[2024-01-25 20:04:20,506] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:04:20,507] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:04:20,508] [INFO] DQC Reference Directory: /var/lib/cwl/stgbbfa417e-bdeb-45c4-9cf4-75ac7b778e22/dqc_reference
[2024-01-25 20:04:21,680] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:04:21,681] [INFO] Task started: Prodigal
[2024-01-25 20:04:21,681] [INFO] Running command: gunzip -c /var/lib/cwl/stgfb0d31e0-c662-4dcc-a55e-7aa9dcbffe1f/GCF_003260015.1_ASM326001v1_genomic.fna.gz | prodigal -d GCF_003260015.1_ASM326001v1_genomic.fna/cds.fna -a GCF_003260015.1_ASM326001v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:04:33,581] [INFO] Task succeeded: Prodigal
[2024-01-25 20:04:33,582] [INFO] Task started: HMMsearch
[2024-01-25 20:04:33,582] [INFO] Running command: hmmsearch --tblout GCF_003260015.1_ASM326001v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbbfa417e-bdeb-45c4-9cf4-75ac7b778e22/dqc_reference/reference_markers.hmm GCF_003260015.1_ASM326001v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:04:33,849] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:04:33,850] [INFO] Found 6/6 markers.
[2024-01-25 20:04:33,893] [INFO] Query marker FASTA was written to GCF_003260015.1_ASM326001v1_genomic.fna/markers.fasta
[2024-01-25 20:04:33,894] [INFO] Task started: Blastn
[2024-01-25 20:04:33,894] [INFO] Running command: blastn -query GCF_003260015.1_ASM326001v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbbfa417e-bdeb-45c4-9cf4-75ac7b778e22/dqc_reference/reference_markers.fasta -out GCF_003260015.1_ASM326001v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:04:35,128] [INFO] Task succeeded: Blastn
[2024-01-25 20:04:35,131] [INFO] Selected 15 target genomes.
[2024-01-25 20:04:35,131] [INFO] Target genome list was writen to GCF_003260015.1_ASM326001v1_genomic.fna/target_genomes.txt
[2024-01-25 20:04:35,154] [INFO] Task started: fastANI
[2024-01-25 20:04:35,155] [INFO] Running command: fastANI --query /var/lib/cwl/stgfb0d31e0-c662-4dcc-a55e-7aa9dcbffe1f/GCF_003260015.1_ASM326001v1_genomic.fna.gz --refList GCF_003260015.1_ASM326001v1_genomic.fna/target_genomes.txt --output GCF_003260015.1_ASM326001v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:04:52,482] [INFO] Task succeeded: fastANI
[2024-01-25 20:04:52,482] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbbfa417e-bdeb-45c4-9cf4-75ac7b778e22/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:04:52,483] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbbfa417e-bdeb-45c4-9cf4-75ac7b778e22/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:04:52,493] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:04:52,493] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:04:52,493] [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
Nakamurella deserti	strain=12Sc4-1	GCA_003260015.1	2164074	2164074	type	True	100.0	1539	1539	95	conclusive
Nakamurella flava	strain=N5BH11	GCA_005298075.1	2576308	2576308	type	True	78.4718	571	1539	95	below_threshold
Nakamurella leprariae	strain=YIM 132084	GCA_016918035.1	2803911	2803911	type	True	78.457	565	1539	95	below_threshold
Nakamurella multipartita	strain=DSM 44233	GCA_000024365.1	53461	53461	type	True	78.2696	647	1539	95	below_threshold
Nakamurella endophytica	strain=CGMCC 4.7308	GCA_014646215.1	1748367	1748367	type	True	78.1477	639	1539	95	below_threshold
Nakamurella aerolata	strain=DB0629	GCA_013002705.1	1656892	1656892	type	True	77.6156	406	1539	95	below_threshold
Saccharopolyspora flava	strain=DSM 44771	GCA_900116135.1	95161	95161	type	True	77.1154	447	1539	95	below_threshold
Nakamurella antarctica	strain=S14-144	GCA_003860405.1	1902245	1902245	type	True	77.0408	202	1539	95	below_threshold
Actinokineospora pegani	strain=TRM 65233	GCA_009745975.1	2654637	2654637	type	True	76.9127	479	1539	95	below_threshold
Geodermatophilus tzadiensis	strain=DSM 45416	GCA_003002915.1	1137988	1137988	type	True	76.7078	521	1539	95	below_threshold
Saccharothrix algeriensis	strain=DSM 44581	GCA_016907655.1	173560	173560	type	True	76.6241	529	1539	95	below_threshold
Nocardia thailandica	strain=NBRC 100428	GCA_000308795.1	257275	257275	type	True	76.5012	456	1539	95	below_threshold
Nocardioides solisilvae	strain=Ka25	GCA_003194625.1	1542435	1542435	type	True	76.322	315	1539	95	below_threshold
Pseudonocardia endophytica	strain=DSM 44969	GCA_004339565.1	401976	401976	type	True	76.2586	483	1539	95	below_threshold
Pseudonocardia acaciae	strain=DSM 45401	GCA_000620785.1	551276	551276	type	True	76.2096	565	1539	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:04:52,494] [INFO] DFAST Taxonomy check result was written to GCF_003260015.1_ASM326001v1_genomic.fna/tc_result.tsv
