[2024-01-24 13:31:12,116] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:12,118] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:12,118] [INFO] DQC Reference Directory: /var/lib/cwl/stg53fcc9f4-dde1-489e-b544-e81f4eaeb7ed/dqc_reference
[2024-01-24 13:31:13,276] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:13,277] [INFO] Task started: Prodigal
[2024-01-24 13:31:13,277] [INFO] Running command: gunzip -c /var/lib/cwl/stg818957ce-50b0-49c1-b0e3-b798aeca2a64/GCF_002938425.1_ASM293842v1_genomic.fna.gz | prodigal -d GCF_002938425.1_ASM293842v1_genomic.fna/cds.fna -a GCF_002938425.1_ASM293842v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:31:22,774] [INFO] Task succeeded: Prodigal
[2024-01-24 13:31:22,775] [INFO] Task started: HMMsearch
[2024-01-24 13:31:22,775] [INFO] Running command: hmmsearch --tblout GCF_002938425.1_ASM293842v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg53fcc9f4-dde1-489e-b544-e81f4eaeb7ed/dqc_reference/reference_markers.hmm GCF_002938425.1_ASM293842v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:31:22,966] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:31:22,967] [INFO] Found 6/6 markers.
[2024-01-24 13:31:22,999] [INFO] Query marker FASTA was written to GCF_002938425.1_ASM293842v1_genomic.fna/markers.fasta
[2024-01-24 13:31:23,000] [INFO] Task started: Blastn
[2024-01-24 13:31:23,000] [INFO] Running command: blastn -query GCF_002938425.1_ASM293842v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg53fcc9f4-dde1-489e-b544-e81f4eaeb7ed/dqc_reference/reference_markers.fasta -out GCF_002938425.1_ASM293842v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:31:24,220] [INFO] Task succeeded: Blastn
[2024-01-24 13:31:24,223] [INFO] Selected 11 target genomes.
[2024-01-24 13:31:24,224] [INFO] Target genome list was writen to GCF_002938425.1_ASM293842v1_genomic.fna/target_genomes.txt
[2024-01-24 13:31:24,228] [INFO] Task started: fastANI
[2024-01-24 13:31:24,228] [INFO] Running command: fastANI --query /var/lib/cwl/stg818957ce-50b0-49c1-b0e3-b798aeca2a64/GCF_002938425.1_ASM293842v1_genomic.fna.gz --refList GCF_002938425.1_ASM293842v1_genomic.fna/target_genomes.txt --output GCF_002938425.1_ASM293842v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:31:36,126] [INFO] Task succeeded: fastANI
[2024-01-24 13:31:36,126] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg53fcc9f4-dde1-489e-b544-e81f4eaeb7ed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:31:36,127] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg53fcc9f4-dde1-489e-b544-e81f4eaeb7ed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:31:36,136] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:31:36,136] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:31:36,137] [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 atacamensis	strain=P6	GCA_002938425.1	2070508	2070508	type	True	100.0	1206	1214	95	conclusive
Blastococcus saxobsidens	strain=DSM 44509	GCA_002938435.1	138336	138336	type	True	85.8532	926	1214	95	below_threshold
Blastococcus saxobsidens	strain=DSM 44509	GCA_004217455.1	138336	138336	type	True	85.8132	940	1214	95	below_threshold
Blastococcus xanthinilyticus	strain=DSM 46842	GCA_008124835.1	1564164	1564164	type	True	84.7369	916	1214	95	below_threshold
Blastococcus aggregatus	strain=DSM 4725	GCA_900221005.1	38502	38502	type	True	83.7796	833	1214	95	below_threshold
Blastococcus litoris	strain=GP-S2-8	GCA_003075095.1	2171622	2171622	type	True	83.7774	882	1214	95	below_threshold
Geodermatophilus tzadiensis	strain=DSM 45416	GCA_003002915.1	1137988	1137988	type	True	82.9481	827	1214	95	below_threshold
Geodermatophilus telluris	strain=DSM 45421	GCA_900102745.1	1190417	1190417	type	True	82.8277	837	1214	95	below_threshold
Geodermatophilus nigrescens	strain=DSM 45408	GCA_900129495.1	1070870	1070870	type	True	82.8058	863	1214	95	below_threshold
Geodermatophilus normandii	strain=DSM 45417	GCA_003182485.1	1137989	1137989	type	True	82.7441	841	1214	95	below_threshold
Klenkia taihuensis	strain=DSM 45962	GCA_900112525.1	1225127	1225127	type	True	81.5773	735	1214	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:31:36,138] [INFO] DFAST Taxonomy check result was written to GCF_002938425.1_ASM293842v1_genomic.fna/tc_result.tsv
