[2024-01-24 14:30:47,297] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:30:47,299] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:30:47,299] [INFO] DQC Reference Directory: /var/lib/cwl/stg73aeeb31-60b8-49ee-8767-b58e960f4696/dqc_reference
[2024-01-24 14:30:48,515] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:30:48,516] [INFO] Task started: Prodigal
[2024-01-24 14:30:48,516] [INFO] Running command: gunzip -c /var/lib/cwl/stg2820ecf6-64fc-46bd-85bf-1be05e310785/GCF_012395945.1_ASM1239594v1_genomic.fna.gz | prodigal -d GCF_012395945.1_ASM1239594v1_genomic.fna/cds.fna -a GCF_012395945.1_ASM1239594v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:31:12,579] [INFO] Task succeeded: Prodigal
[2024-01-24 14:31:12,580] [INFO] Task started: HMMsearch
[2024-01-24 14:31:12,580] [INFO] Running command: hmmsearch --tblout GCF_012395945.1_ASM1239594v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg73aeeb31-60b8-49ee-8767-b58e960f4696/dqc_reference/reference_markers.hmm GCF_012395945.1_ASM1239594v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:31:13,039] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:31:13,040] [INFO] Found 6/6 markers.
[2024-01-24 14:31:13,141] [INFO] Query marker FASTA was written to GCF_012395945.1_ASM1239594v1_genomic.fna/markers.fasta
[2024-01-24 14:31:13,141] [INFO] Task started: Blastn
[2024-01-24 14:31:13,141] [INFO] Running command: blastn -query GCF_012395945.1_ASM1239594v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg73aeeb31-60b8-49ee-8767-b58e960f4696/dqc_reference/reference_markers.fasta -out GCF_012395945.1_ASM1239594v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:14,711] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:14,715] [INFO] Selected 7 target genomes.
[2024-01-24 14:31:14,716] [INFO] Target genome list was writen to GCF_012395945.1_ASM1239594v1_genomic.fna/target_genomes.txt
[2024-01-24 14:31:14,720] [INFO] Task started: fastANI
[2024-01-24 14:31:14,720] [INFO] Running command: fastANI --query /var/lib/cwl/stg2820ecf6-64fc-46bd-85bf-1be05e310785/GCF_012395945.1_ASM1239594v1_genomic.fna.gz --refList GCF_012395945.1_ASM1239594v1_genomic.fna/target_genomes.txt --output GCF_012395945.1_ASM1239594v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:31:29,246] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:29,247] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg73aeeb31-60b8-49ee-8767-b58e960f4696/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:31:29,247] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg73aeeb31-60b8-49ee-8767-b58e960f4696/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:31:29,255] [INFO] Found 7 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 14:31:29,255] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 14:31:29,256] [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 coubleae	strain=DSM 44960	GCA_012395945.1	356147	356147	type	True	100.0	2198	2198	95	inconclusive
Nocardia coubleae	strain=NBRC 108252	GCA_001612805.1	356147	356147	type	True	99.9903	2178	2198	95	inconclusive
Nocardia ignorata	strain=DSM 44496	GCA_004362495.1	145285	145285	type	True	97.0234	1928	2198	95	inconclusive
Nocardia ignorata	strain=NBRC 108230	GCA_001612905.1	145285	145285	type	True	96.9485	1929	2198	95	inconclusive
Nocardia rosealba	strain=NEAU-G4	GCA_020216065.1	2878563	2878563	type	True	95.5753	1903	2198	95	inconclusive
Nocardia salmonicida	strain=NBRC 13393	GCA_001613085.1	53431	53431	type	True	84.8518	1555	2198	95	below_threshold
Nocardia salmonicida subsp. cummidelens	strain=NBRC 100378	GCA_001612865.1	2800120	53431	type	True	84.6796	1540	2198	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:31:29,257] [INFO] DFAST Taxonomy check result was written to GCF_012395945.1_ASM1239594v1_genomic.fna/tc_result.tsv
[2024-01-24 14:31:29,258] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:31:29,258] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:31:29,258] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg73aeeb31-60b8-49ee-8767-b58e960f4696/dqc_reference/checkm_data
[2024-01-24 14:31:29,260] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:31:29,322] [INFO] Task started: CheckM
[2024-01-24 14:31:29,323] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_012395945.1_ASM1239594v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_012395945.1_ASM1239594v1_genomic.fna/checkm_input GCF_012395945.1_ASM1239594v1_genomic.fna/checkm_result
[2024-01-24 14:32:50,851] [INFO] Task succeeded: CheckM
[2024-01-24 14:32:50,853] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.78%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:32:50,880] [INFO] ===== Completeness check finished =====
[2024-01-24 14:32:50,881] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:32:50,881] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_012395945.1_ASM1239594v1_genomic.fna/markers.fasta)
[2024-01-24 14:32:50,882] [INFO] Task started: Blastn
[2024-01-24 14:32:50,882] [INFO] Running command: blastn -query GCF_012395945.1_ASM1239594v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg73aeeb31-60b8-49ee-8767-b58e960f4696/dqc_reference/reference_markers_gtdb.fasta -out GCF_012395945.1_ASM1239594v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:32:52,917] [INFO] Task succeeded: Blastn
[2024-01-24 14:32:52,921] [INFO] Selected 7 target genomes.
[2024-01-24 14:32:52,921] [INFO] Target genome list was writen to GCF_012395945.1_ASM1239594v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:32:52,926] [INFO] Task started: fastANI
[2024-01-24 14:32:52,926] [INFO] Running command: fastANI --query /var/lib/cwl/stg2820ecf6-64fc-46bd-85bf-1be05e310785/GCF_012395945.1_ASM1239594v1_genomic.fna.gz --refList GCF_012395945.1_ASM1239594v1_genomic.fna/target_genomes_gtdb.txt --output GCF_012395945.1_ASM1239594v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:33:05,890] [INFO] Task succeeded: fastANI
[2024-01-24 14:33:05,897] [INFO] Found 7 fastANI hits (2 hits with ANI > circumscription radius)
[2024-01-24 14:33:05,897] [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_001612805.1	s__Nocardia coubleae	99.9903	2178	2198	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	96.9719	100.00	100.00	1.00	1.00	2	inconclusive
GCF_001612905.1	s__Nocardia ignorata	96.9526	1929	2198	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	96.9719	100.00	100.00	1.00	1.00	2	-
GCF_013839555.1	s__Nocardia sp013839555	95.2941	1496	2198	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.2705	N/A	N/A	N/A	N/A	1	inconclusive
GCF_001612825.1	s__Nocardia caishijiensis	91.7388	1733	2198	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014646295.1	s__Nocardia rhizosphaerihabitans	85.4932	1612	2198	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001613085.1	s__Nocardia salmonicida	84.8393	1557	2198	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	97.01	95.63	0.88	0.85	5	-
GCF_001612665.1	s__Nocardia alba	84.4456	1472	2198	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 14:33:05,899] [INFO] GTDB search result was written to GCF_012395945.1_ASM1239594v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:33:05,900] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:33:05,902] [INFO] DFAST_QC result json was written to GCF_012395945.1_ASM1239594v1_genomic.fna/dqc_result.json
[2024-01-24 14:33:05,902] [INFO] DFAST_QC completed!
[2024-01-24 14:33:05,902] [INFO] Total running time: 0h2m19s