[2024-01-24 11:51:09,578] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:09,580] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:09,580] [INFO] DQC Reference Directory: /var/lib/cwl/stg51bb9c81-8e4f-4eff-a10a-5b5cc8f98959/dqc_reference
[2024-01-24 11:51:10,863] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:10,864] [INFO] Task started: Prodigal
[2024-01-24 11:51:10,864] [INFO] Running command: gunzip -c /var/lib/cwl/stg38ce3699-712f-4516-ab4a-8226e20bb0ed/GCF_020733635.1_ASM2073363v1_genomic.fna.gz | prodigal -d GCF_020733635.1_ASM2073363v1_genomic.fna/cds.fna -a GCF_020733635.1_ASM2073363v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:52,602] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:52,602] [INFO] Task started: HMMsearch
[2024-01-24 11:51:52,602] [INFO] Running command: hmmsearch --tblout GCF_020733635.1_ASM2073363v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg51bb9c81-8e4f-4eff-a10a-5b5cc8f98959/dqc_reference/reference_markers.hmm GCF_020733635.1_ASM2073363v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:52,878] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:52,879] [INFO] Found 6/6 markers.
[2024-01-24 11:51:52,936] [INFO] Query marker FASTA was written to GCF_020733635.1_ASM2073363v1_genomic.fna/markers.fasta
[2024-01-24 11:51:52,936] [INFO] Task started: Blastn
[2024-01-24 11:51:52,936] [INFO] Running command: blastn -query GCF_020733635.1_ASM2073363v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg51bb9c81-8e4f-4eff-a10a-5b5cc8f98959/dqc_reference/reference_markers.fasta -out GCF_020733635.1_ASM2073363v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:54,125] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:54,128] [INFO] Selected 13 target genomes.
[2024-01-24 11:51:54,128] [INFO] Target genome list was writen to GCF_020733635.1_ASM2073363v1_genomic.fna/target_genomes.txt
[2024-01-24 11:51:54,136] [INFO] Task started: fastANI
[2024-01-24 11:51:54,136] [INFO] Running command: fastANI --query /var/lib/cwl/stg38ce3699-712f-4516-ab4a-8226e20bb0ed/GCF_020733635.1_ASM2073363v1_genomic.fna.gz --refList GCF_020733635.1_ASM2073363v1_genomic.fna/target_genomes.txt --output GCF_020733635.1_ASM2073363v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:52:16,751] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:16,752] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg51bb9c81-8e4f-4eff-a10a-5b5cc8f98959/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:52:16,752] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg51bb9c81-8e4f-4eff-a10a-5b5cc8f98959/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:52:16,763] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:52:16,763] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:52:16,764] [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 aobensis	strain=NBRC 100429	GCA_000308375.1	257277	257277	type	True	85.4611	1654	2353	95	below_threshold
Nocardia cerradoensis	strain=NBRC 101014	GCA_000308535.1	85688	85688	type	True	85.4513	1627	2353	95	below_threshold
Nocardia africana	strain=FDAARGOS_1597	GCA_020731565.1	134964	134964	type	True	85.4004	1707	2353	95	below_threshold
Nocardia kruczakiae	strain=NBRC 101016	GCA_001612965.1	261477	261477	type	True	85.394	1694	2353	95	below_threshold
Nocardia africana	strain=NBRC 100379	GCA_001612635.1	134964	134964	type	True	85.3906	1711	2353	95	below_threshold
Nocardia elegans	strain=NBRC 108235	GCA_001612845.1	300029	300029	type	True	85.3033	1684	2353	95	below_threshold
Nocardia mikamii	strain=NBRC 108933	GCA_001613505.1	508464	508464	type	True	85.2811	1716	2353	95	below_threshold
Nocardia nova	strain=NBRC 15556	GCA_001613005.1	37330	37330	type	True	85.2471	1670	2353	95	below_threshold
Nocardia veterana	strain=DSM 44445	GCA_012396305.1	132249	132249	type	True	84.7577	1578	2353	95	below_threshold
Nocardia veterana	strain=NBRC 100344	GCA_000308855.1	132249	132249	type	True	84.7271	1556	2353	95	below_threshold
Nocardia miyunensis	strain=NBRC 108239	GCA_001613065.1	282684	282684	type	True	80.6122	1211	2353	95	below_threshold
Nocardia coffeae	strain=CA2R105	GCA_019890715.1	2873381	2873381	type	True	80.611	1240	2353	95	below_threshold
Nocardia vaccinii	strain=NBRC 15922	GCA_001613305.1	1822	1822	type	True	80.5439	1155	2353	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:52:16,765] [INFO] DFAST Taxonomy check result was written to GCF_020733635.1_ASM2073363v1_genomic.fna/tc_result.tsv
