[2024-01-24 11:42:20,304] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:42:20,306] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:42:20,307] [INFO] DQC Reference Directory: /var/lib/cwl/stgb8149b12-6499-42f9-b56d-7fd4f27dcf2f/dqc_reference
[2024-01-24 11:42:24,522] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:42:24,524] [INFO] Task started: Prodigal
[2024-01-24 11:42:24,524] [INFO] Running command: gunzip -c /var/lib/cwl/stgf000c2d4-1dbe-4bb2-b4cc-a3c7bb8bb150/GCF_013002705.1_ASM1300270v1_genomic.fna.gz | prodigal -d GCF_013002705.1_ASM1300270v1_genomic.fna/cds.fna -a GCF_013002705.1_ASM1300270v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:42:38,733] [INFO] Task succeeded: Prodigal
[2024-01-24 11:42:38,734] [INFO] Task started: HMMsearch
[2024-01-24 11:42:38,734] [INFO] Running command: hmmsearch --tblout GCF_013002705.1_ASM1300270v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb8149b12-6499-42f9-b56d-7fd4f27dcf2f/dqc_reference/reference_markers.hmm GCF_013002705.1_ASM1300270v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:42:38,976] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:42:38,978] [INFO] Found 6/6 markers.
[2024-01-24 11:42:39,019] [INFO] Query marker FASTA was written to GCF_013002705.1_ASM1300270v1_genomic.fna/markers.fasta
[2024-01-24 11:42:39,019] [INFO] Task started: Blastn
[2024-01-24 11:42:39,019] [INFO] Running command: blastn -query GCF_013002705.1_ASM1300270v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb8149b12-6499-42f9-b56d-7fd4f27dcf2f/dqc_reference/reference_markers.fasta -out GCF_013002705.1_ASM1300270v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:42:40,205] [INFO] Task succeeded: Blastn
[2024-01-24 11:42:40,209] [INFO] Selected 14 target genomes.
[2024-01-24 11:42:40,210] [INFO] Target genome list was writen to GCF_013002705.1_ASM1300270v1_genomic.fna/target_genomes.txt
[2024-01-24 11:42:40,216] [INFO] Task started: fastANI
[2024-01-24 11:42:40,216] [INFO] Running command: fastANI --query /var/lib/cwl/stgf000c2d4-1dbe-4bb2-b4cc-a3c7bb8bb150/GCF_013002705.1_ASM1300270v1_genomic.fna.gz --refList GCF_013002705.1_ASM1300270v1_genomic.fna/target_genomes.txt --output GCF_013002705.1_ASM1300270v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:42:53,483] [INFO] Task succeeded: fastANI
[2024-01-24 11:42:53,484] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb8149b12-6499-42f9-b56d-7fd4f27dcf2f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:42:53,485] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb8149b12-6499-42f9-b56d-7fd4f27dcf2f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:42:53,497] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:42:53,498] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:42:53,498] [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 aerolata	strain=DB0629	GCA_013002705.1	1656892	1656892	type	True	100.0	1437	1440	95	conclusive
Nakamurella lactea	strain=DSM 19367	GCA_000426645.1	459515	459515	type	True	78.9043	630	1440	95	below_threshold
Nakamurella multipartita	strain=DSM 44233	GCA_000024365.1	53461	53461	type	True	77.8579	469	1440	95	below_threshold
Nakamurella leprariae	strain=YIM 132084	GCA_016918035.1	2803911	2803911	type	True	77.7601	410	1440	95	below_threshold
Nakamurella endophytica	strain=CGMCC 4.7308	GCA_014646215.1	1748367	1748367	type	True	77.7367	484	1440	95	below_threshold
Nakamurella deserti	strain=12Sc4-1	GCA_003260015.1	2164074	2164074	type	True	77.7137	423	1440	95	below_threshold
Nakamurella flava	strain=N5BH11	GCA_005298075.1	2576308	2576308	type	True	77.4215	404	1440	95	below_threshold
Saccharopolyspora antimicrobica	strain=DSM 45119	GCA_003635025.1	455193	455193	type	True	76.8351	391	1440	95	below_threshold
Tsukamurella pulmonis	strain=DSM 44142	GCA_900103175.1	47312	47312	type	True	76.6087	276	1440	95	below_threshold
Saccharothrix tamanrassetensis	strain=CECT 8640	GCA_014203665.1	1051531	1051531	type	True	76.5458	376	1440	95	below_threshold
Tsukamurella pulmonis	strain=NCTC13230	GCA_900460155.1	47312	47312	type	True	76.5424	277	1440	95	below_threshold
Tsukamurella pulmonis	strain=CCUG 35732	GCA_001575165.1	47312	47312	type	True	76.4715	270	1440	95	below_threshold
Pseudonocardia broussonetiae	strain=Gen 01	GCA_013155125.1	2736640	2736640	type	True	76.3007	408	1440	95	below_threshold
Nocardioides donggukensis	strain=MJB4	GCA_014842875.1	2774019	2774019	type	True	76.2055	241	1440	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:42:53,499] [INFO] DFAST Taxonomy check result was written to GCF_013002705.1_ASM1300270v1_genomic.fna/tc_result.tsv
