[2024-01-24 11:20:19,753] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:20:19,755] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:20:19,755] [INFO] DQC Reference Directory: /var/lib/cwl/stgb7e16313-8a01-4ecd-998d-d4d73566d3d5/dqc_reference
[2024-01-24 11:20:20,967] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:20:20,968] [INFO] Task started: Prodigal
[2024-01-24 11:20:20,968] [INFO] Running command: gunzip -c /var/lib/cwl/stgb5f126ee-43bd-4744-8a4e-5354ad6040f1/GCF_006717095.1_ASM671709v1_genomic.fna.gz | prodigal -d GCF_006717095.1_ASM671709v1_genomic.fna/cds.fna -a GCF_006717095.1_ASM671709v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:20:34,960] [INFO] Task succeeded: Prodigal
[2024-01-24 11:20:34,961] [INFO] Task started: HMMsearch
[2024-01-24 11:20:34,961] [INFO] Running command: hmmsearch --tblout GCF_006717095.1_ASM671709v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb7e16313-8a01-4ecd-998d-d4d73566d3d5/dqc_reference/reference_markers.hmm GCF_006717095.1_ASM671709v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:20:35,276] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:20:35,277] [INFO] Found 6/6 markers.
[2024-01-24 11:20:35,325] [INFO] Query marker FASTA was written to GCF_006717095.1_ASM671709v1_genomic.fna/markers.fasta
[2024-01-24 11:20:35,326] [INFO] Task started: Blastn
[2024-01-24 11:20:35,326] [INFO] Running command: blastn -query GCF_006717095.1_ASM671709v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb7e16313-8a01-4ecd-998d-d4d73566d3d5/dqc_reference/reference_markers.fasta -out GCF_006717095.1_ASM671709v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:20:36,496] [INFO] Task succeeded: Blastn
[2024-01-24 11:20:36,500] [INFO] Selected 15 target genomes.
[2024-01-24 11:20:36,500] [INFO] Target genome list was writen to GCF_006717095.1_ASM671709v1_genomic.fna/target_genomes.txt
[2024-01-24 11:20:36,529] [INFO] Task started: fastANI
[2024-01-24 11:20:36,529] [INFO] Running command: fastANI --query /var/lib/cwl/stgb5f126ee-43bd-4744-8a4e-5354ad6040f1/GCF_006717095.1_ASM671709v1_genomic.fna.gz --refList GCF_006717095.1_ASM671709v1_genomic.fna/target_genomes.txt --output GCF_006717095.1_ASM671709v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:20:55,050] [INFO] Task succeeded: fastANI
[2024-01-24 11:20:55,051] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb7e16313-8a01-4ecd-998d-d4d73566d3d5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:20:55,051] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb7e16313-8a01-4ecd-998d-d4d73566d3d5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:20:55,063] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:20:55,063] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:20:55,063] [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
Blastococcus colisei	strain=DSM 46837	GCA_006717095.1	1564162	1564162	type	True	100.0	1719	1719	95	conclusive
Blastococcus litoris	strain=GP-S2-8	GCA_003075095.1	2171622	2171622	type	True	85.3236	1097	1719	95	below_threshold
Blastococcus saxobsidens	strain=DSM 44509	GCA_004217455.1	138336	138336	type	True	83.4692	1015	1719	95	below_threshold
Blastococcus aggregatus	strain=DSM 4725	GCA_900221005.1	38502	38502	type	True	83.4411	945	1719	95	below_threshold
Blastococcus saxobsidens	strain=DSM 44509	GCA_002938435.1	138336	138336	type	True	83.4306	1000	1719	95	below_threshold
Blastococcus xanthinilyticus	strain=DSM 46842	GCA_008124835.1	1564164	1564164	type	True	83.3522	1010	1719	95	below_threshold
Blastococcus atacamensis	strain=P6	GCA_002938425.1	2070508	2070508	type	True	83.1841	876	1719	95	below_threshold
Geodermatophilus ruber	strain=DSM 45317	GCA_900114385.1	504800	504800	type	True	82.6047	936	1719	95	below_threshold
Geodermatophilus obscurus	strain=DSM 43160	GCA_000025345.1	1861	1861	type	True	82.5958	973	1719	95	below_threshold
Geodermatophilus sabuli	strain=CECT 8820	GCA_014191795.1	1564158	1564158	type	True	82.5843	975	1719	95	below_threshold
Geodermatophilus chilensis	strain=B12	GCA_002802985.1	2035835	2035835	type	True	82.5715	940	1719	95	below_threshold
Geodermatophilus bullaregiensis	strain=DSM 46841	GCA_016907675.1	1564160	1564160	type	True	82.4294	975	1719	95	below_threshold
Geodermatophilus tzadiensis	strain=DSM 45416	GCA_003002915.1	1137988	1137988	type	True	82.3538	969	1719	95	below_threshold
Geodermatophilus africanus	strain=DSM 45422	GCA_900107105.1	1137993	1137993	type	True	82.3417	978	1719	95	below_threshold
Geodermatophilus normandii	strain=DSM 45417	GCA_003182485.1	1137989	1137989	type	True	82.1798	960	1719	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:20:55,065] [INFO] DFAST Taxonomy check result was written to GCF_006717095.1_ASM671709v1_genomic.fna/tc_result.tsv
