[2024-01-24 14:14:18,836] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:14:18,838] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:14:18,839] [INFO] DQC Reference Directory: /var/lib/cwl/stg1d64611b-b36e-45c0-a4a1-f1cd6a00278c/dqc_reference
[2024-01-24 14:14:20,087] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:14:20,088] [INFO] Task started: Prodigal
[2024-01-24 14:14:20,088] [INFO] Running command: gunzip -c /var/lib/cwl/stge2979bc1-6463-48f9-baeb-73d85a4f0de5/GCF_002846365.1_ASM284636v1_genomic.fna.gz | prodigal -d GCF_002846365.1_ASM284636v1_genomic.fna/cds.fna -a GCF_002846365.1_ASM284636v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:14:48,662] [INFO] Task succeeded: Prodigal
[2024-01-24 14:14:48,662] [INFO] Task started: HMMsearch
[2024-01-24 14:14:48,662] [INFO] Running command: hmmsearch --tblout GCF_002846365.1_ASM284636v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1d64611b-b36e-45c0-a4a1-f1cd6a00278c/dqc_reference/reference_markers.hmm GCF_002846365.1_ASM284636v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:14:48,976] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:14:48,978] [INFO] Found 6/6 markers.
[2024-01-24 14:14:49,044] [INFO] Query marker FASTA was written to GCF_002846365.1_ASM284636v1_genomic.fna/markers.fasta
[2024-01-24 14:14:49,044] [INFO] Task started: Blastn
[2024-01-24 14:14:49,044] [INFO] Running command: blastn -query GCF_002846365.1_ASM284636v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1d64611b-b36e-45c0-a4a1-f1cd6a00278c/dqc_reference/reference_markers.fasta -out GCF_002846365.1_ASM284636v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:50,314] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:50,317] [INFO] Selected 9 target genomes.
[2024-01-24 14:14:50,317] [INFO] Target genome list was writen to GCF_002846365.1_ASM284636v1_genomic.fna/target_genomes.txt
[2024-01-24 14:14:50,325] [INFO] Task started: fastANI
[2024-01-24 14:14:50,325] [INFO] Running command: fastANI --query /var/lib/cwl/stge2979bc1-6463-48f9-baeb-73d85a4f0de5/GCF_002846365.1_ASM284636v1_genomic.fna.gz --refList GCF_002846365.1_ASM284636v1_genomic.fna/target_genomes.txt --output GCF_002846365.1_ASM284636v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:15:08,499] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:08,500] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1d64611b-b36e-45c0-a4a1-f1cd6a00278c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:15:08,500] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1d64611b-b36e-45c0-a4a1-f1cd6a00278c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:15:08,508] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:15:08,509] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:15:08,509] [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 fluminea	strain=DSM 44489	GCA_002846365.1	134984	134984	type	True	100.0	2682	2683	95	conclusive
Nocardia salmonicida	strain=NBRC 13393	GCA_001613085.1	53431	53431	type	True	91.0136	2076	2683	95	below_threshold
Nocardia salmonicida subsp. cummidelens	strain=NBRC 100378	GCA_001612865.1	2800120	53431	type	True	90.6366	2009	2683	95	below_threshold
Nocardia alba	strain=DSM 44684	GCA_004339125.1	225051	225051	type	True	90.6333	1908	2683	95	below_threshold
Nocardia alba	strain=NBRC 108234	GCA_001612665.1	225051	225051	type	True	90.5692	1888	2683	95	below_threshold
Nocardia mangyaensis	strain=Y48	GCA_001886715.1	2213200	2213200	type	True	85.6239	1665	2683	95	below_threshold
Nocardia asteroides	strain=NBRC 15531	GCA_000308355.2	1824	1824	suspected-type	True	85.6194	1660	2683	95	below_threshold
Nocardia asteroides	strain=DSM 43373	GCA_900114685.1	1824	1824	suspected-type	True	85.5977	1687	2683	95	below_threshold
Nocardia asteroides	strain=ATCC 19247	GCA_005863255.1	1824	1824	suspected-type	True	85.5895	1617	2683	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:15:08,510] [INFO] DFAST Taxonomy check result was written to GCF_002846365.1_ASM284636v1_genomic.fna/tc_result.tsv
