[2024-01-24 14:14:19,531] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:14:19,532] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:14:19,533] [INFO] DQC Reference Directory: /var/lib/cwl/stg820fc5d3-de4a-4034-9e6c-77dc25bc9dd7/dqc_reference
[2024-01-24 14:14:20,854] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:14:20,855] [INFO] Task started: Prodigal
[2024-01-24 14:14:20,855] [INFO] Running command: gunzip -c /var/lib/cwl/stg70ad3eb4-38b4-456b-a4c9-aa2c2b07cc68/GCF_002938435.1_ASM293843v1_genomic.fna.gz | prodigal -d GCF_002938435.1_ASM293843v1_genomic.fna/cds.fna -a GCF_002938435.1_ASM293843v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:14:32,904] [INFO] Task succeeded: Prodigal
[2024-01-24 14:14:32,904] [INFO] Task started: HMMsearch
[2024-01-24 14:14:32,904] [INFO] Running command: hmmsearch --tblout GCF_002938435.1_ASM293843v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg820fc5d3-de4a-4034-9e6c-77dc25bc9dd7/dqc_reference/reference_markers.hmm GCF_002938435.1_ASM293843v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:14:33,197] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:14:33,199] [INFO] Found 6/6 markers.
[2024-01-24 14:14:33,262] [INFO] Query marker FASTA was written to GCF_002938435.1_ASM293843v1_genomic.fna/markers.fasta
[2024-01-24 14:14:33,262] [INFO] Task started: Blastn
[2024-01-24 14:14:33,263] [INFO] Running command: blastn -query GCF_002938435.1_ASM293843v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg820fc5d3-de4a-4034-9e6c-77dc25bc9dd7/dqc_reference/reference_markers.fasta -out GCF_002938435.1_ASM293843v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:34,527] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:34,532] [INFO] Selected 13 target genomes.
[2024-01-24 14:14:34,533] [INFO] Target genome list was writen to GCF_002938435.1_ASM293843v1_genomic.fna/target_genomes.txt
[2024-01-24 14:14:34,546] [INFO] Task started: fastANI
[2024-01-24 14:14:34,547] [INFO] Running command: fastANI --query /var/lib/cwl/stg70ad3eb4-38b4-456b-a4c9-aa2c2b07cc68/GCF_002938435.1_ASM293843v1_genomic.fna.gz --refList GCF_002938435.1_ASM293843v1_genomic.fna/target_genomes.txt --output GCF_002938435.1_ASM293843v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:14:50,024] [INFO] Task succeeded: fastANI
[2024-01-24 14:14:50,025] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg820fc5d3-de4a-4034-9e6c-77dc25bc9dd7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:14:50,025] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg820fc5d3-de4a-4034-9e6c-77dc25bc9dd7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:14:50,037] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:14:50,037] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:14:50,038] [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 saxobsidens	strain=DSM 44509	GCA_002938435.1	138336	138336	type	True	100.0	1452	1461	95	conclusive
Blastococcus saxobsidens	strain=DSM 44509	GCA_004217455.1	138336	138336	type	True	99.9949	1456	1461	95	conclusive
Blastococcus atacamensis	strain=P6	GCA_002938425.1	2070508	2070508	type	True	85.8352	924	1461	95	below_threshold
Blastococcus xanthinilyticus	strain=DSM 46842	GCA_008124835.1	1564164	1564164	type	True	85.2957	1010	1461	95	below_threshold
Blastococcus aggregatus	strain=DSM 4725	GCA_900221005.1	38502	38502	type	True	83.9221	914	1461	95	below_threshold
Blastococcus litoris	strain=GP-S2-8	GCA_003075095.1	2171622	2171622	type	True	83.7196	958	1461	95	below_threshold
Geodermatophilus telluris	strain=DSM 45421	GCA_900102745.1	1190417	1190417	type	True	82.9603	900	1461	95	below_threshold
Geodermatophilus chilensis	strain=B12	GCA_002802985.1	2035835	2035835	type	True	82.9553	889	1461	95	below_threshold
Geodermatophilus normandii	strain=DSM 45417	GCA_003182485.1	1137989	1137989	type	True	82.8133	897	1461	95	below_threshold
Geodermatophilus tzadiensis	strain=DSM 45416	GCA_003002915.1	1137988	1137988	type	True	82.8097	928	1461	95	below_threshold
Geodermatophilus poikilotrophus	strain=DSM 44209	GCA_900111455.1	1333667	1333667	type	True	82.7316	919	1461	95	below_threshold
Geodermatophilus aquaeductus	strain=DSM 46834	GCA_900182545.1	1564161	1564161	type	True	82.6454	955	1461	95	below_threshold
Modestobacter roseus	strain=DSM 45764	GCA_007994135.1	1181884	1181884	type	True	81.9031	857	1461	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:14:50,039] [INFO] DFAST Taxonomy check result was written to GCF_002938435.1_ASM293843v1_genomic.fna/tc_result.tsv
