFAST Taxonomy check result was written to GCF_016863055.1_ASM1686305v1_genomic.fna/tc_result.tsv
[2024-01-25 19:51:25,586] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:51:25,586] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:51:25,586] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg53bd812b-130c-48a3-b652-d47a3340b07e/dqc_reference/checkm_data
[2024-01-25 19:51:25,587] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:51:25,667] [INFO] Task started: CheckM
[2024-01-25 19:51:25,667] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016863055.1_ASM1686305v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016863055.1_ASM1686305v1_genomic.fna/checkm_input GCF_016863055.1_ASM1686305v1_genomic.fna/checkm_result
[2024-01-25 19:52:38,096] [INFO] Task succeeded: CheckM
[2024-01-25 19:52:38,097] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:52:38,117] [INFO] ===== Completeness check finished =====
[2024-01-25 19:52:38,117] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:52:38,118] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016863055.1_ASM1686305v1_genomic.fna/markers.fasta)
[2024-01-25 19:52:38,119] [INFO] Task started: Blastn
[2024-01-25 19:52:38,119] [INFO] Running command: blastn -query GCF_016863055.1_ASM1686305v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg53bd812b-130c-48a3-b652-d47a3340b07e/dqc_reference/reference_markers_gtdb.fasta -out GCF_016863055.1_ASM1686305v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:52:40,257] [INFO] Task succeeded: Blastn
[2024-01-25 19:52:40,260] [INFO] Selected 8 target genomes.
[2024-01-25 19:52:40,260] [INFO] Target genome list was writen to GCF_016863055.1_ASM1686305v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:52:40,272] [INFO] Task started: fastANI
[2024-01-25 19:52:40,272] [INFO] Running command: fastANI --query /var/lib/cwl/stga2403048-70a9-4f3d-8b8f-db3553c5a571/GCF_016863055.1_ASM1686305v1_genomic.fna.gz --refList GCF_016863055.1_ASM1686305v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016863055.1_ASM1686305v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:52:59,803] [INFO] Task succeeded: fastANI
[2024-01-25 19:52:59,810] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:52:59,810] [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_900156315.1	s__Microbispora rosea	99.9901	2875	2883	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	99.16	98.33	0.97	0.94	3	conclusive
GCF_006874475.1	s__Microbispora hainanensis	93.6547	2350	2883	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	95.41	95.40	0.85	0.85	4	-
GCF_006334915.2	s__Microbispora catharanthi	93.4267	2360	2883	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	96.79	95.45	0.89	0.84	4	-
GCF_006874465.1	s__Microbispora bryophytorum	93.0754	2286	2883	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	99.22	97.66	0.97	0.91	4	-
GCF_016863095.1	s__Microbispora siamensis	92.8205	2243	2883	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	96.99	95.83	0.88	0.87	3	-
GCF_014161445.1	s__Microbispora sp014161445	91.2055	2200	2883	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	98.71	98.71	0.93	0.93	2	-
GCF_012999535.1	s__Microbispora sp012999535	89.9967	1966	2883	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003260025.2	s__Microbispora triticiradicis	87.5987	1819	2883	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	98.16	96.98	0.92	0.88	7	-
--------------------------------------------------------------------------------
[2024-01-25 19:52:59,811] [INFO] GTDB search result was written to GCF_016863055.1_ASM1686305v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:52:59,812] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:52:59,815] [INFO] DFAST_QC result json was written to GCF_016863055.1_ASM1686305v1_genomic.fna/dqc_result.json
[2024-01-25 19:52:59,815] [INFO] DFAST_QC completed!
[2024-01-25 19:52:59,815] [INFO] Total running time: 0h2m24s