[2023-06-29 14:26:42,826] [INFO] DFAST_QC pipeline started.
[2023-06-29 14:26:42,831] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 14:26:42,832] [INFO] DQC Reference Directory: /var/lib/cwl/stg4048a684-cede-4aa1-b57d-71ca12a829e5/dqc_reference
[2023-06-29 14:26:44,079] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 14:26:44,080] [INFO] Task started: Prodigal
[2023-06-29 14:26:44,080] [INFO] Running command: gunzip -c /var/lib/cwl/stgd4b7f60e-1164-4f7c-aa66-0ccfccf2c7d9/GCA_021741585.1_ASM2174158v1_genomic.fna.gz | prodigal -d GCA_021741585.1_ASM2174158v1_genomic.fna/cds.fna -a GCA_021741585.1_ASM2174158v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 14:26:48,107] [INFO] Task succeeded: Prodigal
[2023-06-29 14:26:48,108] [INFO] Task started: HMMsearch
[2023-06-29 14:26:48,108] [INFO] Running command: hmmsearch --tblout GCA_021741585.1_ASM2174158v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4048a684-cede-4aa1-b57d-71ca12a829e5/dqc_reference/reference_markers.hmm GCA_021741585.1_ASM2174158v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 14:26:48,350] [INFO] Task succeeded: HMMsearch
[2023-06-29 14:26:48,351] [INFO] Found 6/6 markers.
[2023-06-29 14:26:48,377] [INFO] Query marker FASTA was written to GCA_021741585.1_ASM2174158v1_genomic.fna/markers.fasta
[2023-06-29 14:26:48,378] [INFO] Task started: Blastn
[2023-06-29 14:26:48,378] [INFO] Running command: blastn -query GCA_021741585.1_ASM2174158v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4048a684-cede-4aa1-b57d-71ca12a829e5/dqc_reference/reference_markers.fasta -out GCA_021741585.1_ASM2174158v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 14:26:49,090] [INFO] Task succeeded: Blastn
[2023-06-29 14:26:49,102] [INFO] Selected 19 target genomes.
[2023-06-29 14:26:49,102] [INFO] Target genome list was writen to GCA_021741585.1_ASM2174158v1_genomic.fna/target_genomes.txt
[2023-06-29 14:26:49,109] [INFO] Task started: fastANI
[2023-06-29 14:26:49,109] [INFO] Running command: fastANI --query /var/lib/cwl/stgd4b7f60e-1164-4f7c-aa66-0ccfccf2c7d9/GCA_021741585.1_ASM2174158v1_genomic.fna.gz --refList GCA_021741585.1_ASM2174158v1_genomic.fna/target_genomes.txt --output GCA_021741585.1_ASM2174158v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 14:26:58,224] [INFO] Task succeeded: fastANI
[2023-06-29 14:26:58,225] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4048a684-cede-4aa1-b57d-71ca12a829e5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 14:26:58,225] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4048a684-cede-4aa1-b57d-71ca12a829e5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 14:26:58,231] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 14:26:58,232] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 14:26:58,232] [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
Aquiluna borgnonia	strain=15G-AUS-rot	GCA_013283855.1	2499157	2499157	type	True	78.5635	121	461	95	below_threshold
Rhodoluna lacicola	strain=MWH-Ta8	GCA_000699505.1	529884	529884	type	True	78.1093	53	461	95	below_threshold
Candidatus Rhodoluna planktonica	strain=MWH-Dar1	GCA_001854225.1	535712	535712	type	True	78.0511	58	461	95	below_threshold
Rhodoluna limnophila	strain=27D-LEPI	GCA_005845365.1	232537	232537	type	True	77.5735	72	461	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 14:26:58,234] [INFO] DFAST Taxonomy check result was written to GCA_021741585.1_ASM2174158v1_genomic.fna/tc_result.tsv
[2023-06-29 14:26:58,234] [INFO] ===== Taxonomy check completed =====
[2023-06-29 14:26:58,235] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 14:26:58,235] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4048a684-cede-4aa1-b57d-71ca12a829e5/dqc_reference/checkm_data
[2023-06-29 14:26:58,236] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 14:26:58,253] [INFO] Task started: CheckM
[2023-06-29 14:26:58,253] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_021741585.1_ASM2174158v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_021741585.1_ASM2174158v1_genomic.fna/checkm_input GCA_021741585.1_ASM2174158v1_genomic.fna/checkm_result
