[2024-01-25 19:54:20,779] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:54:20,780] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:54:20,780] [INFO] DQC Reference Directory: /var/lib/cwl/stge5f85685-b907-40e2-9458-d6baacc1ec9c/dqc_reference
[2024-01-25 19:54:21,903] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:54:21,903] [INFO] Task started: Prodigal
[2024-01-25 19:54:21,904] [INFO] Running command: gunzip -c /var/lib/cwl/stg48b9e06f-60eb-4fb8-8e91-5889870362ff/GCF_000308355.2_ASM30835v2_genomic.fna.gz | prodigal -d GCF_000308355.2_ASM30835v2_genomic.fna/cds.fna -a GCF_000308355.2_ASM30835v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:54:45,745] [INFO] Task succeeded: Prodigal
[2024-01-25 19:54:45,745] [INFO] Task started: HMMsearch
[2024-01-25 19:54:45,745] [INFO] Running command: hmmsearch --tblout GCF_000308355.2_ASM30835v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge5f85685-b907-40e2-9458-d6baacc1ec9c/dqc_reference/reference_markers.hmm GCF_000308355.2_ASM30835v2_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:54:46,011] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:54:46,012] [INFO] Found 6/6 markers.
[2024-01-25 19:54:46,067] [INFO] Query marker FASTA was written to GCF_000308355.2_ASM30835v2_genomic.fna/markers.fasta
[2024-01-25 19:54:46,067] [INFO] Task started: Blastn
[2024-01-25 19:54:46,067] [INFO] Running command: blastn -query GCF_000308355.2_ASM30835v2_genomic.fna/markers.fasta -db /var/lib/cwl/stge5f85685-b907-40e2-9458-d6baacc1ec9c/dqc_reference/reference_markers.fasta -out GCF_000308355.2_ASM30835v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:54:47,337] [INFO] Task succeeded: Blastn
[2024-01-25 19:54:47,341] [INFO] Selected 6 target genomes.
[2024-01-25 19:54:47,341] [INFO] Target genome list was writen to GCF_000308355.2_ASM30835v2_genomic.fna/target_genomes.txt
[2024-01-25 19:54:47,345] [INFO] Task started: fastANI
[2024-01-25 19:54:47,345] [INFO] Running command: fastANI --query /var/lib/cwl/stg48b9e06f-60eb-4fb8-8e91-5889870362ff/GCF_000308355.2_ASM30835v2_genomic.fna.gz --refList GCF_000308355.2_ASM30835v2_genomic.fna/target_genomes.txt --output GCF_000308355.2_ASM30835v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:55:00,756] [INFO] Task succeeded: fastANI
[2024-01-25 19:55:00,757] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge5f85685-b907-40e2-9458-d6baacc1ec9c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:55:00,757] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge5f85685-b907-40e2-9458-d6baacc1ec9c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:55:00,763] [INFO] Found 6 fastANI hits (4 hits with ANI > threshold)
[2024-01-25 19:55:00,763] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:55:00,763] [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 asteroides	strain=NBRC 15531	GCA_000308355.2	1824	1824	suspected-type	True	100.0	2295	2298	95	conclusive
Nocardia asteroides	strain=NCTC11293	GCA_900637185.1	1824	1824	suspected-type	True	99.9992	2297	2298	95	conclusive
Nocardia asteroides	strain=DSM 43373	GCA_900114685.1	1824	1824	suspected-type	True	99.9989	2285	2298	95	conclusive
Nocardia asteroides	strain=ATCC 19247	GCA_005863255.1	1824	1824	suspected-type	True	99.9947	2199	2298	95	conclusive
Nocardia rhizosphaerihabitans	strain=CGMCC 4.7329	GCA_014646295.1	1691570	1691570	type	True	88.6376	1782	2298	95	below_threshold
Nocardia neocaledoniensis	strain=NBRC 108232	GCA_007990735.1	236511	236511	type	True	87.8484	1623	2298	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:55:00,765] [INFO] DFAST Taxonomy check result was written to GCF_000308355.2_ASM30835v2_genomic.fna/tc_result.tsv
[2024-01-25 19:55:00,765] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:55:00,765] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:55:00,765] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge5f85685-b907-40e2-9458-d6baacc1ec9c/dqc_reference/checkm_data
[2024-01-25 19:55:00,766] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:55:00,831] [INFO] Task started: CheckM
[2024-01-25 19:55:00,832] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000308355.2_ASM30835v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000308355.2_ASM30835v2_genomic.fna/checkm_input GCF_000308355.2_ASM30835v2_genomic.fna/checkm_result
[2024-01-25 19:56:27,442] [INFO] Task succeeded: CheckM
[2024-01-25 19:56:27,443] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.78%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:56:27,462] [INFO] ===== Completeness check finished =====
[2024-01-25 19:56:27,463] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:56:27,464] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000308355.2_ASM30835v2_genomic.fna/markers.fasta)
[2024-01-25 19:56:27,464] [INFO] Task started: Blastn
[2024-01-25 19:56:27,464] [INFO] Running command: blastn -query GCF_000308355.2_ASM30835v2_genomic.fna/markers.fasta -db /var/lib/cwl/stge5f85685-b907-40e2-9458-d6baacc1ec9c/dqc_reference/reference_markers_gtdb.fasta -out GCF_000308355.2_ASM30835v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:56:29,388] [INFO] Task succeeded: Blastn
[2024-01-25 19:56:29,391] [INFO] Selected 10 target genomes.
[2024-01-25 19:56:29,391] [INFO] Target genome list was writen to GCF_000308355.2_ASM30835v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:56:29,400] [INFO] Task started: fastANI
[2024-01-25 19:56:29,400] [INFO] Running command: fastANI --query /var/lib/cwl/stg48b9e06f-60eb-4fb8-8e91-5889870362ff/GCF_000308355.2_ASM30835v2_genomic.fna.gz --refList GCF_000308355.2_ASM30835v2_genomic.fna/target_genomes_gtdb.txt --output GCF_000308355.2_ASM30835v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:56:49,887] [INFO] Task succeeded: fastANI
[2024-01-25 19:56:49,893] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:56:49,894] [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_900637185.1	s__Nocardia asteroides	99.9992	2297	2298	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	100.00	100.00	1.00	1.00	5	conclusive
GCF_014646295.1	s__Nocardia rhizosphaerihabitans	88.6151	1786	2298	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003182135.1	s__Nocardia neocaledoniensis	87.8299	1786	2298	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001886715.1	s__Nocardia mangyaensis	86.202	1554	2298	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002846365.1	s__Nocardia fluminea	85.6079	1680	2298	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001612805.1	s__Nocardia coubleae	85.5648	1565	2298	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	96.9719	100.00	100.00	1.00	1.00	2	-
GCF_001612825.1	s__Nocardia caishijiensis	85.288	1502	2298	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013839555.1	s__Nocardia sp013839555	85.2455	1201	2298	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.2705	N/A	N/A	N/A	N/A	1	-
GCF_000308795.1	s__Nocardia thailandica	84.0116	1453	2298	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011801125.1	s__Nocardia brasiliensis_C	81.4782	1242	2298	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:56:49,895] [INFO] GTDB search result was written to GCF_000308355.2_ASM30835v2_genomic.fna/result_gtdb.tsv
[2024-01-25 19:56:49,896] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:56:49,898] [INFO] DFAST_QC result json was written to GCF_000308355.2_ASM30835v2_genomic.fna/dqc_result.json
[2024-01-25 19:56:49,898] [INFO] DFAST_QC completed!
[2024-01-25 19:56:49,899] [INFO] Total running time: 0h2m29s