[2024-01-24 12:22:37,844] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:22:37,846] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:22:37,846] [INFO] DQC Reference Directory: /var/lib/cwl/stg5818a922-7aab-4b98-af88-4ae03ea9a9aa/dqc_reference
[2024-01-24 12:22:39,175] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:22:39,176] [INFO] Task started: Prodigal
[2024-01-24 12:22:39,176] [INFO] Running command: gunzip -c /var/lib/cwl/stge350045e-5b3d-4af1-86ab-01a56438f270/GCF_001613505.1_ASM161350v1_genomic.fna.gz | prodigal -d GCF_001613505.1_ASM161350v1_genomic.fna/cds.fna -a GCF_001613505.1_ASM161350v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:23:14,769] [INFO] Task succeeded: Prodigal
[2024-01-24 12:23:14,769] [INFO] Task started: HMMsearch
[2024-01-24 12:23:14,769] [INFO] Running command: hmmsearch --tblout GCF_001613505.1_ASM161350v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5818a922-7aab-4b98-af88-4ae03ea9a9aa/dqc_reference/reference_markers.hmm GCF_001613505.1_ASM161350v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:23:15,106] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:23:15,107] [INFO] Found 6/6 markers.
[2024-01-24 12:23:15,170] [INFO] Query marker FASTA was written to GCF_001613505.1_ASM161350v1_genomic.fna/markers.fasta
[2024-01-24 12:23:15,171] [INFO] Task started: Blastn
[2024-01-24 12:23:15,171] [INFO] Running command: blastn -query GCF_001613505.1_ASM161350v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5818a922-7aab-4b98-af88-4ae03ea9a9aa/dqc_reference/reference_markers.fasta -out GCF_001613505.1_ASM161350v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:16,429] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:16,433] [INFO] Selected 14 target genomes.
[2024-01-24 12:23:16,433] [INFO] Target genome list was writen to GCF_001613505.1_ASM161350v1_genomic.fna/target_genomes.txt
[2024-01-24 12:23:16,441] [INFO] Task started: fastANI
[2024-01-24 12:23:16,442] [INFO] Running command: fastANI --query /var/lib/cwl/stge350045e-5b3d-4af1-86ab-01a56438f270/GCF_001613505.1_ASM161350v1_genomic.fna.gz --refList GCF_001613505.1_ASM161350v1_genomic.fna/target_genomes.txt --output GCF_001613505.1_ASM161350v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:23:43,356] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:43,356] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5818a922-7aab-4b98-af88-4ae03ea9a9aa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:23:43,356] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5818a922-7aab-4b98-af88-4ae03ea9a9aa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:23:43,368] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:23:43,368] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:23:43,368] [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 mikamii	strain=NBRC 108933	GCA_001613505.1	508464	508464	type	True	100.0	2501	2502	95	conclusive
Nocardia kruczakiae	strain=NBRC 101016	GCA_001612965.1	261477	261477	type	True	94.7683	2154	2502	95	below_threshold
Nocardia aobensis	strain=NBRC 100429	GCA_000308375.1	257277	257277	type	True	94.5084	2024	2502	95	below_threshold
Nocardia cerradoensis	strain=NBRC 101014	GCA_000308535.1	85688	85688	type	True	94.3784	1968	2502	95	below_threshold
Nocardia nova	strain=NBRC 15556	GCA_001613005.1	37330	37330	type	True	92.2209	2006	2502	95	below_threshold
Nocardia africana	strain=NBRC 100379	GCA_001612635.1	134964	134964	type	True	92.1883	1974	2502	95	below_threshold
Nocardia elegans	strain=NBRC 108235	GCA_001612845.1	300029	300029	type	True	92.1656	2014	2502	95	below_threshold
Nocardia africana	strain=FDAARGOS_1597	GCA_020731565.1	134964	134964	type	True	92.1494	1991	2502	95	below_threshold
Nocardia vermiculata	strain=JCM 12354	GCA_012396005.1	257274	257274	type	True	83.1428	1412	2502	95	below_threshold
Nocardia vermiculata	strain=NBRC 100427	GCA_001613265.1	257274	257274	type	True	83.0905	1420	2502	95	below_threshold
Nocardia coffeae	strain=CA2R105	GCA_019890715.1	2873381	2873381	type	True	80.7969	1316	2502	95	below_threshold
Nocardia miyunensis	strain=NBRC 108239	GCA_001613065.1	282684	282684	type	True	80.7947	1297	2502	95	below_threshold
