[2024-01-24 12:53:57,208] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:53:57,210] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:53:57,210] [INFO] DQC Reference Directory: /var/lib/cwl/stg5bb50816-3d33-4317-b6f0-7af7e6657706/dqc_reference
[2024-01-24 12:53:58,467] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:53:58,468] [INFO] Task started: Prodigal
[2024-01-24 12:53:58,468] [INFO] Running command: gunzip -c /var/lib/cwl/stgd1ab7f58-9500-45f0-bf7c-27d422b5c20e/GCF_001613205.1_ASM161320v1_genomic.fna.gz | prodigal -d GCF_001613205.1_ASM161320v1_genomic.fna/cds.fna -a GCF_001613205.1_ASM161320v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:54:23,516] [INFO] Task succeeded: Prodigal
[2024-01-24 12:54:23,516] [INFO] Task started: HMMsearch
[2024-01-24 12:54:23,516] [INFO] Running command: hmmsearch --tblout GCF_001613205.1_ASM161320v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5bb50816-3d33-4317-b6f0-7af7e6657706/dqc_reference/reference_markers.hmm GCF_001613205.1_ASM161320v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:54:23,899] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:54:23,901] [INFO] Found 6/6 markers.
[2024-01-24 12:54:23,967] [INFO] Query marker FASTA was written to GCF_001613205.1_ASM161320v1_genomic.fna/markers.fasta
[2024-01-24 12:54:23,967] [INFO] Task started: Blastn
[2024-01-24 12:54:23,968] [INFO] Running command: blastn -query GCF_001613205.1_ASM161320v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5bb50816-3d33-4317-b6f0-7af7e6657706/dqc_reference/reference_markers.fasta -out GCF_001613205.1_ASM161320v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:25,122] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:25,126] [INFO] Selected 6 target genomes.
[2024-01-24 12:54:25,126] [INFO] Target genome list was writen to GCF_001613205.1_ASM161320v1_genomic.fna/target_genomes.txt
[2024-01-24 12:54:25,142] [INFO] Task started: fastANI
[2024-01-24 12:54:25,143] [INFO] Running command: fastANI --query /var/lib/cwl/stgd1ab7f58-9500-45f0-bf7c-27d422b5c20e/GCF_001613205.1_ASM161320v1_genomic.fna.gz --refList GCF_001613205.1_ASM161320v1_genomic.fna/target_genomes.txt --output GCF_001613205.1_ASM161320v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:54:36,437] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:36,437] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5bb50816-3d33-4317-b6f0-7af7e6657706/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:54:36,438] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5bb50816-3d33-4317-b6f0-7af7e6657706/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:54:36,445] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:54:36,445] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:54:36,446] [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
Nocardia sienata	strain=NBRC 100364	GCA_001613205.1	248552	248552	type	True	100.0	2205	2211	95	conclusive
Nocardia rhamnosiphila	strain=NRRL B-24637	GCA_000720425.1	426716	426716	type	True	92.1441	1886	2211	95	below_threshold
Nocardia rhamnosiphila	strain=NRRL B-24637	GCA_000721005.1	426716	426716	type	True	92.1358	1888	2211	95	below_threshold
Nocardia rhamnosiphila	strain=NBRC 108938	GCA_001613485.1	426716	426716	type	True	92.1175	1847	2211	95	below_threshold
Nocardia grenadensis	strain=NBRC 108939	GCA_001613445.1	931537	931537	type	True	91.1541	1666	2211	95	below_threshold
Nocardia testacea	strain=NBRC 100365	GCA_000308775.1	248551	248551	type	True	90.7933	1771	2211	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:54:36,447] [INFO] DFAST Taxonomy check result was written to GCF_001613205.1_ASM161320v1_genomic.fna/tc_result.tsv
[2024-01-24 12:54:36,448] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:54:36,448] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:54:36,449] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5bb50816-3d33-4317-b6f0-7af7e6657706/dqc_reference/checkm_data
[2024-01-24 12:54:36,450] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:54:36,518] [INFO] Task started: CheckM
[2024-01-24 12:54:36,519] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001613205.1_ASM161320v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001613205.1_ASM161320v1_genomic.fna/checkm_input GCF_001613205.1_ASM161320v1_genomic.fna/checkm_result
[2024-01-24 12:55:41,966] [INFO] Task succeeded: CheckM
[2024-01-24 12:55:41,967] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 1.85%
Strain heterogeneity: 25.00%
--------------------------------------------------------------------------------
[2024-01-24 12:55:41,990] [INFO] ===== Completeness check finished =====
[2024-01-24 12:55:41,990] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:55:41,990] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001613205.1_ASM161320v1_genomic.fna/markers.fasta)
[2024-01-24 12:55:41,990] [INFO] Task started: Blastn
[2024-01-24 12:55:41,990] [INFO] Running command: blastn -query GCF_001613205.1_ASM161320v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5bb50816-3d33-4317-b6f0-7af7e6657706/dqc_reference/reference_markers_gtdb.fasta -out GCF_001613205.1_ASM161320v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:55:43,497] [INFO] Task succeeded: Blastn
[2024-01-24 12:55:43,500] [INFO] Selected 6 target genomes.
[2024-01-24 12:55:43,500] [INFO] Target genome list was writen to GCF_001613205.1_ASM161320v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:55:43,528] [INFO] Task started: fastANI
[2024-01-24 12:55:43,528] [INFO] Running command: fastANI --query /var/lib/cwl/stgd1ab7f58-9500-45f0-bf7c-27d422b5c20e/GCF_001613205.1_ASM161320v1_genomic.fna.gz --refList GCF_001613205.1_ASM161320v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001613205.1_ASM161320v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:55:54,369] [INFO] Task succeeded: fastANI
[2024-01-24 12:55:54,375] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:55:54,376] [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_001613205.1	s__Nocardia sienata	100.0	2205	2211	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000720425.1	s__Nocardia rhamnosiphila	92.116	1889	2211	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	99.99	99.99	0.99	0.99	3	-
GCF_001618425.1	s__Nocardia fusca	92.0755	1809	2211	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001613445.1	s__Nocardia grenadensis	91.1745	1664	2211	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000308775.1	s__Nocardia testacea	90.7759	1774	2211	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001613245.1	s__Nocardia speluncae	82.6537	1389	2211	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:55:54,377] [INFO] GTDB search result was written to GCF_001613205.1_ASM161320v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:55:54,378] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:55:54,380] [INFO] DFAST_QC result json was written to GCF_001613205.1_ASM161320v1_genomic.fna/dqc_result.json
[2024-01-24 12:55:54,380] [INFO] DFAST_QC completed!
[2024-01-24 12:55:54,380] [INFO] Total running time: 0h1m57s