[2024-01-24 14:14:50,040] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:14:50,040] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:14:50,040] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg820fc5d3-de4a-4034-9e6c-77dc25bc9dd7/dqc_reference/checkm_data
[2024-01-24 14:14:50,042] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:14:50,091] [INFO] Task started: CheckM
[2024-01-24 14:14:50,091] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002938435.1_ASM293843v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002938435.1_ASM293843v1_genomic.fna/checkm_input GCF_002938435.1_ASM293843v1_genomic.fna/checkm_result
[2024-01-24 14:15:47,555] [INFO] Task succeeded: CheckM
[2024-01-24 14:15:47,556] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:15:47,573] [INFO] ===== Completeness check finished =====
[2024-01-24 14:15:47,573] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:15:47,573] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002938435.1_ASM293843v1_genomic.fna/markers.fasta)
[2024-01-24 14:15:47,573] [INFO] Task started: Blastn
[2024-01-24 14:15:47,574] [INFO] Running command: blastn -query GCF_002938435.1_ASM293843v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg820fc5d3-de4a-4034-9e6c-77dc25bc9dd7/dqc_reference/reference_markers_gtdb.fasta -out GCF_002938435.1_ASM293843v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:49,321] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:49,324] [INFO] Selected 16 target genomes.
[2024-01-24 14:15:49,324] [INFO] Target genome list was writen to GCF_002938435.1_ASM293843v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:15:49,349] [INFO] Task started: fastANI
[2024-01-24 14:15:49,349] [INFO] Running command: fastANI --query /var/lib/cwl/stg70ad3eb4-38b4-456b-a4c9-aa2c2b07cc68/GCF_002938435.1_ASM293843v1_genomic.fna.gz --refList GCF_002938435.1_ASM293843v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002938435.1_ASM293843v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:16:07,357] [INFO] Task succeeded: fastANI
[2024-01-24 14:16:07,370] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:16:07,371] [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_002938435.1	s__Blastococcus saxobsidens	100.0	1452	1461	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Blastococcus	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_010682065.1	s__Blastococcus saxobsidens_B	89.7432	986	1461	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Blastococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003319095.1	s__Blastococcus sp003319095	86.3593	1014	1461	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	86.1864	958	1461	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Blastococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002938425.1	s__Blastococcus atacamensis	85.897	919	1461	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	85.4413	956	1461	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	85.3171	1008	1461	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	85.1975	997	1461	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	84.1902	947	1461	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	83.8825	863	1461	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Blastococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112815.1	s__Blastococcus sp900112815	83.7031	964	1461	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	83.0438	939	1461	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Blastococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102745.1	s__Geodermatophilus telluris	82.8976	907	1461	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Geodermatophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900143215.1	s__Geodermatophilus obscurus_A	82.7174	907	1461	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	82.405	913	1461	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	82.3175	917	1461	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 14:16:07,372] [INFO] GTDB search result was written to GCF_002938435.1_ASM293843v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:16:07,373] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:16:07,377] [INFO] DFAST_QC result json was written to GCF_002938435.1_ASM293843v1_genomic.fna/dqc_result.json
[2024-01-24 14:16:07,377] [INFO] DFAST_QC completed!
[2024-01-24 14:16:07,377] [INFO] Total running time: 0h1m48s