[2024-01-24 13:09:33,975] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:09:33,977] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:09:33,978] [INFO] DQC Reference Directory: /var/lib/cwl/stg1b5bc96a-087f-4cbe-898a-3a22c35ada72/dqc_reference
[2024-01-24 13:09:35,216] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:09:35,217] [INFO] Task started: Prodigal
[2024-01-24 13:09:35,217] [INFO] Running command: gunzip -c /var/lib/cwl/stgfae65d70-c072-42e7-867e-3cf88347991b/GCF_019222765.1_ASM1922276v1_genomic.fna.gz | prodigal -d GCF_019222765.1_ASM1922276v1_genomic.fna/cds.fna -a GCF_019222765.1_ASM1922276v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:10:36,941] [INFO] Task succeeded: Prodigal
[2024-01-24 13:10:36,941] [INFO] Task started: HMMsearch
[2024-01-24 13:10:36,941] [INFO] Running command: hmmsearch --tblout GCF_019222765.1_ASM1922276v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1b5bc96a-087f-4cbe-898a-3a22c35ada72/dqc_reference/reference_markers.hmm GCF_019222765.1_ASM1922276v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:10:37,251] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:10:37,252] [INFO] Found 6/6 markers.
[2024-01-24 13:10:37,334] [INFO] Query marker FASTA was written to GCF_019222765.1_ASM1922276v1_genomic.fna/markers.fasta
[2024-01-24 13:10:37,334] [INFO] Task started: Blastn
[2024-01-24 13:10:37,335] [INFO] Running command: blastn -query GCF_019222765.1_ASM1922276v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1b5bc96a-087f-4cbe-898a-3a22c35ada72/dqc_reference/reference_markers.fasta -out GCF_019222765.1_ASM1922276v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:38,562] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:38,565] [INFO] Selected 11 target genomes.
[2024-01-24 13:10:38,566] [INFO] Target genome list was writen to GCF_019222765.1_ASM1922276v1_genomic.fna/target_genomes.txt
[2024-01-24 13:10:38,619] [INFO] Task started: fastANI
[2024-01-24 13:10:38,619] [INFO] Running command: fastANI --query /var/lib/cwl/stgfae65d70-c072-42e7-867e-3cf88347991b/GCF_019222765.1_ASM1922276v1_genomic.fna.gz --refList GCF_019222765.1_ASM1922276v1_genomic.fna/target_genomes.txt --output GCF_019222765.1_ASM1922276v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:11:01,169] [INFO] Task succeeded: fastANI
[2024-01-24 13:11:01,170] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1b5bc96a-087f-4cbe-898a-3a22c35ada72/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:11:01,170] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1b5bc96a-087f-4cbe-898a-3a22c35ada72/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:11:01,180] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:11:01,180] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:11:01,180] [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 iowensis	strain=NRRL 5646	GCA_019222765.1	204891	204891	type	True	100.0	2981	2982	95	conclusive
Nocardia suismassiliense	strain=S-137	GCA_900269665.1	2077092	2077092	type	True	87.2123	2108	2982	95	below_threshold
Nocardia ninae	strain=NBRC 108245	GCA_007990755.1	356145	356145	type	True	87.0705	2083	2982	95	below_threshold
Nocardia colli	strain=CICC 11023	GCA_008704205.1	2545717	2545717	type	True	86.6102	2028	2982	95	below_threshold
Nocardia altamirensis	strain=NBRC 108246	GCA_001612685.1	472158	472158	type	True	85.3116	1936	2982	95	below_threshold
Nocardia brasiliensis	strain=NBRC 14402	GCA_000308475.2	37326	37326	suspected-type	True	85.0692	1873	2982	95	below_threshold
Nocardia vulneris	strain=NBRC 108936	GCA_001613425.1	1141657	1141657	type	True	85.0663	1911	2982	95	below_threshold
Nocardia vulneris	strain=W9851	GCA_000811985.1	1141657	1141657	type	True	85.0306	1889	2982	95	below_threshold
Nocardia rhizosphaerihabitans	strain=CGMCC 4.7329	GCA_014646295.1	1691570	1691570	type	True	80.9335	1204	2982	95	below_threshold
Nocardia salmonicida subsp. cummidelens	strain=NBRC 100378	GCA_001612865.1	2800120	53431	type	True	80.2639	1138	2982	95	below_threshold
Nocardia salmonicida	strain=NBRC 13393	GCA_001613085.1	53431	53431	type	True	80.2358	1140	2982	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:11:01,183] [INFO] DFAST Taxonomy check result was written to GCF_019222765.1_ASM1922276v1_genomic.fna/tc_result.tsv
