[2024-01-25 18:05:50,614] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:05:50,616] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:05:50,616] [INFO] DQC Reference Directory: /var/lib/cwl/stgd88fdd69-88c5-41ee-a0aa-74b0b80953a3/dqc_reference
[2024-01-25 18:05:51,831] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:05:51,831] [INFO] Task started: Prodigal
[2024-01-25 18:05:51,832] [INFO] Running command: gunzip -c /var/lib/cwl/stge8f79c35-ade2-48b3-bac7-36eebc04328c/GCF_025264705.1_ASM2526470v1_genomic.fna.gz | prodigal -d GCF_025264705.1_ASM2526470v1_genomic.fna/cds.fna -a GCF_025264705.1_ASM2526470v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:06:33,199] [INFO] Task succeeded: Prodigal
[2024-01-25 18:06:33,199] [INFO] Task started: HMMsearch
[2024-01-25 18:06:33,199] [INFO] Running command: hmmsearch --tblout GCF_025264705.1_ASM2526470v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd88fdd69-88c5-41ee-a0aa-74b0b80953a3/dqc_reference/reference_markers.hmm GCF_025264705.1_ASM2526470v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:06:33,663] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:06:33,664] [INFO] Found 6/6 markers.
[2024-01-25 18:06:33,745] [INFO] Query marker FASTA was written to GCF_025264705.1_ASM2526470v1_genomic.fna/markers.fasta
[2024-01-25 18:06:33,746] [INFO] Task started: Blastn
[2024-01-25 18:06:33,746] [INFO] Running command: blastn -query GCF_025264705.1_ASM2526470v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd88fdd69-88c5-41ee-a0aa-74b0b80953a3/dqc_reference/reference_markers.fasta -out GCF_025264705.1_ASM2526470v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:06:34,951] [INFO] Task succeeded: Blastn
[2024-01-25 18:06:34,955] [INFO] Selected 8 target genomes.
[2024-01-25 18:06:34,955] [INFO] Target genome list was writen to GCF_025264705.1_ASM2526470v1_genomic.fna/target_genomes.txt
[2024-01-25 18:06:34,960] [INFO] Task started: fastANI
[2024-01-25 18:06:34,960] [INFO] Running command: fastANI --query /var/lib/cwl/stge8f79c35-ade2-48b3-bac7-36eebc04328c/GCF_025264705.1_ASM2526470v1_genomic.fna.gz --refList GCF_025264705.1_ASM2526470v1_genomic.fna/target_genomes.txt --output GCF_025264705.1_ASM2526470v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:07:04,921] [INFO] Task succeeded: fastANI
[2024-01-25 18:07:04,921] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd88fdd69-88c5-41ee-a0aa-74b0b80953a3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:07:04,921] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd88fdd69-88c5-41ee-a0aa-74b0b80953a3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:07:04,928] [INFO] Found 8 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:07:04,928] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:07:04,928] [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 aurantiacum	strain=NRRL B-8018	GCA_025264705.1	35754	35754	type	True	100.0	3841	3841	95	conclusive
Dactylosporangium aurantiacum	strain=NRRL B-8018	GCA_000716715.1	35754	35754	type	True	99.9551	3730	3841	95	conclusive
Dactylosporangium siamense	strain=NBRC 106093	GCA_016862795.1	685454	685454	type	True	88.1206	2742	3841	95	below_threshold
Dactylosporangium sucinum	strain=JCM 19831	GCA_014647515.1	1424081	1424081	type	True	82.613	2225	3841	95	below_threshold
Dactylosporangium fulvum	strain=NRRL B-16292	GCA_025137375.1	53359	53359	type	True	82.5388	2052	3841	95	below_threshold
Dactylosporangium roseum	strain=NRRL B-16295	GCA_025264685.1	47989	47989	type	True	82.2309	1686	3841	95	below_threshold
Dactylosporangium matsuzakiense	strain=NRRL B-16293	GCA_025264725.1	53360	53360	type	True	81.341	2136	3841	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	78.1626	1093	3841	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:07:04,933] [INFO] DFAST Taxonomy check result was written to GCF_025264705.1_ASM2526470v1_genomic.fna/tc_result.tsv
[2024-01-25 18:07:04,934] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:07:04,934] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:07:04,934] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd88fdd69-88c5-41ee-a0aa-74b0b80953a3/dqc_reference/checkm_data
[2024-01-25 18:07:04,935] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:07:05,039] [INFO] Task started: CheckM
[2024-01-25 18:07:05,039] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025264705.1_ASM2526470v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025264705.1_ASM2526470v1_genomic.fna/checkm_input GCF_025264705.1_ASM2526470v1_genomic.fna/checkm_result
[2024-01-25 18:14:07,259] [INFO] Task succeeded: CheckM
