[2024-01-24 14:19:31,537] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:31,544] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:31,544] [INFO] DQC Reference Directory: /var/lib/cwl/stg814d1fbf-bd4c-4294-b435-a6da11562970/dqc_reference
[2024-01-24 14:19:32,957] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:32,959] [INFO] Task started: Prodigal
[2024-01-24 14:19:32,959] [INFO] Running command: gunzip -c /var/lib/cwl/stg1516779a-fdd5-481e-b2a3-a7ad3df55beb/GCF_000720965.1_ASM72096v1_genomic.fna.gz | prodigal -d GCF_000720965.1_ASM72096v1_genomic.fna/cds.fna -a GCF_000720965.1_ASM72096v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:19:54,235] [INFO] Task succeeded: Prodigal
[2024-01-24 14:19:54,235] [INFO] Task started: HMMsearch
[2024-01-24 14:19:54,235] [INFO] Running command: hmmsearch --tblout GCF_000720965.1_ASM72096v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg814d1fbf-bd4c-4294-b435-a6da11562970/dqc_reference/reference_markers.hmm GCF_000720965.1_ASM72096v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:19:54,631] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:19:54,633] [INFO] Found 6/6 markers.
[2024-01-24 14:19:54,705] [INFO] Query marker FASTA was written to GCF_000720965.1_ASM72096v1_genomic.fna/markers.fasta
[2024-01-24 14:19:54,706] [INFO] Task started: Blastn
[2024-01-24 14:19:54,706] [INFO] Running command: blastn -query GCF_000720965.1_ASM72096v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg814d1fbf-bd4c-4294-b435-a6da11562970/dqc_reference/reference_markers.fasta -out GCF_000720965.1_ASM72096v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:19:56,089] [INFO] Task succeeded: Blastn
[2024-01-24 14:19:56,092] [INFO] Selected 15 target genomes.
[2024-01-24 14:19:56,093] [INFO] Target genome list was writen to GCF_000720965.1_ASM72096v1_genomic.fna/target_genomes.txt
[2024-01-24 14:19:56,121] [INFO] Task started: fastANI
[2024-01-24 14:19:56,122] [INFO] Running command: fastANI --query /var/lib/cwl/stg1516779a-fdd5-481e-b2a3-a7ad3df55beb/GCF_000720965.1_ASM72096v1_genomic.fna.gz --refList GCF_000720965.1_ASM72096v1_genomic.fna/target_genomes.txt --output GCF_000720965.1_ASM72096v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:20:22,817] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:22,818] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg814d1fbf-bd4c-4294-b435-a6da11562970/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:20:22,818] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg814d1fbf-bd4c-4294-b435-a6da11562970/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:20:22,833] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:20:22,833] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:20:22,833] [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
Actinocatenispora sera	strain=NRRL B-24477	GCA_000720965.1	390989	390989	type	True	100.0	2289	2291	95	conclusive
Actinocatenispora sera	strain=NBRC 101916	GCA_018324685.1	390989	390989	type	True	99.9869	2290	2291	95	conclusive
Actinocatenispora comari	strain=NUM-2625	GCA_017312725.1	2807577	2807577	type	True	92.7597	1972	2291	95	below_threshold
Micromonospora olivasterospora	strain=DSM 43868	GCA_007830265.1	1880	1880	type	True	77.7607	812	2291	95	below_threshold
Micromonospora rifamycinica	strain=DSM 44983	GCA_900090265.1	291594	291594	type	True	77.6922	845	2291	95	below_threshold
Micromonospora radicis	strain=AZ1-13	GCA_003583405.1	1894971	1894971	type	True	77.6855	725	2291	95	below_threshold
Micromonospora wenchangensis	strain=CCTCC AA 2012002	GCA_002210435.1	1185415	1185415	type	True	77.5623	865	2291	95	below_threshold
Micromonospora maris	strain=NRRL B-24793	GCA_001507315.1	1003110	1003110	type	True	77.5578	726	2291	95	below_threshold
Micromonospora maris	strain=AB-18-032	GCA_000204155.1	1003110	1003110	type	True	77.5084	731	2291	95	below_threshold
Micromonospora polyrhachis	strain=DSM 45886	GCA_014203835.1	1282883	1282883	type	True	77.2695	634	2291	95	below_threshold
Longispora albida	strain=DSM 44784	GCA_000379825.1	203523	203523	type	True	77.2283	639	2291	95	below_threshold
Catellatospora citrea	strain=NBRC 14495	GCA_016862615.1	53366	53366	type	True	77.1892	887	2291	95	below_threshold
Catellatospora methionotrophica	strain=NBRC 14553	GCA_016862655.1	121620	121620	type	True	77.0464	860	2291	95	below_threshold
Couchioplanes caeruleus	strain=DSM 43634	GCA_003751945.1	56438	56438	type	True	76.8865	761	2291	95	below_threshold