[2024-01-24 11:20:55,066] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:20:55,066] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:20:55,066] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb7e16313-8a01-4ecd-998d-d4d73566d3d5/dqc_reference/checkm_data
[2024-01-24 11:20:55,067] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:20:55,117] [INFO] Task started: CheckM
[2024-01-24 11:20:55,117] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006717095.1_ASM671709v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006717095.1_ASM671709v1_genomic.fna/checkm_input GCF_006717095.1_ASM671709v1_genomic.fna/checkm_result
[2024-01-24 11:22:11,373] [INFO] Task succeeded: CheckM
[2024-01-24 11:22:11,375] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:22:11,398] [INFO] ===== Completeness check finished =====
[2024-01-24 11:22:11,398] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:22:11,399] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006717095.1_ASM671709v1_genomic.fna/markers.fasta)
[2024-01-24 11:22:11,399] [INFO] Task started: Blastn
[2024-01-24 11:22:11,399] [INFO] Running command: blastn -query GCF_006717095.1_ASM671709v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb7e16313-8a01-4ecd-998d-d4d73566d3d5/dqc_reference/reference_markers_gtdb.fasta -out GCF_006717095.1_ASM671709v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:22:13,129] [INFO] Task succeeded: Blastn
[2024-01-24 11:22:13,134] [INFO] Selected 12 target genomes.
[2024-01-24 11:22:13,134] [INFO] Target genome list was writen to GCF_006717095.1_ASM671709v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:22:13,182] [INFO] Task started: fastANI
[2024-01-24 11:22:13,182] [INFO] Running command: fastANI --query /var/lib/cwl/stgb5f126ee-43bd-4744-8a4e-5354ad6040f1/GCF_006717095.1_ASM671709v1_genomic.fna.gz --refList GCF_006717095.1_ASM671709v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006717095.1_ASM671709v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:22:28,149] [INFO] Task succeeded: fastANI
[2024-01-24 11:22:28,165] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:22:28,165] [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_006717095.1	s__Blastococcus colisei	100.0	1717	1719	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Blastococcus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900112815.1	s__Blastococcus sp900112815	86.9523	1166	1719	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Blastococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013410015.1	s__Blastococcus sp013410015	85.8624	1135	1719	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Blastococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902805535.1	s__Blastococcus sp902805535	85.4064	820	1719	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Blastococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900230285.1	s__Blastococcus sp900230285	85.3232	1078	1719	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Blastococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188025.1	s__Blastococcus sp900188025	85.2465	1058	1719	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Blastococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004570345.1	s__Blastococcus sp004570345	84.0634	961	1719	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Blastococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000284015.1	s__Blastococcus saxobsidens_A	83.9346	1073	1719	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Blastococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000702465.1	s__Blastococcus sp000702465	83.439	956	1719	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Blastococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003319105.1	s__Blastococcus sp003319105	83.1211	921	1719	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Blastococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010686765.1	s__Geodermatophilus sabuli_A	82.621	972	1719	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Geodermatophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003428645.1	s__Geodermatophilus sp003428645	82.2623	981	1719	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Geodermatophilus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:22:28,167] [INFO] GTDB search result was written to GCF_006717095.1_ASM671709v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:22:28,168] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:22:28,171] [INFO] DFAST_QC result json was written to GCF_006717095.1_ASM671709v1_genomic.fna/dqc_result.json
[2024-01-24 11:22:28,171] [INFO] DFAST_QC completed!
[2024-01-24 11:22:28,171] [INFO] Total running time: 0h2m8s