[2024-01-24 13:17:13,683] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:13,685] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:13,685] [INFO] DQC Reference Directory: /var/lib/cwl/stg40c19dd2-b15d-4d9c-8f27-74a287c9cdb8/dqc_reference
[2024-01-24 13:17:14,975] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:14,976] [INFO] Task started: Prodigal
[2024-01-24 13:17:14,977] [INFO] Running command: gunzip -c /var/lib/cwl/stg6d78e97c-d401-4bc5-a5ed-4ba0dc6b9cad/GCF_000308855.1_ASM30885v1_genomic.fna.gz | prodigal -d GCF_000308855.1_ASM30885v1_genomic.fna/cds.fna -a GCF_000308855.1_ASM30885v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:41,151] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:41,151] [INFO] Task started: HMMsearch
[2024-01-24 13:17:41,152] [INFO] Running command: hmmsearch --tblout GCF_000308855.1_ASM30885v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg40c19dd2-b15d-4d9c-8f27-74a287c9cdb8/dqc_reference/reference_markers.hmm GCF_000308855.1_ASM30885v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:41,520] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:41,522] [INFO] Found 6/6 markers.
[2024-01-24 13:17:41,581] [INFO] Query marker FASTA was written to GCF_000308855.1_ASM30885v1_genomic.fna/markers.fasta
[2024-01-24 13:17:41,582] [INFO] Task started: Blastn
[2024-01-24 13:17:41,582] [INFO] Running command: blastn -query GCF_000308855.1_ASM30885v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg40c19dd2-b15d-4d9c-8f27-74a287c9cdb8/dqc_reference/reference_markers.fasta -out GCF_000308855.1_ASM30885v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:42,810] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:42,814] [INFO] Selected 9 target genomes.
[2024-01-24 13:17:42,815] [INFO] Target genome list was writen to GCF_000308855.1_ASM30885v1_genomic.fna/target_genomes.txt
[2024-01-24 13:17:42,824] [INFO] Task started: fastANI
[2024-01-24 13:17:42,825] [INFO] Running command: fastANI --query /var/lib/cwl/stg6d78e97c-d401-4bc5-a5ed-4ba0dc6b9cad/GCF_000308855.1_ASM30885v1_genomic.fna.gz --refList GCF_000308855.1_ASM30885v1_genomic.fna/target_genomes.txt --output GCF_000308855.1_ASM30885v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:17:58,545] [INFO] Task succeeded: fastANI
[2024-01-24 13:17:58,546] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg40c19dd2-b15d-4d9c-8f27-74a287c9cdb8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:17:58,546] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg40c19dd2-b15d-4d9c-8f27-74a287c9cdb8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:17:58,555] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:17:58,555] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:17:58,555] [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 veterana	strain=NBRC 100344	GCA_000308855.1	132249	132249	type	True	100.0	2167	2180	95	conclusive
Nocardia veterana	strain=DSM 44445	GCA_012396305.1	132249	132249	type	True	99.9987	2178	2180	95	conclusive
Nocardia africana	strain=NBRC 100379	GCA_001612635.1	134964	134964	type	True	86.2483	1656	2180	95	below_threshold
Nocardia africana	strain=FDAARGOS_1597	GCA_020731565.1	134964	134964	type	True	86.1817	1673	2180	95	below_threshold
Nocardia cerradoensis	strain=NBRC 101014	GCA_000308535.1	85688	85688	type	True	86.0984	1532	2180	95	below_threshold
Nocardia elegans	strain=NBRC 108235	GCA_001612845.1	300029	300029	type	True	86.0451	1576	2180	95	below_threshold
Nocardia mikamii	strain=NBRC 108933	GCA_001613505.1	508464	508464	type	True	85.9965	1655	2180	95	below_threshold
Nocardia nova	strain=NBRC 15556	GCA_001613005.1	37330	37330	type	True	85.9759	1555	2180	95	below_threshold
Nocardia kruczakiae	strain=NBRC 101016	GCA_001612965.1	261477	261477	type	True	85.964	1600	2180	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:17:58,557] [INFO] DFAST Taxonomy check result was written to GCF_000308855.1_ASM30885v1_genomic.fna/tc_result.tsv
[2024-01-24 13:17:58,558] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:17:58,558] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:17:58,559] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg40c19dd2-b15d-4d9c-8f27-74a287c9cdb8/dqc_reference/checkm_data
[2024-01-24 13:17:58,560] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:17:58,643] [INFO] Task started: CheckM
[2024-01-24 13:17:58,643] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000308855.1_ASM30885v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000308855.1_ASM30885v1_genomic.fna/checkm_input GCF_000308855.1_ASM30885v1_genomic.fna/checkm_result
[2024-01-24 13:19:16,406] [INFO] Task succeeded: CheckM
[2024-01-24 13:19:16,407] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:19:16,432] [INFO] ===== Completeness check finished =====
[2024-01-24 13:19:16,433] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:19:16,433] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000308855.1_ASM30885v1_genomic.fna/markers.fasta)
[2024-01-24 13:19:16,433] [INFO] Task started: Blastn
[2024-01-24 13:19:16,434] [INFO] Running command: blastn -query GCF_000308855.1_ASM30885v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg40c19dd2-b15d-4d9c-8f27-74a287c9cdb8/dqc_reference/reference_markers_gtdb.fasta -out GCF_000308855.1_ASM30885v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:18,203] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:18,207] [INFO] Selected 10 target genomes.
[2024-01-24 13:19:18,207] [INFO] Target genome list was writen to GCF_000308855.1_ASM30885v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:19:18,214] [INFO] Task started: fastANI
[2024-01-24 13:19:18,214] [INFO] Running command: fastANI --query /var/lib/cwl/stg6d78e97c-d401-4bc5-a5ed-4ba0dc6b9cad/GCF_000308855.1_ASM30885v1_genomic.fna.gz --refList GCF_000308855.1_ASM30885v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000308855.1_ASM30885v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:19:35,897] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:35,915] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:19:35,915] [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_000308855.1	s__Nocardia veterana	100.0	2167	2180	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_001612635.1	s__Nocardia africana	86.2295	1659	2180	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	99.93	99.93	0.99	0.99	2	-
GCF_000308535.1	s__Nocardia cerradoensis	86.1011	1530	2180	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0231	99.71	99.43	1.00	0.99	3	-
GCF_000308375.1	s__Nocardia aobensis	86.0628	1558	2180	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.6988	98.11	97.03	0.89	0.86	3	-
GCF_001612845.1	s__Nocardia elegans	86.0238	1580	2180	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	86.0024	1655	2180	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	85.9803	1555	2180	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	96.9334	98.75	97.55	0.88	0.84	13	-
GCF_001612965.1	s__Nocardia kruczakiae	85.9715	1600	2180	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.6988	N/A	N/A	N/A	N/A	1	-
GCF_002933465.1	s__Nocardia nova_B	85.7519	1539	2180	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	99.92	99.92	0.99	0.99	2	-
GCF_015354405.1	s__Nocardia sp015354405	85.7087	1615	2180	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 13:19:35,918] [INFO] GTDB search result was written to GCF_000308855.1_ASM30885v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:19:35,918] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:19:35,925] [INFO] DFAST_QC result json was written to GCF_000308855.1_ASM30885v1_genomic.fna/dqc_result.json
[2024-01-24 13:19:35,925] [INFO] DFAST_QC completed!
[2024-01-24 13:19:35,925] [INFO] Total running time: 0h2m22s