[2024-01-24 15:18:38,833] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:18:38,835] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:18:38,835] [INFO] DQC Reference Directory: /var/lib/cwl/stg12c8eb1c-31a1-48bf-b7b4-4333651338fa/dqc_reference
[2024-01-24 15:18:40,224] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:18:40,225] [INFO] Task started: Prodigal
[2024-01-24 15:18:40,225] [INFO] Running command: gunzip -c /var/lib/cwl/stg968f5605-3b9b-4f51-b87a-8a64130a52c2/GCF_014648555.1_ASM1464855v1_genomic.fna.gz | prodigal -d GCF_014648555.1_ASM1464855v1_genomic.fna/cds.fna -a GCF_014648555.1_ASM1464855v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:19:04,201] [INFO] Task succeeded: Prodigal
[2024-01-24 15:19:04,201] [INFO] Task started: HMMsearch
[2024-01-24 15:19:04,201] [INFO] Running command: hmmsearch --tblout GCF_014648555.1_ASM1464855v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg12c8eb1c-31a1-48bf-b7b4-4333651338fa/dqc_reference/reference_markers.hmm GCF_014648555.1_ASM1464855v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:19:04,696] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:19:04,697] [INFO] Found 6/6 markers.
[2024-01-24 15:19:04,770] [INFO] Query marker FASTA was written to GCF_014648555.1_ASM1464855v1_genomic.fna/markers.fasta
[2024-01-24 15:19:04,771] [INFO] Task started: Blastn
[2024-01-24 15:19:04,771] [INFO] Running command: blastn -query GCF_014648555.1_ASM1464855v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg12c8eb1c-31a1-48bf-b7b4-4333651338fa/dqc_reference/reference_markers.fasta -out GCF_014648555.1_ASM1464855v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:06,206] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:06,209] [INFO] Selected 11 target genomes.
[2024-01-24 15:19:06,209] [INFO] Target genome list was writen to GCF_014648555.1_ASM1464855v1_genomic.fna/target_genomes.txt
[2024-01-24 15:19:06,224] [INFO] Task started: fastANI
[2024-01-24 15:19:06,225] [INFO] Running command: fastANI --query /var/lib/cwl/stg968f5605-3b9b-4f51-b87a-8a64130a52c2/GCF_014648555.1_ASM1464855v1_genomic.fna.gz --refList GCF_014648555.1_ASM1464855v1_genomic.fna/target_genomes.txt --output GCF_014648555.1_ASM1464855v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:19:34,946] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:34,946] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg12c8eb1c-31a1-48bf-b7b4-4333651338fa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:19:34,947] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg12c8eb1c-31a1-48bf-b7b4-4333651338fa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:19:34,960] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:19:34,961] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:19:34,961] [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
Kitasatospora griseola	strain=JCM 3339	GCA_014648555.1	2064	2064	type	True	100.0	2706	2716	95	conclusive
Kitasatospora cheerisanensis	strain=KCTC 2395	GCA_000696185.1	81942	81942	type	True	91.0579	2102	2716	95	below_threshold
Kitasatospora phosalacinea	strain=NRRL B-16230	GCA_000716545.1	2065	2065	type	True	88.0447	1751	2716	95	below_threshold
Kitasatospora setae	strain=KM-6054	GCA_000269985.1	2066	2066	type	True	87.8009	1871	2716	95	below_threshold
Kitasatospora setae	strain=NRRL B-16185	GCA_000716965.1	2066	2066	type	True	87.7504	1814	2716	95	below_threshold
Kitasatospora paracochleata	strain=DSM 41656	GCA_024172095.1	58354	58354	type	True	84.1503	1608	2716	95	below_threshold
Kitasatospora aureofaciens	strain=NRRL 2209	GCA_000978515.1	1894	1894	type	True	82.7723	1325	2716	95	below_threshold
Kitasatospora purpeofusca	strain=NRRL B-1817	GCA_000718025.1	67352	67352	type	True	82.6606	1592	2716	95	below_threshold
Kitasatospora humi	strain=RB6PN24	GCA_020907985.1	2893891	2893891	type	True	82.0826	1290	2716	95	below_threshold
Streptomyces rubrisoli	strain=DSM 42083	GCA_024436055.1	1387313	1387313	type	True	79.1513	944	2716	95	below_threshold
Streptomyces spinosus	strain=SBTS01	GCA_020400655.1	2872623	2872623	type	True	78.6983	1129	2716	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:19:34,963] [INFO] DFAST Taxonomy check result was written to GCF_014648555.1_ASM1464855v1_genomic.fna/tc_result.tsv
[2024-01-24 15:19:34,964] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:19:34,964] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:19:34,964] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg12c8eb1c-31a1-48bf-b7b4-4333651338fa/dqc_reference/checkm_data
[2024-01-24 15:19:34,966] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:19:35,046] [INFO] Task started: CheckM
[2024-01-24 15:19:35,046] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014648555.1_ASM1464855v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014648555.1_ASM1464855v1_genomic.fna/checkm_input GCF_014648555.1_ASM1464855v1_genomic.fna/checkm_result
[2024-01-24 15:21:30,168] [INFO] Task succeeded: CheckM
[2024-01-24 15:21:30,170] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:21:30,193] [INFO] ===== Completeness check finished =====
[2024-01-24 15:21:30,193] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:21:30,194] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014648555.1_ASM1464855v1_genomic.fna/markers.fasta)
[2024-01-24 15:21:30,194] [INFO] Task started: Blastn
[2024-01-24 15:21:30,194] [INFO] Running command: blastn -query GCF_014648555.1_ASM1464855v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg12c8eb1c-31a1-48bf-b7b4-4333651338fa/dqc_reference/reference_markers_gtdb.fasta -out GCF_014648555.1_ASM1464855v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:21:32,423] [INFO] Task succeeded: Blastn
[2024-01-24 15:21:32,430] [INFO] Selected 6 target genomes.
[2024-01-24 15:21:32,430] [INFO] Target genome list was writen to GCF_014648555.1_ASM1464855v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:21:32,435] [INFO] Task started: fastANI
[2024-01-24 15:21:32,435] [INFO] Running command: fastANI --query /var/lib/cwl/stg968f5605-3b9b-4f51-b87a-8a64130a52c2/GCF_014648555.1_ASM1464855v1_genomic.fna.gz --refList GCF_014648555.1_ASM1464855v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014648555.1_ASM1464855v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:21:49,166] [INFO] Task succeeded: fastANI
[2024-01-24 15:21:49,174] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:21:49,175] [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_014648555.1	s__Kitasatospora griseola	100.0	2706	2716	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	97.80	97.68	0.89	0.89	3	conclusive
GCF_001905465.1	s__Kitasatospora sp001905465	91.9398	2104	2716	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000696185.1	s__Kitasatospora cheerisanensis	91.0783	2099	2716	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002754615.1	s__Kitasatospora sp002754615	88.3516	1860	2716	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	100.00	100.00	0.99	0.99	2	-
GCF_003751605.1	s__Kitasatospora cineracea	88.1134	1900	2716	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	97.58	96.37	0.89	0.86	4	-
GCF_000716545.1	s__Kitasatospora phosalacinea	88.0925	1745	2716	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:21:49,184] [INFO] GTDB search result was written to GCF_014648555.1_ASM1464855v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:21:49,185] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:21:49,188] [INFO] DFAST_QC result json was written to GCF_014648555.1_ASM1464855v1_genomic.fna/dqc_result.json
[2024-01-24 15:21:49,188] [INFO] DFAST_QC completed!
[2024-01-24 15:21:49,189] [INFO] Total running time: 0h3m10s