[2023-06-29 14:27:17,815] [INFO] Task succeeded: CheckM
[2023-06-29 14:27:17,816] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 14:27:17,835] [INFO] ===== Completeness check finished =====
[2023-06-29 14:27:17,836] [INFO] ===== Start GTDB Search =====
[2023-06-29 14:27:17,836] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_021741585.1_ASM2174158v1_genomic.fna/markers.fasta)
[2023-06-29 14:27:17,837] [INFO] Task started: Blastn
[2023-06-29 14:27:17,837] [INFO] Running command: blastn -query GCA_021741585.1_ASM2174158v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4048a684-cede-4aa1-b57d-71ca12a829e5/dqc_reference/reference_markers_gtdb.fasta -out GCA_021741585.1_ASM2174158v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 14:27:18,940] [INFO] Task succeeded: Blastn
[2023-06-29 14:27:18,945] [INFO] Selected 22 target genomes.
[2023-06-29 14:27:18,946] [INFO] Target genome list was writen to GCA_021741585.1_ASM2174158v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 14:27:18,959] [INFO] Task started: fastANI
[2023-06-29 14:27:18,959] [INFO] Running command: fastANI --query /var/lib/cwl/stgd4b7f60e-1164-4f7c-aa66-0ccfccf2c7d9/GCA_021741585.1_ASM2174158v1_genomic.fna.gz --refList GCA_021741585.1_ASM2174158v1_genomic.fna/target_genomes_gtdb.txt --output GCA_021741585.1_ASM2174158v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 14:27:24,933] [INFO] Task succeeded: fastANI
[2023-06-29 14:27:24,944] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 14:27:24,944] [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
GCA_018402685.1	s__Aquiluna sp018402685	78.9389	110	461	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Aquiluna	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013283855.1	s__Aquiluna borgnonia	78.5635	121	461	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Aquiluna	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002479805.1	s__Aquiluna sp002479805	78.5239	128	461	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Aquiluna	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002333405.1	s__Aquiluna sp002333405	78.4683	106	461	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Aquiluna	95.0	97.62	97.20	0.92	0.89	8	-
GCA_017854485.1	s__Aquiluna sp017854485	78.3726	100	461	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Aquiluna	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905182225.1	s__Aquiluna sp905182225	78.2763	64	461	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Aquiluna	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009923455.1	s__Aquiluna sp009923455	78.2109	110	461	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Aquiluna	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000257665.1	s__Aquiluna sp000257665	78.1077	68	461	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Aquiluna	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003149555.1	s__Aquiluna sp003149555	78.0406	76	461	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Aquiluna	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100865.1	s__Aquiluna sp900100865	77.9089	102	461	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Aquiluna	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002478545.1	s__Aquiluna sp002478545	77.7363	74	461	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Aquiluna	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018402615.1	s__Aquiluna sp018402615	77.2541	60	461	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Aquiluna	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 14:27:24,949] [INFO] GTDB search result was written to GCA_021741585.1_ASM2174158v1_genomic.fna/result_gtdb.tsv
[2023-06-29 14:27:24,949] [INFO] ===== GTDB Search completed =====
[2023-06-29 14:27:24,953] [INFO] DFAST_QC result json was written to GCA_021741585.1_ASM2174158v1_genomic.fna/dqc_result.json
[2023-06-29 14:27:24,953] [INFO] DFAST_QC completed!
[2023-06-29 14:27:24,953] [INFO] Total running time: 0h0m42s