Nocardia jiangxiensis	strain=NBRC 101359	GCA_000308615.1	282685	282685	type	True	80.6914	1308	2502	95	below_threshold
Nocardia albiluteola	strain=NEAU-G5	GCA_018860155.1	2842303	2842303	type	True	80.6638	1229	2502	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:23:43,371] [INFO] DFAST Taxonomy check result was written to GCF_001613505.1_ASM161350v1_genomic.fna/tc_result.tsv
[2024-01-24 12:23:43,372] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:23:43,372] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:23:43,372] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5818a922-7aab-4b98-af88-4ae03ea9a9aa/dqc_reference/checkm_data
[2024-01-24 12:23:43,373] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:23:43,442] [INFO] Task started: CheckM
[2024-01-24 12:23:43,442] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001613505.1_ASM161350v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001613505.1_ASM161350v1_genomic.fna/checkm_input GCF_001613505.1_ASM161350v1_genomic.fna/checkm_result
[2024-01-24 12:25:23,308] [INFO] Task succeeded: CheckM
[2024-01-24 12:25:23,309] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.31%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:25:23,344] [INFO] ===== Completeness check finished =====
[2024-01-24 12:25:23,345] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:25:23,345] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001613505.1_ASM161350v1_genomic.fna/markers.fasta)
[2024-01-24 12:25:23,346] [INFO] Task started: Blastn
[2024-01-24 12:25:23,346] [INFO] Running command: blastn -query GCF_001613505.1_ASM161350v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5818a922-7aab-4b98-af88-4ae03ea9a9aa/dqc_reference/reference_markers_gtdb.fasta -out GCF_001613505.1_ASM161350v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:25:25,211] [INFO] Task succeeded: Blastn
[2024-01-24 12:25:25,215] [INFO] Selected 10 target genomes.
[2024-01-24 12:25:25,216] [INFO] Target genome list was writen to GCF_001613505.1_ASM161350v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:25:25,226] [INFO] Task started: fastANI
[2024-01-24 12:25:25,226] [INFO] Running command: fastANI --query /var/lib/cwl/stge350045e-5b3d-4af1-86ab-01a56438f270/GCF_001613505.1_ASM161350v1_genomic.fna.gz --refList GCF_001613505.1_ASM161350v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001613505.1_ASM161350v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:25:44,163] [INFO] Task succeeded: fastANI
[2024-01-24 12:25:44,181] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:25:44,182] [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_001613505.1	s__Nocardia mikamii	100.0	2501	2502	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_001612965.1	s__Nocardia kruczakiae	94.7683	2154	2502	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.6988	N/A	N/A	N/A	N/A	1	-
GCF_015354405.1	s__Nocardia sp015354405	94.5878	2004	2502	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	94.5172	2023	2502	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	94.3606	1970	2502	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0231	99.71	99.43	1.00	0.99	3	-
GCF_001612635.1	s__Nocardia africana	92.1815	1975	2502	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	99.93	99.93	0.99	0.99	2	-
GCF_002933465.1	s__Nocardia nova_B	91.6181	1793	2502	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	99.92	99.92	0.99	0.99	2	-
GCF_000523235.1	s__Nocardia nova_A	84.8458	1730	2502	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001613265.1	s__Nocardia vermiculata	83.077	1423	2502	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000308615.1	s__Nocardia jiangxiensis	80.7026	1306	2502	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 12:25:44,184] [INFO] GTDB search result was written to GCF_001613505.1_ASM161350v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:25:44,185] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:25:44,190] [INFO] DFAST_QC result json was written to GCF_001613505.1_ASM161350v1_genomic.fna/dqc_result.json
[2024-01-24 12:25:44,190] [INFO] DFAST_QC completed!
[2024-01-24 12:25:44,190] [INFO] Total running time: 0h3m6s