[2024-01-25 18:14:07,261] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:14:07,288] [INFO] ===== Completeness check finished =====
[2024-01-25 18:14:07,289] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:14:07,291] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025264705.1_ASM2526470v1_genomic.fna/markers.fasta)
[2024-01-25 18:14:07,291] [INFO] Task started: Blastn
[2024-01-25 18:14:07,291] [INFO] Running command: blastn -query GCF_025264705.1_ASM2526470v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd88fdd69-88c5-41ee-a0aa-74b0b80953a3/dqc_reference/reference_markers_gtdb.fasta -out GCF_025264705.1_ASM2526470v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:14:09,287] [INFO] Task succeeded: Blastn
[2024-01-25 18:14:09,290] [INFO] Selected 18 target genomes.
[2024-01-25 18:14:09,290] [INFO] Target genome list was writen to GCF_025264705.1_ASM2526470v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:14:09,306] [INFO] Task started: fastANI
[2024-01-25 18:14:09,306] [INFO] Running command: fastANI --query /var/lib/cwl/stge8f79c35-ade2-48b3-bac7-36eebc04328c/GCF_025264705.1_ASM2526470v1_genomic.fna.gz --refList GCF_025264705.1_ASM2526470v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025264705.1_ASM2526470v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:14:55,896] [INFO] Task succeeded: fastANI
[2024-01-25 18:14:55,907] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:14:55,908] [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_000716715.1	s__Dactylosporangium aurantiacum	99.9551	3730	3841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Dactylosporangium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_016862795.1	s__Dactylosporangium siamense	88.1557	2734	3841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Dactylosporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014647515.1	s__Dactylosporangium sucinum	82.6445	2215	3841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Dactylosporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900090295.1	s__Micromonospora coxensis	78.2511	1290	3841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014205165.1	s__Micromonospora carbonacea	78.2402	1429	3841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.5545	99.19	98.38	0.95	0.91	3	-
GCF_016863475.1	s__Spirilliplanes yamanashiensis	78.2082	1375	3841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Spirilliplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900090245.1	s__Micromonospora halophytica	78.166	1171	3841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648395.1	s__Micromonospora fulviviridis	78.1155	1343	3841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	95.01	95.01	0.74	0.74	2	-
GCF_900091515.1	s__Micromonospora purpureochromogenes	78.1118	1238	3841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	96.27	95.68	0.85	0.81	4	-
GCF_004217615.1	s__Micromonospora kangleipakensis	78.0723	1254	3841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900090265.1	s__Micromonospora rifamycinica	78.0482	1262	3841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900091435.1	s__Micromonospora chaiyaphumensis	78.0186	1322	3841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	95.16	95.15	0.86	0.86	3	-
GCF_011297335.1	s__Catellatospora methionotrophica	77.8923	1416	3841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Catellatospora	95.0	99.99	99.99	0.99	0.99	2	-
GCF_018327705.1	s__Catellatospora sp018327705	77.8865	1505	3841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Catellatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009720365.1	s__Catellatospora paridis	77.8605	1463	3841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Catellatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003626655.1	s__Micromonospora costi	77.7796	1275	3841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014204895.1	s__Actinoplanes abujensis	77.5977	1365	3841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016861975.1	s__Actinocatenispora rupis	76.5146	1214	3841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinocatenispora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:14:55,909] [INFO] GTDB search result was written to GCF_025264705.1_ASM2526470v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:14:55,909] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:14:55,914] [INFO] DFAST_QC result json was written to GCF_025264705.1_ASM2526470v1_genomic.fna/dqc_result.json
[2024-01-25 18:14:55,914] [INFO] DFAST_QC completed!
[2024-01-25 18:14:55,914] [INFO] Total running time: 0h9m5s