[2024-01-25 19:47:05,461] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:47:05,465] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:47:05,465] [INFO] DQC Reference Directory: /var/lib/cwl/stg2ee1683e-b5dc-45ed-9c92-7b13f6546e67/dqc_reference
[2024-01-25 19:47:06,637] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:47:06,640] [INFO] Task started: Prodigal
[2024-01-25 19:47:06,640] [INFO] Running command: gunzip -c /var/lib/cwl/stg7ff4d852-dda2-4e4a-baaf-256736784fcb/GCF_027922405.1_ASM2792240v1_genomic.fna.gz | prodigal -d GCF_027922405.1_ASM2792240v1_genomic.fna/cds.fna -a GCF_027922405.1_ASM2792240v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:47:35,377] [INFO] Task succeeded: Prodigal
[2024-01-25 19:47:35,377] [INFO] Task started: HMMsearch
[2024-01-25 19:47:35,377] [INFO] Running command: hmmsearch --tblout GCF_027922405.1_ASM2792240v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2ee1683e-b5dc-45ed-9c92-7b13f6546e67/dqc_reference/reference_markers.hmm GCF_027922405.1_ASM2792240v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:47:35,851] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:47:35,854] [INFO] Found 6/6 markers.
[2024-01-25 19:47:35,944] [INFO] Query marker FASTA was written to GCF_027922405.1_ASM2792240v1_genomic.fna/markers.fasta
[2024-01-25 19:47:35,945] [INFO] Task started: Blastn
[2024-01-25 19:47:35,945] [INFO] Running command: blastn -query GCF_027922405.1_ASM2792240v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2ee1683e-b5dc-45ed-9c92-7b13f6546e67/dqc_reference/reference_markers.fasta -out GCF_027922405.1_ASM2792240v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:47:37,157] [INFO] Task succeeded: Blastn
[2024-01-25 19:47:37,160] [INFO] Selected 9 target genomes.
[2024-01-25 19:47:37,160] [INFO] Target genome list was writen to GCF_027922405.1_ASM2792240v1_genomic.fna/target_genomes.txt
[2024-01-25 19:47:37,178] [INFO] Task started: fastANI
[2024-01-25 19:47:37,178] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ff4d852-dda2-4e4a-baaf-256736784fcb/GCF_027922405.1_ASM2792240v1_genomic.fna.gz --refList GCF_027922405.1_ASM2792240v1_genomic.fna/target_genomes.txt --output GCF_027922405.1_ASM2792240v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:48:05,823] [INFO] Task succeeded: fastANI
[2024-01-25 19:48:05,824] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2ee1683e-b5dc-45ed-9c92-7b13f6546e67/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:48:05,825] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2ee1683e-b5dc-45ed-9c92-7b13f6546e67/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:48:05,832] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:48:05,832] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-25 19:48:05,832] [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
Dactylosporangium matsuzakiense	strain=NRRL B-16293	GCA_025264725.1	53360	53360	type	True	99.9173	3415	3764	95	inconclusive
Dactylosporangium vinaceum	strain=NRRL B-16297	GCA_019904175.1	53362	53362	type	True	97.6539	3383	3764	95	inconclusive
Dactylosporangium sucinum	strain=JCM 19831	GCA_014647515.1	1424081	1424081	type	True	81.6473	2034	3764	95	below_threshold
Dactylosporangium fulvum	strain=NRRL B-16292	GCA_025137375.1	53359	53359	type	True	81.5899	1843	3764	95	below_threshold
Dactylosporangium aurantiacum	strain=NRRL B-8018	GCA_025264705.1	35754	35754	type	True	81.3717	2150	3764	95	below_threshold
Dactylosporangium roseum	strain=NRRL B-16295	GCA_025264685.1	47989	47989	type	True	81.3112	1558	3764	95	below_threshold
Dactylosporangium aurantiacum	strain=NRRL B-8018	GCA_000716715.1	35754	35754	type	True	81.2929	2152	3764	95	below_threshold
Dactylosporangium siamense	strain=NBRC 106093	GCA_016862795.1	685454	685454	type	True	81.0118	2071	3764	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	77.6741	990	3764	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:48:05,833] [INFO] DFAST Taxonomy check result was written to GCF_027922405.1_ASM2792240v1_genomic.fna/tc_result.tsv
[2024-01-25 19:48:05,834] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:48:05,834] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:48:05,834] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2ee1683e-b5dc-45ed-9c92-7b13f6546e67/dqc_reference/checkm_data
[2024-01-25 19:48:05,835] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:48:05,938] [INFO] Task started: CheckM
[2024-01-25 19:48:05,938] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_027922405.1_ASM2792240v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_027922405.1_ASM2792240v1_genomic.fna/checkm_input GCF_027922405.1_ASM2792240v1_genomic.fna/checkm_result
[2024-01-25 19:50:12,701] [INFO] Task succeeded: CheckM