Actinokineospora enzanensis	strain=DSM 44649	GCA_000374445.1	155975	155975	type	True	76.4785	597	2291	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:20:22,835] [INFO] DFAST Taxonomy check result was written to GCF_000720965.1_ASM72096v1_genomic.fna/tc_result.tsv
[2024-01-24 14:20:22,835] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:20:22,835] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:20:22,836] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg814d1fbf-bd4c-4294-b435-a6da11562970/dqc_reference/checkm_data
[2024-01-24 14:20:22,837] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:20:22,902] [INFO] Task started: CheckM
[2024-01-24 14:20:22,903] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000720965.1_ASM72096v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000720965.1_ASM72096v1_genomic.fna/checkm_input GCF_000720965.1_ASM72096v1_genomic.fna/checkm_result
[2024-01-24 14:21:30,628] [INFO] Task succeeded: CheckM
[2024-01-24 14:21:30,630] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:21:30,652] [INFO] ===== Completeness check finished =====
[2024-01-24 14:21:30,653] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:21:30,653] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000720965.1_ASM72096v1_genomic.fna/markers.fasta)
[2024-01-24 14:21:30,653] [INFO] Task started: Blastn
[2024-01-24 14:21:30,654] [INFO] Running command: blastn -query GCF_000720965.1_ASM72096v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg814d1fbf-bd4c-4294-b435-a6da11562970/dqc_reference/reference_markers_gtdb.fasta -out GCF_000720965.1_ASM72096v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:21:32,639] [INFO] Task succeeded: Blastn
[2024-01-24 14:21:32,643] [INFO] Selected 10 target genomes.
[2024-01-24 14:21:32,643] [INFO] Target genome list was writen to GCF_000720965.1_ASM72096v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:21:32,684] [INFO] Task started: fastANI
[2024-01-24 14:21:32,684] [INFO] Running command: fastANI --query /var/lib/cwl/stg1516779a-fdd5-481e-b2a3-a7ad3df55beb/GCF_000720965.1_ASM72096v1_genomic.fna.gz --refList GCF_000720965.1_ASM72096v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000720965.1_ASM72096v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:21:52,780] [INFO] Task succeeded: fastANI
[2024-01-24 14:21:52,790] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:21:52,791] [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_018324685.1	s__Actinocatenispora sera	99.9869	2290	2291	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinocatenispora	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_017312725.1	s__Actinocatenispora sp017312725	92.7997	1968	2291	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinocatenispora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016865425.1	s__Actinocatenispora thailandica	89.8273	1963	2291	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinocatenispora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016861975.1	s__Actinocatenispora rupis	82.219	1444	2291	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinocatenispora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003583405.1	s__Micromonospora radicis	77.7068	721	2291	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002210435.1	s__Micromonospora wenchangensis	77.5717	864	2291	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	95.84	95.43	0.85	0.83	5	-
GCF_014203835.1	s__Micromonospora_H polyrhachis	77.2839	632	2291	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora_H	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016863475.1	s__Spirilliplanes yamanashiensis	77.1672	907	2291	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Spirilliplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003610235.1	s__Catellatospora citrea	77.1085	908	2291	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Catellatospora	95.0	97.34	95.99	0.88	0.83	4	-
GCF_000374445.1	s__Actinokineospora enzanensis	76.4612	602	2291	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:21:52,792] [INFO] GTDB search result was written to GCF_000720965.1_ASM72096v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:21:52,793] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:21:52,798] [INFO] DFAST_QC result json was written to GCF_000720965.1_ASM72096v1_genomic.fna/dqc_result.json
[2024-01-24 14:21:52,798] [INFO] DFAST_QC completed!
[2024-01-24 14:21:52,798] [INFO] Total running time: 0h2m21s