[2024-01-24 12:53:49,413] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:53:49,415] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:53:49,416] [INFO] DQC Reference Directory: /var/lib/cwl/stg16d8b8cd-9ba5-4b90-bba6-2d9caad87a0f/dqc_reference
[2024-01-24 12:53:51,729] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:53:51,730] [INFO] Task started: Prodigal
[2024-01-24 12:53:51,730] [INFO] Running command: gunzip -c /var/lib/cwl/stg8747b785-d347-4794-aa7b-5c68b146d4e3/GCF_000721005.1_ASM72100v1_genomic.fna.gz | prodigal -d GCF_000721005.1_ASM72100v1_genomic.fna/cds.fna -a GCF_000721005.1_ASM72100v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:54:16,658] [INFO] Task succeeded: Prodigal
[2024-01-24 12:54:16,658] [INFO] Task started: HMMsearch
[2024-01-24 12:54:16,658] [INFO] Running command: hmmsearch --tblout GCF_000721005.1_ASM72100v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg16d8b8cd-9ba5-4b90-bba6-2d9caad87a0f/dqc_reference/reference_markers.hmm GCF_000721005.1_ASM72100v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:54:17,027] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:54:17,028] [INFO] Found 6/6 markers.
[2024-01-24 12:54:17,087] [INFO] Query marker FASTA was written to GCF_000721005.1_ASM72100v1_genomic.fna/markers.fasta
[2024-01-24 12:54:17,088] [INFO] Task started: Blastn
[2024-01-24 12:54:17,088] [INFO] Running command: blastn -query GCF_000721005.1_ASM72100v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg16d8b8cd-9ba5-4b90-bba6-2d9caad87a0f/dqc_reference/reference_markers.fasta -out GCF_000721005.1_ASM72100v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:18,171] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:18,175] [INFO] Selected 6 target genomes.
[2024-01-24 12:54:18,175] [INFO] Target genome list was writen to GCF_000721005.1_ASM72100v1_genomic.fna/target_genomes.txt
[2024-01-24 12:54:18,182] [INFO] Task started: fastANI
[2024-01-24 12:54:18,182] [INFO] Running command: fastANI --query /var/lib/cwl/stg8747b785-d347-4794-aa7b-5c68b146d4e3/GCF_000721005.1_ASM72100v1_genomic.fna.gz --refList GCF_000721005.1_ASM72100v1_genomic.fna/target_genomes.txt --output GCF_000721005.1_ASM72100v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:54:30,057] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:30,062] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg16d8b8cd-9ba5-4b90-bba6-2d9caad87a0f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:54:30,064] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg16d8b8cd-9ba5-4b90-bba6-2d9caad87a0f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:54:30,077] [INFO] Found 6 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 12:54:30,077] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:54:30,077] [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 rhamnosiphila	strain=NRRL B-24637	GCA_000721005.1	426716	426716	type	True	100.0	2526	2527	95	conclusive
Nocardia rhamnosiphila	strain=NRRL B-24637	GCA_000720425.1	426716	426716	type	True	99.9948	2521	2527	95	conclusive
Nocardia rhamnosiphila	strain=NBRC 108938	GCA_001613485.1	426716	426716	type	True	99.9734	2476	2527	95	conclusive
Nocardia sienata	strain=NBRC 100364	GCA_001613205.1	248552	248552	type	True	92.101	1888	2527	95	below_threshold
Nocardia grenadensis	strain=NBRC 108939	GCA_001613445.1	931537	931537	type	True	91.9719	1813	2527	95	below_threshold
Nocardia testacea	strain=NBRC 100365	GCA_000308775.1	248551	248551	type	True	91.187	1944	2527	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:54:30,080] [INFO] DFAST Taxonomy check result was written to GCF_000721005.1_ASM72100v1_genomic.fna/tc_result.tsv
[2024-01-24 12:54:30,081] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:54:30,081] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:54:30,081] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg16d8b8cd-9ba5-4b90-bba6-2d9caad87a0f/dqc_reference/checkm_data
[2024-01-24 12:54:30,083] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:54:30,159] [INFO] Task started: CheckM
[2024-01-24 12:54:30,159] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000721005.1_ASM72100v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000721005.1_ASM72100v1_genomic.fna/checkm_input GCF_000721005.1_ASM72100v1_genomic.fna/checkm_result
[2024-01-24 12:55:45,373] [INFO] Task succeeded: CheckM
[2024-01-24 12:55:45,375] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.31%
Strain heterogeneity: 40.00%
--------------------------------------------------------------------------------
[2024-01-24 12:55:45,403] [INFO] ===== Completeness check finished =====
[2024-01-24 12:55:45,403] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:55:45,403] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000721005.1_ASM72100v1_genomic.fna/markers.fasta)
[2024-01-24 12:55:45,404] [INFO] Task started: Blastn
[2024-01-24 12:55:45,404] [INFO] Running command: blastn -query GCF_000721005.1_ASM72100v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg16d8b8cd-9ba5-4b90-bba6-2d9caad87a0f/dqc_reference/reference_markers_gtdb.fasta -out GCF_000721005.1_ASM72100v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:55:47,034] [INFO] Task succeeded: Blastn
[2024-01-24 12:55:47,038] [INFO] Selected 7 target genomes.
[2024-01-24 12:55:47,038] [INFO] Target genome list was writen to GCF_000721005.1_ASM72100v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:55:47,043] [INFO] Task started: fastANI
[2024-01-24 12:55:47,044] [INFO] Running command: fastANI --query /var/lib/cwl/stg8747b785-d347-4794-aa7b-5c68b146d4e3/GCF_000721005.1_ASM72100v1_genomic.fna.gz --refList GCF_000721005.1_ASM72100v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000721005.1_ASM72100v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:56:01,071] [INFO] Task succeeded: fastANI
[2024-01-24 12:56:01,080] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:56:01,081] [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_000720425.1	s__Nocardia rhamnosiphila	99.9948	2521	2527	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	99.99	99.99	0.99	0.99	3	conclusive
GCF_001618425.1	s__Nocardia fusca	93.7393	2024	2527	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	92.0964	1889	2527	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	91.9743	1813	2527	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	91.202	1942	2527	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014645735.1	s__Nocardia jinanensis	87.1321	1846	2527	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	99.99	99.97	1.00	1.00	3	-
GCF_001613245.1	s__Nocardia speluncae	82.7114	1488	2527	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 12:56:01,082] [INFO] GTDB search result was written to GCF_000721005.1_ASM72100v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:56:01,083] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:56:01,087] [INFO] DFAST_QC result json was written to GCF_000721005.1_ASM72100v1_genomic.fna/dqc_result.json
[2024-01-24 12:56:01,087] [INFO] DFAST_QC completed!
[2024-01-24 12:56:01,087] [INFO] Total running time: 0h2m12s