[2024-01-24 11:52:16,766] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:52:16,766] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:52:16,766] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg51bb9c81-8e4f-4eff-a10a-5b5cc8f98959/dqc_reference/checkm_data
[2024-01-24 11:52:16,767] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:52:16,829] [INFO] Task started: CheckM
[2024-01-24 11:52:16,829] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020733635.1_ASM2073363v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020733635.1_ASM2073363v1_genomic.fna/checkm_input GCF_020733635.1_ASM2073363v1_genomic.fna/checkm_result
[2024-01-24 11:54:16,696] [INFO] Task succeeded: CheckM
[2024-01-24 11:54:16,697] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.31%
Strain heterogeneity: 40.00%
--------------------------------------------------------------------------------
[2024-01-24 11:54:16,722] [INFO] ===== Completeness check finished =====
[2024-01-24 11:54:16,722] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:54:16,723] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020733635.1_ASM2073363v1_genomic.fna/markers.fasta)
[2024-01-24 11:54:16,723] [INFO] Task started: Blastn
[2024-01-24 11:54:16,723] [INFO] Running command: blastn -query GCF_020733635.1_ASM2073363v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg51bb9c81-8e4f-4eff-a10a-5b5cc8f98959/dqc_reference/reference_markers_gtdb.fasta -out GCF_020733635.1_ASM2073363v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:54:18,396] [INFO] Task succeeded: Blastn
[2024-01-24 11:54:18,399] [INFO] Selected 13 target genomes.
[2024-01-24 11:54:18,399] [INFO] Target genome list was writen to GCF_020733635.1_ASM2073363v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:54:18,407] [INFO] Task started: fastANI
[2024-01-24 11:54:18,407] [INFO] Running command: fastANI --query /var/lib/cwl/stg38ce3699-712f-4516-ab4a-8226e20bb0ed/GCF_020733635.1_ASM2073363v1_genomic.fna.gz --refList GCF_020733635.1_ASM2073363v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020733635.1_ASM2073363v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:54:40,594] [INFO] Task succeeded: fastANI
[2024-01-24 11:54:40,605] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:54:40,605] [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_000523235.1	s__Nocardia nova_A	85.9048	1713	2353	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000308375.1	s__Nocardia aobensis	85.4801	1651	2353	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.6988	98.11	97.03	0.89	0.86	3	-
GCF_000308535.1	s__Nocardia cerradoensis	85.4684	1624	2353	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0231	99.71	99.43	1.00	0.99	3	-
GCF_001612965.1	s__Nocardia kruczakiae	85.41	1691	2353	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.6988	N/A	N/A	N/A	N/A	1	-
GCF_001612635.1	s__Nocardia africana	85.3953	1710	2353	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	99.93	99.93	0.99	0.99	2	-
GCF_001612845.1	s__Nocardia elegans	85.3027	1684	2353	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	96.9334	99.79	99.59	0.97	0.94	3	-
GCF_001613505.1	s__Nocardia mikamii	85.2986	1713	2353	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001613005.1	s__Nocardia nova	85.2566	1668	2353	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	96.9334	98.75	97.55	0.88	0.84	13	-
GCF_015354405.1	s__Nocardia sp015354405	85.2107	1665	2353	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002933465.1	s__Nocardia nova_B	85.19	1524	2353	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	99.92	99.92	0.99	0.99	2	-
GCF_000308855.1	s__Nocardia veterana	84.7427	1553	2353	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000526215.1	s__Nocardia sp000526215	80.9174	1203	2353	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001613305.1	s__Nocardia vaccinii	80.5432	1155	2353	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 11:54:40,606] [INFO] GTDB search result was written to GCF_020733635.1_ASM2073363v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:54:40,607] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:54:40,610] [INFO] DFAST_QC result json was written to GCF_020733635.1_ASM2073363v1_genomic.fna/dqc_result.json
[2024-01-24 11:54:40,611] [INFO] DFAST_QC completed!
[2024-01-24 11:54:40,611] [INFO] Total running time: 0h3m31s