[2024-01-24 13:57:56,031] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:56,033] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:56,033] [INFO] DQC Reference Directory: /var/lib/cwl/stg777a42b9-de12-4e36-8c10-cad200de168f/dqc_reference
[2024-01-24 13:57:57,346] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:57,347] [INFO] Task started: Prodigal
[2024-01-24 13:57:57,347] [INFO] Running command: gunzip -c /var/lib/cwl/stg69b57521-f401-4677-9cb3-c49d14b9e6ff/GCF_001528665.1_ASM152866v1_genomic.fna.gz | prodigal -d GCF_001528665.1_ASM152866v1_genomic.fna/cds.fna -a GCF_001528665.1_ASM152866v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:22,041] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:22,042] [INFO] Task started: HMMsearch
[2024-01-24 13:58:22,042] [INFO] Running command: hmmsearch --tblout GCF_001528665.1_ASM152866v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg777a42b9-de12-4e36-8c10-cad200de168f/dqc_reference/reference_markers.hmm GCF_001528665.1_ASM152866v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:22,536] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:22,537] [INFO] Found 6/6 markers.
[2024-01-24 13:58:22,606] [INFO] Query marker FASTA was written to GCF_001528665.1_ASM152866v1_genomic.fna/markers.fasta
[2024-01-24 13:58:22,607] [INFO] Task started: Blastn
[2024-01-24 13:58:22,607] [INFO] Running command: blastn -query GCF_001528665.1_ASM152866v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg777a42b9-de12-4e36-8c10-cad200de168f/dqc_reference/reference_markers.fasta -out GCF_001528665.1_ASM152866v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:24,032] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:24,036] [INFO] Selected 21 target genomes.
[2024-01-24 13:58:24,036] [INFO] Target genome list was writen to GCF_001528665.1_ASM152866v1_genomic.fna/target_genomes.txt
[2024-01-24 13:58:24,043] [INFO] Task started: fastANI
[2024-01-24 13:58:24,044] [INFO] Running command: fastANI --query /var/lib/cwl/stg69b57521-f401-4677-9cb3-c49d14b9e6ff/GCF_001528665.1_ASM152866v1_genomic.fna.gz --refList GCF_001528665.1_ASM152866v1_genomic.fna/target_genomes.txt --output GCF_001528665.1_ASM152866v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:59:03,820] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:03,821] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg777a42b9-de12-4e36-8c10-cad200de168f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:59:03,821] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg777a42b9-de12-4e36-8c10-cad200de168f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:59:03,838] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:59:03,838] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:59:03,838] [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
Microtetraspora malaysiensis	strain=NBRC 100735	GCA_001528665.1	161358	161358	type	True	100.0	2908	2914	95	conclusive
Microtetraspora fusca	strain=NBRC 13915	GCA_001570365.1	1997	1997	type	True	93.7989	2279	2914	95	below_threshold
Microtetraspora niveoalba	strain=NBRC 15239	GCA_001570405.1	46175	46175	type	True	89.6211	2017	2914	95	below_threshold
Microbispora siamensis	strain=NBRC 104113	GCA_016863095.1	564413	564413	type	True	81.5542	1509	2914	95	below_threshold
Microbispora rosea subsp. aerata	strain=NBRC 14624	GCA_016863075.1	147065	58117	type	True	81.4334	1258	2914	95	below_threshold
Microbispora bryophytorum	strain=DSM 46710	GCA_006874465.1	1460882	1460882	type	True	81.411	1337	2914	95	below_threshold
Sphaerimonospora thailandensis	strain=NBRC 107569	GCA_016863115.1	795644	795644	type	True	81.3779	1066	2914	95	below_threshold
Microbispora bryophytorum	strain=NEAU-TX2-2	GCA_014712735.1	1460882	1460882	type	True	81.3693	1352	2914	95	below_threshold
Microbispora rosea	strain=ATCC 12950	GCA_900156315.1	58117	58117	type	True	81.3384	1448	2914	95	below_threshold
Microbispora rosea subsp. aerata	strain=JCM 3076	GCA_014647835.1	147065	58117	type	True	81.3317	1267	2914	95	below_threshold
Microbispora bryophytorum	strain=CGMCC 4.7138	GCA_014645855.1	1460882	1460882	type	True	81.3107	1355	2914	95	below_threshold
Microbispora rosea subsp. rosea	strain=NBRC 14044	GCA_016863055.1	58118	58117	type	True	81.3088	1453	2914	95	below_threshold
Microbispora fusca	strain=NEAU-HEGS1-5	GCA_005864065.1	2576905	2576905	type	True	81.2253	1309	2914	95	below_threshold
Planotetraspora phitsanulokensis	strain=NBRC 104273	GCA_016863295.1	575192	575192	type	True	80.9404	1304	2914	95	below_threshold
Microbispora oryzae	strain=RL4-1S	GCA_017896165.1	2806554	2806554	type	True	80.8929	1184	2914	95	below_threshold
Planotetraspora mira	strain=NBRC 15435	GCA_016863275.1	58121	58121	type	True	80.8344	1296	2914	95	below_threshold
Planotetraspora thailandica	strain=NBRC 104271	GCA_016863335.1	487172	487172	type	True	80.8248	1258	2914	95	below_threshold
Nonomuraea pusilla	strain=DSM 43357	GCA_900109355.1	46177	46177	type	True	80.1968	1407	2914	95	below_threshold
Nonomuraea rhizosphaerae	strain=CGMCC 4.7431	GCA_019396405.1	2665663	2665663	type	True	79.7292	844	2914	95	below_threshold