[2024-01-24 13:11:01,184] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:11:01,184] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:11:01,184] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1b5bc96a-087f-4cbe-898a-3a22c35ada72/dqc_reference/checkm_data
[2024-01-24 13:11:01,186] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:11:01,262] [INFO] Task started: CheckM
[2024-01-24 13:11:01,262] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019222765.1_ASM1922276v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019222765.1_ASM1922276v1_genomic.fna/checkm_input GCF_019222765.1_ASM1922276v1_genomic.fna/checkm_result
[2024-01-24 13:13:41,241] [INFO] Task succeeded: CheckM
[2024-01-24 13:13:41,242] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.31%
Strain heterogeneity: 40.00%
--------------------------------------------------------------------------------
[2024-01-24 13:13:41,281] [INFO] ===== Completeness check finished =====
[2024-01-24 13:13:41,282] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:13:41,282] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019222765.1_ASM1922276v1_genomic.fna/markers.fasta)
[2024-01-24 13:13:41,282] [INFO] Task started: Blastn
[2024-01-24 13:13:41,282] [INFO] Running command: blastn -query GCF_019222765.1_ASM1922276v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1b5bc96a-087f-4cbe-898a-3a22c35ada72/dqc_reference/reference_markers_gtdb.fasta -out GCF_019222765.1_ASM1922276v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:43,183] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:43,187] [INFO] Selected 11 target genomes.
[2024-01-24 13:13:43,187] [INFO] Target genome list was writen to GCF_019222765.1_ASM1922276v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:13:43,240] [INFO] Task started: fastANI
[2024-01-24 13:13:43,240] [INFO] Running command: fastANI --query /var/lib/cwl/stgfae65d70-c072-42e7-867e-3cf88347991b/GCF_019222765.1_ASM1922276v1_genomic.fna.gz --refList GCF_019222765.1_ASM1922276v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019222765.1_ASM1922276v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:14:07,990] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:08,001] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:14:08,001] [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_019222765.1	s__Nocardia iowensis	100.0	2981	2982	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_900269665.1	s__Nocardia suismassiliense	87.1976	2109	2982	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	95.20	95.20	0.87	0.87	2	-
GCF_007990755.1	s__Nocardia ninae	87.0635	2084	2982	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	95.51	95.51	0.86	0.86	2	-
GCF_008704205.1	s__Nocardia colli	86.6045	2030	2982	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001612685.1	s__Nocardia altamirensis	85.309	1936	2982	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001613425.1	s__Nocardia vulneris	85.061	1911	2982	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.8238	100.00	100.00	0.99	0.99	2	-
GCF_000308475.2	s__Nocardia brasiliensis	85.0574	1875	2982	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.8238	100.00	99.99	1.00	1.00	3	-
GCF_000250675.2	s__Nocardia brasiliensis_B	85.0164	1922	2982	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.2192	100.00	100.00	1.00	1.00	2	-
GCF_000284035.1	s__Nocardia cyriacigeorgica_B	81.471	1183	2982	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	98.41	98.27	0.93	0.91	5	-
GCF_010858045.1	s__Nocardia cyriacigeorgica_E	81.4255	1148	2982	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	98.94	98.91	0.92	0.91	4	-
GCF_014646295.1	s__Nocardia rhizosphaerihabitans	80.9521	1200	2982	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:14:08,002] [INFO] GTDB search result was written to GCF_019222765.1_ASM1922276v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:14:08,003] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:14:08,006] [INFO] DFAST_QC result json was written to GCF_019222765.1_ASM1922276v1_genomic.fna/dqc_result.json
[2024-01-24 13:14:08,007] [INFO] DFAST_QC completed!
[2024-01-24 13:14:08,007] [INFO] Total running time: 0h4m34s