[2024-01-24 13:55:41,071] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:55:41,074] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:55:41,076] [INFO] DQC Reference Directory: /var/lib/cwl/stg505015db-95a7-42b3-83cc-a35493060738/dqc_reference
[2024-01-24 13:55:42,424] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:55:42,425] [INFO] Task started: Prodigal
[2024-01-24 13:55:42,425] [INFO] Running command: gunzip -c /var/lib/cwl/stg9a5beac8-d47f-4818-86d2-31843e84eb00/GCF_014144965.1_ASM1414496v1_genomic.fna.gz | prodigal -d GCF_014144965.1_ASM1414496v1_genomic.fna/cds.fna -a GCF_014144965.1_ASM1414496v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:55:50,535] [INFO] Task succeeded: Prodigal
[2024-01-24 13:55:50,536] [INFO] Task started: HMMsearch
[2024-01-24 13:55:50,536] [INFO] Running command: hmmsearch --tblout GCF_014144965.1_ASM1414496v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg505015db-95a7-42b3-83cc-a35493060738/dqc_reference/reference_markers.hmm GCF_014144965.1_ASM1414496v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:55:50,796] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:55:50,797] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg9a5beac8-d47f-4818-86d2-31843e84eb00/GCF_014144965.1_ASM1414496v1_genomic.fna.gz]
[2024-01-24 13:55:50,840] [INFO] Query marker FASTA was written to GCF_014144965.1_ASM1414496v1_genomic.fna/markers.fasta
[2024-01-24 13:55:50,840] [INFO] Task started: Blastn
[2024-01-24 13:55:50,841] [INFO] Running command: blastn -query GCF_014144965.1_ASM1414496v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg505015db-95a7-42b3-83cc-a35493060738/dqc_reference/reference_markers.fasta -out GCF_014144965.1_ASM1414496v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:55:52,054] [INFO] Task succeeded: Blastn
[2024-01-24 13:55:52,057] [INFO] Selected 6 target genomes.
[2024-01-24 13:55:52,058] [INFO] Target genome list was writen to GCF_014144965.1_ASM1414496v1_genomic.fna/target_genomes.txt
[2024-01-24 13:55:52,081] [INFO] Task started: fastANI
[2024-01-24 13:55:52,081] [INFO] Running command: fastANI --query /var/lib/cwl/stg9a5beac8-d47f-4818-86d2-31843e84eb00/GCF_014144965.1_ASM1414496v1_genomic.fna.gz --refList GCF_014144965.1_ASM1414496v1_genomic.fna/target_genomes.txt --output GCF_014144965.1_ASM1414496v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:55:55,932] [INFO] Task succeeded: fastANI
[2024-01-24 13:55:55,933] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg505015db-95a7-42b3-83cc-a35493060738/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:55:55,933] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg505015db-95a7-42b3-83cc-a35493060738/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:55:55,940] [INFO] Found 6 fastANI hits (6 hits with ANI > threshold)
[2024-01-24 13:55:55,941] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:55:55,941] [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
Dietzia kunjamensis	strain=K30-10T	GCA_014144965.1	322509	322509	type	True	100.0	761	775	95	inconclusive
Dietzia kunjamensis	strain=DSM 44907	GCA_003610395.1	322509	322509	type	True	99.9937	774	775	95	inconclusive
Dietzia kunjamensis subsp. schimae	strain=DSM 45139	GCA_900182685.1	498198	322509	type	True	97.0118	714	775	95	inconclusive
Dietzia maris	strain=IMV 195	GCA_009806365.1	37915	37915	suspected-type	True	96.9288	591	775	95	inconclusive
Dietzia maris	strain=IMV 195T	GCA_014144855.1	37915	37915	suspected-type	True	96.9127	577	775	95	inconclusive
Dietzia kunjamensis subsp. schimae	strain=YIM 65001T	GCA_014144975.1	498198	322509	type	True	96.235	513	775	95	inconclusive
--------------------------------------------------------------------------------
[2024-01-24 13:55:55,944] [INFO] DFAST Taxonomy check result was written to GCF_014144965.1_ASM1414496v1_genomic.fna/tc_result.tsv
[2024-01-24 13:55:55,945] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:55:55,945] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:55:55,946] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg505015db-95a7-42b3-83cc-a35493060738/dqc_reference/checkm_data
[2024-01-24 13:55:55,948] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:55:55,981] [INFO] Task started: CheckM
[2024-01-24 13:55:55,982] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014144965.1_ASM1414496v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014144965.1_ASM1414496v1_genomic.fna/checkm_input GCF_014144965.1_ASM1414496v1_genomic.fna/checkm_result
[2024-01-24 13:56:24,048] [INFO] Task succeeded: CheckM
[2024-01-24 13:56:24,050] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:56:24,072] [INFO] ===== Completeness check finished =====
[2024-01-24 13:56:24,072] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:56:24,072] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014144965.1_ASM1414496v1_genomic.fna/markers.fasta)
[2024-01-24 13:56:24,073] [INFO] Task started: Blastn
[2024-01-24 13:56:24,073] [INFO] Running command: blastn -query GCF_014144965.1_ASM1414496v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg505015db-95a7-42b3-83cc-a35493060738/dqc_reference/reference_markers_gtdb.fasta -out GCF_014144965.1_ASM1414496v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:56:25,583] [INFO] Task succeeded: Blastn
[2024-01-24 13:56:25,586] [INFO] Selected 7 target genomes.
[2024-01-24 13:56:25,586] [INFO] Target genome list was writen to GCF_014144965.1_ASM1414496v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:56:25,596] [INFO] Task started: fastANI
[2024-01-24 13:56:25,596] [INFO] Running command: fastANI --query /var/lib/cwl/stg9a5beac8-d47f-4818-86d2-31843e84eb00/GCF_014144965.1_ASM1414496v1_genomic.fna.gz --refList GCF_014144965.1_ASM1414496v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014144965.1_ASM1414496v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:56:30,400] [INFO] Task succeeded: fastANI
[2024-01-24 13:56:30,413] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:56:30,413] [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_014144855.1	s__Dietzia maris	96.9127	577	775	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Dietzia	95.0	97.49	96.42	0.87	0.74	16	conclusive
GCF_000186325.1	s__Dietzia cinnamea_A	87.2126	597	775	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Dietzia	95.1735	96.59	96.10	0.87	0.83	4	-
GCF_001571065.1	s__Dietzia cinnamea	86.3604	612	775	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Dietzia	95.1735	97.27	96.55	0.88	0.84	8	-
GCF_003096075.1	s__Dietzia lutea	86.1423	641	775	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Dietzia	95.0	99.99	99.99	1.00	1.00	2	-
GCF_008369165.1	s__Dietzia sp008369165	86.0958	604	775	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Dietzia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014145145.1	s__Dietzia cercidiphylli	84.4791	512	775	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Dietzia	95.0	97.02	96.60	0.78	0.68	10	-
GCF_002289575.1	s__Dietzia natronolimnaea_A	83.7403	600	775	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Dietzia	95.0	96.66	96.66	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:56:30,415] [INFO] GTDB search result was written to GCF_014144965.1_ASM1414496v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:56:30,415] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:56:30,418] [INFO] DFAST_QC result json was written to GCF_014144965.1_ASM1414496v1_genomic.fna/dqc_result.json
[2024-01-24 13:56:30,418] [INFO] DFAST_QC completed!
[2024-01-24 13:56:30,418] [INFO] Total running time: 0h0m49s