[2024-01-24 14:55:18,451] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:55:18,452] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:55:18,453] [INFO] DQC Reference Directory: /var/lib/cwl/stg26595703-9044-4c23-acc6-8bb6fdda4a7d/dqc_reference
[2024-01-24 14:55:19,719] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:55:19,720] [INFO] Task started: Prodigal
[2024-01-24 14:55:19,720] [INFO] Running command: gunzip -c /var/lib/cwl/stgcbc82205-325f-4f0f-ad1f-8ca4bb18ff12/GCF_012395985.1_ASM1239598v1_genomic.fna.gz | prodigal -d GCF_012395985.1_ASM1239598v1_genomic.fna/cds.fna -a GCF_012395985.1_ASM1239598v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:55:53,121] [INFO] Task succeeded: Prodigal
[2024-01-24 14:55:53,122] [INFO] Task started: HMMsearch
[2024-01-24 14:55:53,122] [INFO] Running command: hmmsearch --tblout GCF_012395985.1_ASM1239598v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg26595703-9044-4c23-acc6-8bb6fdda4a7d/dqc_reference/reference_markers.hmm GCF_012395985.1_ASM1239598v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:55:53,433] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:55:53,434] [INFO] Found 6/6 markers.
[2024-01-24 14:55:53,490] [INFO] Query marker FASTA was written to GCF_012395985.1_ASM1239598v1_genomic.fna/markers.fasta
[2024-01-24 14:55:53,491] [INFO] Task started: Blastn
[2024-01-24 14:55:53,491] [INFO] Running command: blastn -query GCF_012395985.1_ASM1239598v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg26595703-9044-4c23-acc6-8bb6fdda4a7d/dqc_reference/reference_markers.fasta -out GCF_012395985.1_ASM1239598v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:55:54,431] [INFO] Task succeeded: Blastn
[2024-01-24 14:55:54,434] [INFO] Selected 8 target genomes.
[2024-01-24 14:55:54,435] [INFO] Target genome list was writen to GCF_012395985.1_ASM1239598v1_genomic.fna/target_genomes.txt
[2024-01-24 14:55:54,439] [INFO] Task started: fastANI
[2024-01-24 14:55:54,439] [INFO] Running command: fastANI --query /var/lib/cwl/stgcbc82205-325f-4f0f-ad1f-8ca4bb18ff12/GCF_012395985.1_ASM1239598v1_genomic.fna.gz --refList GCF_012395985.1_ASM1239598v1_genomic.fna/target_genomes.txt --output GCF_012395985.1_ASM1239598v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:56:09,166] [INFO] Task succeeded: fastANI
[2024-01-24 14:56:09,167] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg26595703-9044-4c23-acc6-8bb6fdda4a7d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:56:09,167] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg26595703-9044-4c23-acc6-8bb6fdda4a7d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:56:09,179] [INFO] Found 8 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:56:09,179] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:56:09,179] [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 speluncae	strain=DSM 45078	GCA_012395985.1	419477	419477	type	True	100.0	2462	2463	95	conclusive
Nocardia speluncae	strain=NBRC 108251	GCA_001613245.1	419477	419477	type	True	99.9828	2430	2463	95	conclusive
Nocardia carnea	strain=NBRC 14403	GCA_000308515.1	37328	37328	type	True	90.4843	1845	2463	95	below_threshold
Nocardia flavorosea	strain=JCM 3332	GCA_012396035.1	53429	53429	type	True	89.8582	1824	2463	95	below_threshold
Nocardia flavorosea	strain=NBRC 108225	GCA_001613385.1	53429	53429	type	True	89.8158	1833	2463	95	below_threshold
Nocardia rhamnosiphila	strain=NBRC 108938	GCA_001613485.1	426716	426716	type	True	82.8766	1467	2463	95	below_threshold
Nocardia rhamnosiphila	strain=NRRL B-24637	GCA_000720425.1	426716	426716	type	True	82.853	1501	2463	95	below_threshold
Nocardia rhamnosiphila	strain=NRRL B-24637	GCA_000721005.1	426716	426716	type	True	82.8486	1483	2463	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:56:09,181] [INFO] DFAST Taxonomy check result was written to GCF_012395985.1_ASM1239598v1_genomic.fna/tc_result.tsv
[2024-01-24 14:56:09,182] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:56:09,182] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:56:09,182] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg26595703-9044-4c23-acc6-8bb6fdda4a7d/dqc_reference/checkm_data
[2024-01-24 14:56:09,184] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:56:09,255] [INFO] Task started: CheckM
[2024-01-24 14:56:09,255] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_012395985.1_ASM1239598v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_012395985.1_ASM1239598v1_genomic.fna/checkm_input GCF_012395985.1_ASM1239598v1_genomic.fna/checkm_result
[2024-01-24 14:57:33,237] [INFO] Task succeeded: CheckM
[2024-01-24 14:57:33,238] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:57:33,255] [INFO] ===== Completeness check finished =====
[2024-01-24 14:57:33,255] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:57:33,255] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_012395985.1_ASM1239598v1_genomic.fna/markers.fasta)
[2024-01-24 14:57:33,256] [INFO] Task started: Blastn
[2024-01-24 14:57:33,256] [INFO] Running command: blastn -query GCF_012395985.1_ASM1239598v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg26595703-9044-4c23-acc6-8bb6fdda4a7d/dqc_reference/reference_markers_gtdb.fasta -out GCF_012395985.1_ASM1239598v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:57:34,617] [INFO] Task succeeded: Blastn
[2024-01-24 14:57:34,626] [INFO] Selected 9 target genomes.
[2024-01-24 14:57:34,627] [INFO] Target genome list was writen to GCF_012395985.1_ASM1239598v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:57:34,638] [INFO] Task started: fastANI
[2024-01-24 14:57:34,639] [INFO] Running command: fastANI --query /var/lib/cwl/stgcbc82205-325f-4f0f-ad1f-8ca4bb18ff12/GCF_012395985.1_ASM1239598v1_genomic.fna.gz --refList GCF_012395985.1_ASM1239598v1_genomic.fna/target_genomes_gtdb.txt --output GCF_012395985.1_ASM1239598v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:57:50,784] [INFO] Task succeeded: fastANI
[2024-01-24 14:57:50,797] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:57:50,798] [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_001613245.1	s__Nocardia speluncae	99.9828	2430	2463	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_000308515.1	s__Nocardia carnea	90.4757	1846	2463	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001613385.1	s__Nocardia flavorosea	89.8216	1831	2463	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	99.99	99.99	1.00	1.00	2	-
GCF_015477805.1	s__Nocardia flavorosea_A	88.5341	1732	2463	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001618425.1	s__Nocardia fusca	83.1334	1462	2463	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	82.8749	1391	2463	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000720425.1	s__Nocardia rhamnosiphila	82.86	1500	2463	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	99.99	99.99	0.99	0.99	3	-
GCF_001613445.1	s__Nocardia grenadensis	82.7983	1396	2463	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	82.7621	1380	2463	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 14:57:50,799] [INFO] GTDB search result was written to GCF_012395985.1_ASM1239598v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:57:50,800] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:57:50,808] [INFO] DFAST_QC result json was written to GCF_012395985.1_ASM1239598v1_genomic.fna/dqc_result.json
[2024-01-24 14:57:50,809] [INFO] DFAST_QC completed!
[2024-01-24 14:57:50,809] [INFO] Total running time: 0h2m32s