[2024-01-25 20:04:52,495] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:04:52,495] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:04:52,495] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbbfa417e-bdeb-45c4-9cf4-75ac7b778e22/dqc_reference/checkm_data
[2024-01-25 20:04:52,496] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:04:52,540] [INFO] Task started: CheckM
[2024-01-25 20:04:52,540] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003260015.1_ASM326001v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003260015.1_ASM326001v1_genomic.fna/checkm_input GCF_003260015.1_ASM326001v1_genomic.fna/checkm_result
[2024-01-25 20:06:34,320] [INFO] Task succeeded: CheckM
[2024-01-25 20:06:34,321] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:06:34,335] [INFO] ===== Completeness check finished =====
[2024-01-25 20:06:34,335] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:06:34,336] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003260015.1_ASM326001v1_genomic.fna/markers.fasta)
[2024-01-25 20:06:34,336] [INFO] Task started: Blastn
[2024-01-25 20:06:34,336] [INFO] Running command: blastn -query GCF_003260015.1_ASM326001v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbbfa417e-bdeb-45c4-9cf4-75ac7b778e22/dqc_reference/reference_markers_gtdb.fasta -out GCF_003260015.1_ASM326001v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:06:36,261] [INFO] Task succeeded: Blastn
[2024-01-25 20:06:36,265] [INFO] Selected 12 target genomes.
[2024-01-25 20:06:36,265] [INFO] Target genome list was writen to GCF_003260015.1_ASM326001v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:06:36,286] [INFO] Task started: fastANI
[2024-01-25 20:06:36,286] [INFO] Running command: fastANI --query /var/lib/cwl/stgfb0d31e0-c662-4dcc-a55e-7aa9dcbffe1f/GCF_003260015.1_ASM326001v1_genomic.fna.gz --refList GCF_003260015.1_ASM326001v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003260015.1_ASM326001v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:06:48,230] [INFO] Task succeeded: fastANI
[2024-01-25 20:06:48,239] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:06:48,239] [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_003260015.1	s__Nakamurella deserti	100.0	1539	1539	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Nakamurellaceae;g__Nakamurella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009707545.1	s__Nakamurella sp009707545	78.7149	618	1539	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Nakamurellaceae;g__Nakamurella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003576535.1	s__Nakamurella silvestris	78.5759	489	1539	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Nakamurellaceae;g__Nakamurella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005298075.1	s__Nakamurella flava	78.4924	568	1539	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Nakamurellaceae;g__Nakamurella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016918035.1	s__Nakamurella sp016918035	78.4639	564	1539	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Nakamurellaceae;g__Nakamurella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000024365.1	s__Nakamurella multipartita	78.2843	645	1539	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Nakamurellaceae;g__Nakamurella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104535.1	s__Nakamurella panacisegetis	78.2257	469	1539	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Nakamurellaceae;g__Nakamurella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014646215.1	s__Nakamurella endophytica	78.1159	644	1539	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Nakamurellaceae;g__Nakamurella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014303395.1	s__Nakamurella sp014303395	77.8576	469	1539	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Nakamurellaceae;g__Nakamurella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017882715.1	s__Nakamurella sp017882715	77.314	345	1539	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Nakamurellaceae;g__Nakamurella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014395785.1	s__Nocardioides_B mesophilus	76.6929	361	1539	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003194625.1	s__Nocardioides solisilvae	76.3157	316	1539	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:06:48,248] [INFO] GTDB search result was written to GCF_003260015.1_ASM326001v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:06:48,249] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:06:48,252] [INFO] DFAST_QC result json was written to GCF_003260015.1_ASM326001v1_genomic.fna/dqc_result.json
[2024-01-25 20:06:48,253] [INFO] DFAST_QC completed!
[2024-01-25 20:06:48,253] [INFO] Total running time: 0h2m28s