[2024-01-24 14:15:08,511] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:15:08,511] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:15:08,511] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1d64611b-b36e-45c0-a4a1-f1cd6a00278c/dqc_reference/checkm_data
[2024-01-24 14:15:08,513] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:15:08,583] [INFO] Task started: CheckM
[2024-01-24 14:15:08,583] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002846365.1_ASM284636v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002846365.1_ASM284636v1_genomic.fna/checkm_input GCF_002846365.1_ASM284636v1_genomic.fna/checkm_result
[2024-01-24 14:16:35,636] [INFO] Task succeeded: CheckM
[2024-01-24 14:16:35,638] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:16:35,657] [INFO] ===== Completeness check finished =====
[2024-01-24 14:16:35,658] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:16:35,658] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002846365.1_ASM284636v1_genomic.fna/markers.fasta)
[2024-01-24 14:16:35,658] [INFO] Task started: Blastn
[2024-01-24 14:16:35,658] [INFO] Running command: blastn -query GCF_002846365.1_ASM284636v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1d64611b-b36e-45c0-a4a1-f1cd6a00278c/dqc_reference/reference_markers_gtdb.fasta -out GCF_002846365.1_ASM284636v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:16:37,521] [INFO] Task succeeded: Blastn
[2024-01-24 14:16:37,524] [INFO] Selected 11 target genomes.
[2024-01-24 14:16:37,524] [INFO] Target genome list was writen to GCF_002846365.1_ASM284636v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:16:37,804] [INFO] Task started: fastANI
[2024-01-24 14:16:37,804] [INFO] Running command: fastANI --query /var/lib/cwl/stge2979bc1-6463-48f9-baeb-73d85a4f0de5/GCF_002846365.1_ASM284636v1_genomic.fna.gz --refList GCF_002846365.1_ASM284636v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002846365.1_ASM284636v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:16:59,294] [INFO] Task succeeded: fastANI
[2024-01-24 14:16:59,305] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:16:59,305] [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_002846365.1	s__Nocardia fluminea	100.0	2683	2683	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_001613085.1	s__Nocardia salmonicida	91.0108	2077	2683	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	97.01	95.63	0.88	0.85	5	-
GCF_001612665.1	s__Nocardia alba	90.5692	1888	2683	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	100.00	100.00	1.00	1.00	2	-
GCA_014360565.1	s__Nocardia sp014360565	88.6517	1470	2683	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014646295.1	s__Nocardia rhizosphaerihabitans	85.8885	1746	2683	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900637185.1	s__Nocardia asteroides	85.708	1684	2683	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	100.00	100.00	1.00	1.00	5	-
GCF_001886715.1	s__Nocardia mangyaensis	85.5908	1671	2683	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	85.2011	1706	2683	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001612905.1	s__Nocardia ignorata	84.9187	1615	2683	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	96.9719	100.00	100.00	1.00	1.00	2	-
GCF_001612805.1	s__Nocardia coubleae	84.845	1584	2683	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	96.9719	100.00	100.00	1.00	1.00	2	-
GCF_011801125.1	s__Nocardia brasiliensis_C	80.59	1205	2683	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 14:16:59,307] [INFO] GTDB search result was written to GCF_002846365.1_ASM284636v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:16:59,307] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:16:59,310] [INFO] DFAST_QC result json was written to GCF_002846365.1_ASM284636v1_genomic.fna/dqc_result.json
[2024-01-24 14:16:59,310] [INFO] DFAST_QC completed!
[2024-01-24 14:16:59,310] [INFO] Total running time: 0h2m40s