[2024-01-24 11:42:53,500] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:42:53,500] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:42:53,500] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb8149b12-6499-42f9-b56d-7fd4f27dcf2f/dqc_reference/checkm_data
[2024-01-24 11:42:53,501] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:42:53,543] [INFO] Task started: CheckM
[2024-01-24 11:42:53,543] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013002705.1_ASM1300270v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013002705.1_ASM1300270v1_genomic.fna/checkm_input GCF_013002705.1_ASM1300270v1_genomic.fna/checkm_result
[2024-01-24 11:43:42,082] [INFO] Task succeeded: CheckM
[2024-01-24 11:43:42,084] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.37%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:43:42,107] [INFO] ===== Completeness check finished =====
[2024-01-24 11:43:42,107] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:43:42,107] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013002705.1_ASM1300270v1_genomic.fna/markers.fasta)
[2024-01-24 11:43:42,108] [INFO] Task started: Blastn
[2024-01-24 11:43:42,108] [INFO] Running command: blastn -query GCF_013002705.1_ASM1300270v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb8149b12-6499-42f9-b56d-7fd4f27dcf2f/dqc_reference/reference_markers_gtdb.fasta -out GCF_013002705.1_ASM1300270v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:43:43,865] [INFO] Task succeeded: Blastn
[2024-01-24 11:43:43,869] [INFO] Selected 13 target genomes.
[2024-01-24 11:43:43,869] [INFO] Target genome list was writen to GCF_013002705.1_ASM1300270v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:43:43,879] [INFO] Task started: fastANI
[2024-01-24 11:43:43,880] [INFO] Running command: fastANI --query /var/lib/cwl/stgf000c2d4-1dbe-4bb2-b4cc-a3c7bb8bb150/GCF_013002705.1_ASM1300270v1_genomic.fna.gz --refList GCF_013002705.1_ASM1300270v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013002705.1_ASM1300270v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:43:57,470] [INFO] Task succeeded: fastANI
[2024-01-24 11:43:57,485] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:43:57,486] [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_013002705.1	s__Nakamurella aerolata	100.0	1437	1440	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_000426645.1	s__Nakamurella lactea	78.9111	629	1440	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	77.8952	464	1440	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Nakamurellaceae;g__Nakamurella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009707545.1	s__Nakamurella sp009707545	77.8871	485	1440	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	77.834	351	1440	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	77.7919	406	1440	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Nakamurellaceae;g__Nakamurella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003260015.1	s__Nakamurella deserti	77.7506	418	1440	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	77.7172	487	1440	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Nakamurellaceae;g__Nakamurella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011058165.1	s__Rhodococcus aetherivorans	76.8501	273	1440	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	98.92	95.74	0.88	0.78	18	-
GCF_003635025.1	s__Saccharopolyspora antimicrobica	76.7717	396	1440	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora	96.3257	100.00	100.00	1.00	1.00	2	-
GCF_900103175.1	s__Tsukamurella pulmonis	76.6241	274	1440	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Tsukamurella	95.0	99.49	98.89	0.96	0.93	5	-
GCA_902805565.1	s__CADCTP01 sp902805565	76.2862	313	1440	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__CADCTP01;g__CADCTP01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900119315.1	s__Actinoplanes sp900119315	76.1228	391	1440	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	3	-
--------------------------------------------------------------------------------
[2024-01-24 11:43:57,487] [INFO] GTDB search result was written to GCF_013002705.1_ASM1300270v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:43:57,488] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:43:57,492] [INFO] DFAST_QC result json was written to GCF_013002705.1_ASM1300270v1_genomic.fna/dqc_result.json
[2024-01-24 11:43:57,492] [INFO] DFAST_QC completed!
[2024-01-24 11:43:57,492] [INFO] Total running time: 0h1m37s