Sphaerisporangium corydalis	strain=NEAU-YHS15	GCA_025506355.1	1441875	1441875	type	True	79.7133	1292	2914	95	below_threshold
Nonomuraea phyllanthi	strain=WYY166	GCA_009497075.1	2219224	2219224	type	True	79.4917	1349	2914	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:59:03,840] [INFO] DFAST Taxonomy check result was written to GCF_001528665.1_ASM152866v1_genomic.fna/tc_result.tsv
[2024-01-24 13:59:03,841] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:59:03,841] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:59:03,841] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg777a42b9-de12-4e36-8c10-cad200de168f/dqc_reference/checkm_data
[2024-01-24 13:59:03,842] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:59:03,926] [INFO] Task started: CheckM
[2024-01-24 13:59:03,926] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001528665.1_ASM152866v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001528665.1_ASM152866v1_genomic.fna/checkm_input GCF_001528665.1_ASM152866v1_genomic.fna/checkm_result
[2024-01-24 14:00:19,016] [INFO] Task succeeded: CheckM
[2024-01-24 14:00:19,018] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:00:19,075] [INFO] ===== Completeness check finished =====
[2024-01-24 14:00:19,076] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:00:19,076] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001528665.1_ASM152866v1_genomic.fna/markers.fasta)
[2024-01-24 14:00:19,077] [INFO] Task started: Blastn
[2024-01-24 14:00:19,077] [INFO] Running command: blastn -query GCF_001528665.1_ASM152866v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg777a42b9-de12-4e36-8c10-cad200de168f/dqc_reference/reference_markers_gtdb.fasta -out GCF_001528665.1_ASM152866v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:00:21,244] [INFO] Task succeeded: Blastn
[2024-01-24 14:00:21,247] [INFO] Selected 15 target genomes.
[2024-01-24 14:00:21,247] [INFO] Target genome list was writen to GCF_001528665.1_ASM152866v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:00:21,259] [INFO] Task started: fastANI
[2024-01-24 14:00:21,260] [INFO] Running command: fastANI --query /var/lib/cwl/stg69b57521-f401-4677-9cb3-c49d14b9e6ff/GCF_001528665.1_ASM152866v1_genomic.fna.gz --refList GCF_001528665.1_ASM152866v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001528665.1_ASM152866v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:00:54,618] [INFO] Task succeeded: fastANI
[2024-01-24 14:00:54,638] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:00:54,639] [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_001528665.1	s__Microtetraspora malaysiensis	100.0	2908	2914	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microtetraspora	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001570365.1	s__Microtetraspora fusca	93.8078	2279	2914	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microtetraspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001570405.1	s__Microtetraspora niveoalba	89.6106	2018	2914	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microtetraspora	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001570385.1	s__Microtetraspora glauca	87.5843	2036	2914	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microtetraspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016863095.1	s__Microbispora siamensis	81.5783	1504	2914	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	96.99	95.83	0.88	0.87	3	-
GCF_006874465.1	s__Microbispora bryophytorum	81.4134	1335	2914	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	99.22	97.66	0.97	0.91	4	-
GCF_014647835.1	s__Microbispora aerata	81.3865	1259	2914	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	100.00	100.00	1.00	1.00	2	-
GCA_003260025.2	s__Microbispora triticiradicis	81.3477	1260	2914	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	98.16	96.98	0.92	0.88	7	-
GCF_016863015.1	s__Microbispora amethystogenes	81.3158	1327	2914	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	97.43	97.43	0.91	0.91	2	-
GCF_900156315.1	s__Microbispora rosea	81.3142	1454	2914	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	99.16	98.33	0.97	0.94	3	-
GCF_016863035.1	s__Microbispora corallina	81.2923	1372	2914	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	97.01	97.01	0.91	0.91	2	-
GCF_016863335.1	s__Planotetraspora thailandica	80.8324	1257	2914	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	80.8299	1297	2914	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planotetraspora	95.2969	N/A	N/A	N/A	N/A	1	-
GCF_900109355.1	s__Nonomuraea pusilla	80.1658	1410	2914	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	99.44	99.44	0.97	0.97	2	-
GCF_900099965.1	s__Nonomuraea jiangxiensis	79.0725	1321	2914	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:00:54,641] [INFO] GTDB search result was written to GCF_001528665.1_ASM152866v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:00:54,642] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:00:54,647] [INFO] DFAST_QC result json was written to GCF_001528665.1_ASM152866v1_genomic.fna/dqc_result.json
[2024-01-24 14:00:54,647] [INFO] DFAST_QC completed!
[2024-01-24 14:00:54,647] [INFO] Total running time: 0h2m59s