[2024-01-25 19:50:12,702] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:50:12,727] [INFO] ===== Completeness check finished =====
[2024-01-25 19:50:12,727] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:50:12,728] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_027922405.1_ASM2792240v1_genomic.fna/markers.fasta)
[2024-01-25 19:50:12,728] [INFO] Task started: Blastn
[2024-01-25 19:50:12,728] [INFO] Running command: blastn -query GCF_027922405.1_ASM2792240v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2ee1683e-b5dc-45ed-9c92-7b13f6546e67/dqc_reference/reference_markers_gtdb.fasta -out GCF_027922405.1_ASM2792240v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:50:14,617] [INFO] Task succeeded: Blastn
[2024-01-25 19:50:14,619] [INFO] Selected 18 target genomes.
[2024-01-25 19:50:14,620] [INFO] Target genome list was writen to GCF_027922405.1_ASM2792240v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:50:14,634] [INFO] Task started: fastANI
[2024-01-25 19:50:14,634] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ff4d852-dda2-4e4a-baaf-256736784fcb/GCF_027922405.1_ASM2792240v1_genomic.fna.gz --refList GCF_027922405.1_ASM2792240v1_genomic.fna/target_genomes_gtdb.txt --output GCF_027922405.1_ASM2792240v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:50:52,208] [INFO] Task succeeded: fastANI
[2024-01-25 19:50:52,218] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 19:50:52,219] [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_014647515.1	s__Dactylosporangium sucinum	81.6999	2017	3764	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Dactylosporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000716715.1	s__Dactylosporangium aurantiacum	81.3585	2127	3764	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Dactylosporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862795.1	s__Dactylosporangium siamense	81.0311	2063	3764	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Dactylosporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016863255.1	s__Planosporangium mesophilum	78.0892	1014	3764	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Planosporangium	95.0	100.00	100.00	0.99	0.99	2	-
GCF_011947225.1	s__Planosporangium flavigriseum	78.087	847	3764	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Planosporangium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_016863475.1	s__Spirilliplanes yamanashiensis	77.8085	1199	3764	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Spirilliplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018070575.1	s__Micromonospora sp018070575	77.6922	1052	3764	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018397995.1	s__NBRC-107566 sp018397995	77.6113	989	3764	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__NBRC-107566	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016863615.1	s__Virgisporangium aliadipatigenens	77.5478	1352	3764	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Virgisporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004217535.1	s__Micromonospora sp004217535	77.5348	1038	3764	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862575.1	s__Catellatospora bangladeshensis	77.4755	1251	3764	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Catellatospora	95.0	95.24	95.24	0.85	0.85	2	-
GCF_018327705.1	s__Catellatospora sp018327705	77.4212	1310	3764	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Catellatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900091615.1	s__Micromonospora yangpuensis	77.4034	952	3764	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	100.00	100.00	1.00	1.00	2	-
GCF_019083965.1	s__Catellatospora sp019083965	77.3954	1206	3764	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Catellatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003711105.1	s__Actinoplanes teichomyceticus	77.357	1266	3764	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	99.99	1.00	1.00	4	-
GCF_001567585.1	s__Micromonospora rosaria	77.2886	1077	3764	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900119315.1	s__Actinoplanes sp900119315	77.2611	1223	3764	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	3	-
GCF_017876755.1	s__Crossiella equi	75.8613	1030	3764	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Crossiella	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:50:52,220] [INFO] GTDB search result was written to GCF_027922405.1_ASM2792240v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:50:52,220] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:50:52,223] [INFO] DFAST_QC result json was written to GCF_027922405.1_ASM2792240v1_genomic.fna/dqc_result.json
[2024-01-25 19:50:52,223] [INFO] DFAST_QC completed!
[2024-01-25 19:50:52,223] [INFO] Total running time: 0h3m47s