[2024-01-24 15:26:39,510] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:26:39,512] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:26:39,513] [INFO] DQC Reference Directory: /var/lib/cwl/stgd72fe583-3b86-4eb3-bbdf-ba8cbccce2b8/dqc_reference
[2024-01-24 15:26:40,900] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:26:40,901] [INFO] Task started: Prodigal
[2024-01-24 15:26:40,901] [INFO] Running command: gunzip -c /var/lib/cwl/stgfaf713b7-1891-4d4b-8149-53ea66483da2/GCF_001613245.1_ASM161324v1_genomic.fna.gz | prodigal -d GCF_001613245.1_ASM161324v1_genomic.fna/cds.fna -a GCF_001613245.1_ASM161324v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:27:08,260] [INFO] Task succeeded: Prodigal
[2024-01-24 15:27:08,260] [INFO] Task started: HMMsearch
[2024-01-24 15:27:08,260] [INFO] Running command: hmmsearch --tblout GCF_001613245.1_ASM161324v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd72fe583-3b86-4eb3-bbdf-ba8cbccce2b8/dqc_reference/reference_markers.hmm GCF_001613245.1_ASM161324v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:27:08,599] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:27:08,600] [INFO] Found 6/6 markers.
[2024-01-24 15:27:08,663] [INFO] Query marker FASTA was written to GCF_001613245.1_ASM161324v1_genomic.fna/markers.fasta
[2024-01-24 15:27:08,663] [INFO] Task started: Blastn
[2024-01-24 15:27:08,663] [INFO] Running command: blastn -query GCF_001613245.1_ASM161324v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd72fe583-3b86-4eb3-bbdf-ba8cbccce2b8/dqc_reference/reference_markers.fasta -out GCF_001613245.1_ASM161324v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:09,626] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:09,629] [INFO] Selected 8 target genomes.
[2024-01-24 15:27:09,629] [INFO] Target genome list was writen to GCF_001613245.1_ASM161324v1_genomic.fna/target_genomes.txt
[2024-01-24 15:27:09,633] [INFO] Task started: fastANI
[2024-01-24 15:27:09,633] [INFO] Running command: fastANI --query /var/lib/cwl/stgfaf713b7-1891-4d4b-8149-53ea66483da2/GCF_001613245.1_ASM161324v1_genomic.fna.gz --refList GCF_001613245.1_ASM161324v1_genomic.fna/target_genomes.txt --output GCF_001613245.1_ASM161324v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:27:24,819] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:24,819] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd72fe583-3b86-4eb3-bbdf-ba8cbccce2b8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:27:24,820] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd72fe583-3b86-4eb3-bbdf-ba8cbccce2b8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:27:24,831] [INFO] Found 8 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 15:27:24,831] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:27:24,831] [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=NBRC 108251	GCA_001613245.1	419477	419477	type	True	100.0	2432	2439	95	conclusive
Nocardia speluncae	strain=DSM 45078	GCA_012395985.1	419477	419477	type	True	99.9997	2439	2439	95	conclusive
Nocardia carnea	strain=NBRC 14403	GCA_000308515.1	37328	37328	type	True	90.5253	1821	2439	95	below_threshold
Nocardia flavorosea	strain=NBRC 108225	GCA_001613385.1	53429	53429	type	True	89.8768	1801	2439	95	below_threshold
Nocardia flavorosea	strain=JCM 3332	GCA_012396035.1	53429	53429	type	True	89.8412	1808	2439	95	below_threshold
Nocardia rhamnosiphila	strain=NRRL B-24637	GCA_000721005.1	426716	426716	type	True	82.9357	1474	2439	95	below_threshold
Nocardia rhamnosiphila	strain=NBRC 108938	GCA_001613485.1	426716	426716	type	True	82.9294	1449	2439	95	below_threshold
Nocardia rhamnosiphila	strain=NRRL B-24637	GCA_000720425.1	426716	426716	type	True	82.8831	1489	2439	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:27:24,833] [INFO] DFAST Taxonomy check result was written to GCF_001613245.1_ASM161324v1_genomic.fna/tc_result.tsv
[2024-01-24 15:27:24,833] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:27:24,834] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:27:24,834] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd72fe583-3b86-4eb3-bbdf-ba8cbccce2b8/dqc_reference/checkm_data
[2024-01-24 15:27:24,835] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:27:24,905] [INFO] Task started: CheckM
[2024-01-24 15:27:24,905] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001613245.1_ASM161324v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001613245.1_ASM161324v1_genomic.fna/checkm_input GCF_001613245.1_ASM161324v1_genomic.fna/checkm_result
[2024-01-24 15:28:36,394] [INFO] Task succeeded: CheckM
[2024-01-24 15:28:36,396] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.63%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:28:36,421] [INFO] ===== Completeness check finished =====
[2024-01-24 15:28:36,421] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:28:36,422] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001613245.1_ASM161324v1_genomic.fna/markers.fasta)
[2024-01-24 15:28:36,422] [INFO] Task started: Blastn
[2024-01-24 15:28:36,422] [INFO] Running command: blastn -query GCF_001613245.1_ASM161324v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd72fe583-3b86-4eb3-bbdf-ba8cbccce2b8/dqc_reference/reference_markers_gtdb.fasta -out GCF_001613245.1_ASM161324v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:28:37,844] [INFO] Task succeeded: Blastn
[2024-01-24 15:28:37,849] [INFO] Selected 9 target genomes.
[2024-01-24 15:28:37,849] [INFO] Target genome list was writen to GCF_001613245.1_ASM161324v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:28:37,857] [INFO] Task started: fastANI
[2024-01-24 15:28:37,857] [INFO] Running command: fastANI --query /var/lib/cwl/stgfaf713b7-1891-4d4b-8149-53ea66483da2/GCF_001613245.1_ASM161324v1_genomic.fna.gz --refList GCF_001613245.1_ASM161324v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001613245.1_ASM161324v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:28:54,175] [INFO] Task succeeded: fastANI
[2024-01-24 15:28:54,191] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:28:54,191] [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	100.0	2432	2439	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	90.512	1823	2439	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	89.8768	1801	2439	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	88.6005	1708	2439	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	83.0801	1451	2439	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	82.912	1372	2439	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	82.8602	1493	2439	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	82.8198	1369	2439	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	82.7276	1355	2439	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 15:28:54,193] [INFO] GTDB search result was written to GCF_001613245.1_ASM161324v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:28:54,194] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:28:54,197] [INFO] DFAST_QC result json was written to GCF_001613245.1_ASM161324v1_genomic.fna/dqc_result.json
[2024-01-24 15:28:54,198] [INFO] DFAST_QC completed!
[2024-01-24 15:28:54,198] [INFO] Total running time: 0h2m15s