[2024-01-24 13:13:26,497] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:13:26,502] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:13:26,502] [INFO] DQC Reference Directory: /var/lib/cwl/stg69426958-443e-494a-8341-69ed43ae1a94/dqc_reference
[2024-01-24 13:13:27,832] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:13:27,833] [INFO] Task started: Prodigal
[2024-01-24 13:13:27,833] [INFO] Running command: gunzip -c /var/lib/cwl/stg96d44bcd-8998-40bd-9007-9af5955e178a/GCF_003182485.1_ASM318248v1_genomic.fna.gz | prodigal -d GCF_003182485.1_ASM318248v1_genomic.fna/cds.fna -a GCF_003182485.1_ASM318248v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:40,090] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:40,091] [INFO] Task started: HMMsearch
[2024-01-24 13:13:40,091] [INFO] Running command: hmmsearch --tblout GCF_003182485.1_ASM318248v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg69426958-443e-494a-8341-69ed43ae1a94/dqc_reference/reference_markers.hmm GCF_003182485.1_ASM318248v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:40,397] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:40,398] [INFO] Found 6/6 markers.
[2024-01-24 13:13:40,444] [INFO] Query marker FASTA was written to GCF_003182485.1_ASM318248v1_genomic.fna/markers.fasta
[2024-01-24 13:13:40,445] [INFO] Task started: Blastn
[2024-01-24 13:13:40,445] [INFO] Running command: blastn -query GCF_003182485.1_ASM318248v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg69426958-443e-494a-8341-69ed43ae1a94/dqc_reference/reference_markers.fasta -out GCF_003182485.1_ASM318248v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:41,839] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:41,842] [INFO] Selected 9 target genomes.
[2024-01-24 13:13:41,843] [INFO] Target genome list was writen to GCF_003182485.1_ASM318248v1_genomic.fna/target_genomes.txt
[2024-01-24 13:13:41,848] [INFO] Task started: fastANI
[2024-01-24 13:13:41,848] [INFO] Running command: fastANI --query /var/lib/cwl/stg96d44bcd-8998-40bd-9007-9af5955e178a/GCF_003182485.1_ASM318248v1_genomic.fna.gz --refList GCF_003182485.1_ASM318248v1_genomic.fna/target_genomes.txt --output GCF_003182485.1_ASM318248v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:13:57,881] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:57,882] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg69426958-443e-494a-8341-69ed43ae1a94/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:13:57,882] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg69426958-443e-494a-8341-69ed43ae1a94/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:13:57,892] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:13:57,892] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:13:57,892] [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
Geodermatophilus normandii	strain=DSM 45417	GCA_003182485.1	1137989	1137989	type	True	100.0	1540	1540	95	conclusive
Geodermatophilus aquaeductus	strain=DSM 46834	GCA_900182545.1	1564161	1564161	type	True	93.1684	1327	1540	95	below_threshold
Geodermatophilus amargosae	strain=DSM 46136	GCA_900116515.1	1296565	1296565	type	True	92.1795	1322	1540	95	below_threshold
Geodermatophilus nigrescens	strain=DSM 45408	GCA_900129495.1	1070870	1070870	type	True	88.0866	1251	1540	95	below_threshold
Geodermatophilus saharensis	strain=DSM 45423	GCA_900188205.1	1137994	1137994	type	True	87.8377	1232	1540	95	below_threshold
Geodermatophilus tzadiensis	strain=DSM 45416	GCA_003002915.1	1137988	1137988	type	True	87.7048	1163	1540	95	below_threshold
Geodermatophilus bullaregiensis	strain=DSM 46841	GCA_016907675.1	1564160	1564160	type	True	87.6409	1185	1540	95	below_threshold
Geodermatophilus siccatus	strain=DSM 45419	GCA_900103785.1	1137991	1137991	type	True	84.5211	1074	1540	95	below_threshold
Blastococcus xanthinilyticus	strain=DSM 46842	GCA_008124835.1	1564164	1564164	type	True	82.9107	958	1540	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:13:57,906] [INFO] DFAST Taxonomy check result was written to GCF_003182485.1_ASM318248v1_genomic.fna/tc_result.tsv
[2024-01-24 13:13:57,907] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:13:57,908] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:13:57,908] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg69426958-443e-494a-8341-69ed43ae1a94/dqc_reference/checkm_data