[2024-01-24 13:31:36,139] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:31:36,140] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:31:36,140] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg53fcc9f4-dde1-489e-b544-e81f4eaeb7ed/dqc_reference/checkm_data
[2024-01-24 13:31:36,141] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:31:36,179] [INFO] Task started: CheckM
[2024-01-24 13:31:36,180] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002938425.1_ASM293842v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002938425.1_ASM293842v1_genomic.fna/checkm_input GCF_002938425.1_ASM293842v1_genomic.fna/checkm_result
[2024-01-24 13:32:23,338] [INFO] Task succeeded: CheckM
[2024-01-24 13:32:23,339] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.39%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:32:23,358] [INFO] ===== Completeness check finished =====
[2024-01-24 13:32:23,359] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:32:23,359] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002938425.1_ASM293842v1_genomic.fna/markers.fasta)
[2024-01-24 13:32:23,359] [INFO] Task started: Blastn
[2024-01-24 13:32:23,359] [INFO] Running command: blastn -query GCF_002938425.1_ASM293842v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg53fcc9f4-dde1-489e-b544-e81f4eaeb7ed/dqc_reference/reference_markers_gtdb.fasta -out GCF_002938425.1_ASM293842v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:25,217] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:25,221] [INFO] Selected 12 target genomes.
[2024-01-24 13:32:25,221] [INFO] Target genome list was writen to GCF_002938425.1_ASM293842v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:32:25,243] [INFO] Task started: fastANI
[2024-01-24 13:32:25,243] [INFO] Running command: fastANI --query /var/lib/cwl/stg818957ce-50b0-49c1-b0e3-b798aeca2a64/GCF_002938425.1_ASM293842v1_genomic.fna.gz --refList GCF_002938425.1_ASM293842v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002938425.1_ASM293842v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:32:37,732] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:37,742] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:32:37,742] [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_002938425.1	s__Blastococcus atacamensis	100.0	1206	1214	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_003319095.1	s__Blastococcus sp003319095	89.0983	973	1214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Blastococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004571075.1	s__Blastococcus sp004571075	87.7731	919	1214	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	86.612	931	1214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Blastococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010682065.1	s__Blastococcus saxobsidens_B	86.0712	861	1214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Blastococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002938435.1	s__Blastococcus saxobsidens	85.8417	927	1214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Blastococcus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_008124835.1	s__Blastococcus xanthinilyticus	84.7145	918	1214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Blastococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003319185.1	s__Blastococcus sp003319185	84.3678	855	1214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Blastococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016612865.1	s__Blastococcus sp016612865	83.8333	830	1214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Blastococcus	95.0	99.95	99.95	0.99	0.99	2	-
GCF_003319105.1	s__Blastococcus sp003319105	83.8001	816	1214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Blastococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000582785.1	s__Blastococcus massiliensis	83.5613	786	1214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Blastococcus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003182485.1	s__Geodermatophilus normandii	82.7647	839	1214	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 13:32:37,749] [INFO] GTDB search result was written to GCF_002938425.1_ASM293842v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:32:37,750] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:32:37,754] [INFO] DFAST_QC result json was written to GCF_002938425.1_ASM293842v1_genomic.fna/dqc_result.json
[2024-01-24 13:32:37,754] [INFO] DFAST_QC completed!
[2024-01-24 13:32:37,754] [INFO] Total running time: 0h1m26s