[2024-01-24 12:22:28,456] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:22:28,549] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:22:28,550] [INFO] DQC Reference Directory: /var/lib/cwl/stg99ed1079-3cad-49f8-8757-6fa5bfe9636f/dqc_reference
[2024-01-24 12:22:29,972] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:22:29,973] [INFO] Task started: Prodigal
[2024-01-24 12:22:29,973] [INFO] Running command: gunzip -c /var/lib/cwl/stg6e523089-354c-4628-ad28-6db49b3bb5ea/GCF_001613445.1_ASM161344v1_genomic.fna.gz | prodigal -d GCF_001613445.1_ASM161344v1_genomic.fna/cds.fna -a GCF_001613445.1_ASM161344v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:22:51,275] [INFO] Task succeeded: Prodigal
[2024-01-24 12:22:51,275] [INFO] Task started: HMMsearch
[2024-01-24 12:22:51,275] [INFO] Running command: hmmsearch --tblout GCF_001613445.1_ASM161344v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg99ed1079-3cad-49f8-8757-6fa5bfe9636f/dqc_reference/reference_markers.hmm GCF_001613445.1_ASM161344v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:51,710] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:51,712] [INFO] Found 6/6 markers.
[2024-01-24 12:22:51,763] [INFO] Query marker FASTA was written to GCF_001613445.1_ASM161344v1_genomic.fna/markers.fasta
[2024-01-24 12:22:51,764] [INFO] Task started: Blastn
[2024-01-24 12:22:51,764] [INFO] Running command: blastn -query GCF_001613445.1_ASM161344v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg99ed1079-3cad-49f8-8757-6fa5bfe9636f/dqc_reference/reference_markers.fasta -out GCF_001613445.1_ASM161344v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:52,885] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:52,890] [INFO] Selected 10 target genomes.
[2024-01-24 12:22:52,890] [INFO] Target genome list was writen to GCF_001613445.1_ASM161344v1_genomic.fna/target_genomes.txt
[2024-01-24 12:22:52,898] [INFO] Task started: fastANI
[2024-01-24 12:22:52,899] [INFO] Running command: fastANI --query /var/lib/cwl/stg6e523089-354c-4628-ad28-6db49b3bb5ea/GCF_001613445.1_ASM161344v1_genomic.fna.gz --refList GCF_001613445.1_ASM161344v1_genomic.fna/target_genomes.txt --output GCF_001613445.1_ASM161344v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:23:10,479] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:10,479] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg99ed1079-3cad-49f8-8757-6fa5bfe9636f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:23:10,479] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg99ed1079-3cad-49f8-8757-6fa5bfe9636f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:23:10,488] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:23:10,489] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:23:10,489] [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 grenadensis	strain=NBRC 108939	GCA_001613445.1	931537	931537	type	True	100.0	2129	2138	95	conclusive
Nocardia rhamnosiphila	strain=NRRL B-24637	GCA_000721005.1	426716	426716	type	True	92.1189	1794	2138	95	below_threshold
Nocardia rhamnosiphila	strain=NBRC 108938	GCA_001613485.1	426716	426716	type	True	92.0878	1778	2138	95	below_threshold
Nocardia rhamnosiphila	strain=NRRL B-24637	GCA_000720425.1	426716	426716	type	True	92.087	1805	2138	95	below_threshold
Nocardia sienata	strain=NBRC 100364	GCA_001613205.1	248552	248552	type	True	91.2158	1653	2138	95	below_threshold
Nocardia testacea	strain=NBRC 100365	GCA_000308775.1	248551	248551	type	True	90.5552	1657	2138	95	below_threshold
Nocardia carnea	strain=NBRC 14403	GCA_000308515.1	37328	37328	type	True	83.1358	1367	2138	95	below_threshold
Nocardia flavorosea	strain=JCM 3332	GCA_012396035.1	53429	53429	type	True	82.9613	1373	2138	95	below_threshold
Nocardia flavorosea	strain=NBRC 108225	GCA_001613385.1	53429	53429	type	True	82.9528	1373	2138	95	below_threshold
Nocardia brevicatena	strain=NBRC 12119	GCA_000308495.1	37327	37327	type	True	80.6469	1065	2138	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:23:10,497] [INFO] DFAST Taxonomy check result was written to GCF_001613445.1_ASM161344v1_genomic.fna/tc_result.tsv
[2024-01-24 12:23:10,501] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:23:10,501] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:23:10,502] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg99ed1079-3cad-49f8-8757-6fa5bfe9636f/dqc_reference/checkm_data
[2024-01-24 12:23:10,503] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:23:10,566] [INFO] Task started: CheckM
[2024-01-24 12:23:10,566] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001613445.1_ASM161344v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001613445.1_ASM161344v1_genomic.fna/checkm_input GCF_001613445.1_ASM161344v1_genomic.fna/checkm_result
[2024-01-24 12:24:09,560] [INFO] Task succeeded: CheckM
[2024-01-24 12:24:09,562] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 6.02%
Strain heterogeneity: 40.00%
--------------------------------------------------------------------------------
[2024-01-24 12:24:09,587] [INFO] ===== Completeness check finished =====
[2024-01-24 12:24:09,587] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:24:09,588] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001613445.1_ASM161344v1_genomic.fna/markers.fasta)
[2024-01-24 12:24:09,588] [INFO] Task started: Blastn
[2024-01-24 12:24:09,588] [INFO] Running command: blastn -query GCF_001613445.1_ASM161344v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg99ed1079-3cad-49f8-8757-6fa5bfe9636f/dqc_reference/reference_markers_gtdb.fasta -out GCF_001613445.1_ASM161344v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:24:11,140] [INFO] Task succeeded: Blastn
[2024-01-24 12:24:11,144] [INFO] Selected 9 target genomes.
[2024-01-24 12:24:11,144] [INFO] Target genome list was writen to GCF_001613445.1_ASM161344v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:24:11,156] [INFO] Task started: fastANI
[2024-01-24 12:24:11,156] [INFO] Running command: fastANI --query /var/lib/cwl/stg6e523089-354c-4628-ad28-6db49b3bb5ea/GCF_001613445.1_ASM161344v1_genomic.fna.gz --refList GCF_001613445.1_ASM161344v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001613445.1_ASM161344v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:24:25,968] [INFO] Task succeeded: fastANI
[2024-01-24 12:24:25,983] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:24:25,983] [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_001613445.1	s__Nocardia grenadensis	100.0	2128	2138	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	92.0908	1804	2138	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	91.8143	1676	2138	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001613205.1	s__Nocardia sienata	91.2056	1654	2138	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	90.5552	1657	2138	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013361595.1	s__Nocardia sp013361595	85.9397	1011	2138	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015477805.1	s__Nocardia flavorosea_A	83.1081	1308	2138	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001613385.1	s__Nocardia flavorosea	82.9736	1369	2138	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000308495.1	s__Nocardia brevicatena	80.6326	1065	2138	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 12:24:25,985] [INFO] GTDB search result was written to GCF_001613445.1_ASM161344v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:24:25,985] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:24:25,989] [INFO] DFAST_QC result json was written to GCF_001613445.1_ASM161344v1_genomic.fna/dqc_result.json
[2024-01-24 12:24:25,989] [INFO] DFAST_QC completed!
[2024-01-24 12:24:25,990] [INFO] Total running time: 0h1m58s