[2024-01-24 13:13:57,911] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:13:57,959] [INFO] Task started: CheckM
[2024-01-24 13:13:57,959] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003182485.1_ASM318248v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003182485.1_ASM318248v1_genomic.fna/checkm_input GCF_003182485.1_ASM318248v1_genomic.fna/checkm_result
[2024-01-24 13:15:14,068] [INFO] Task succeeded: CheckM
[2024-01-24 13:15:14,069] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:15:14,098] [INFO] ===== Completeness check finished =====
[2024-01-24 13:15:14,099] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:15:14,099] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003182485.1_ASM318248v1_genomic.fna/markers.fasta)
[2024-01-24 13:15:14,099] [INFO] Task started: Blastn
[2024-01-24 13:15:14,100] [INFO] Running command: blastn -query GCF_003182485.1_ASM318248v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg69426958-443e-494a-8341-69ed43ae1a94/dqc_reference/reference_markers_gtdb.fasta -out GCF_003182485.1_ASM318248v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:15:16,197] [INFO] Task succeeded: Blastn
[2024-01-24 13:15:16,201] [INFO] Selected 12 target genomes.
[2024-01-24 13:15:16,201] [INFO] Target genome list was writen to GCF_003182485.1_ASM318248v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:15:16,229] [INFO] Task started: fastANI
[2024-01-24 13:15:16,229] [INFO] Running command: fastANI --query /var/lib/cwl/stg96d44bcd-8998-40bd-9007-9af5955e178a/GCF_003182485.1_ASM318248v1_genomic.fna.gz --refList GCF_003182485.1_ASM318248v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003182485.1_ASM318248v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:15:35,228] [INFO] Task succeeded: fastANI
[2024-01-24 13:15:35,242] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:15:35,242] [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_003182485.1	s__Geodermatophilus normandii	100.0	1540	1540	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Geodermatophilus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900182545.1	s__Geodermatophilus aquaeductus	93.1685	1327	1540	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Geodermatophilus	95.0	96.01	96.01	0.85	0.85	2	-
GCF_900116515.1	s__Geodermatophilus amargosae	92.1844	1322	1540	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Geodermatophilus	95.0	95.87	95.87	0.85	0.85	2	-
GCF_900129495.1	s__Geodermatophilus nigrescens	88.0757	1252	1540	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Geodermatophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188205.1	s__Geodermatophilus saharensis	87.8821	1228	1540	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Geodermatophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115395.1	s__Geodermatophilus obscurus_B	87.8327	1222	1540	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Geodermatophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003002915.1	s__Geodermatophilus tzadiensis	87.7173	1162	1540	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Geodermatophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907675.1	s__Geodermatophilus bullaregiensis	87.6041	1191	1540	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Geodermatophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103785.1	s__Geodermatophilus siccatus	84.4483	1083	1540	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Geodermatophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003319095.1	s__Blastococcus sp003319095	83.1097	923	1540	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Blastococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003319175.1	s__Blastococcus sp003319175	82.9788	868	1540	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Blastococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008124835.1	s__Blastococcus xanthinilyticus	82.898	960	1540	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Blastococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:15:35,244] [INFO] GTDB search result was written to GCF_003182485.1_ASM318248v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:15:35,245] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:15:35,251] [INFO] DFAST_QC result json was written to GCF_003182485.1_ASM318248v1_genomic.fna/dqc_result.json
[2024-01-24 13:15:35,251] [INFO] DFAST_QC completed!
[2024-01-24 13:15:35,251] [INFO] Total running time: 0h2m9s