[2024-01-24 13:31:27,759] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:27,760] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:27,760] [INFO] DQC Reference Directory: /var/lib/cwl/stgd1b1e8a0-60ea-4d2e-a5fd-84b6aac7ef47/dqc_reference
[2024-01-24 13:31:28,949] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:28,958] [INFO] Task started: Prodigal
[2024-01-24 13:31:28,958] [INFO] Running command: gunzip -c /var/lib/cwl/stg8c9600ca-9b4c-4690-b254-d69639d85279/GCF_001613265.1_ASM161326v1_genomic.fna.gz | prodigal -d GCF_001613265.1_ASM161326v1_genomic.fna/cds.fna -a GCF_001613265.1_ASM161326v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:31:56,326] [INFO] Task succeeded: Prodigal
[2024-01-24 13:31:56,326] [INFO] Task started: HMMsearch
[2024-01-24 13:31:56,326] [INFO] Running command: hmmsearch --tblout GCF_001613265.1_ASM161326v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd1b1e8a0-60ea-4d2e-a5fd-84b6aac7ef47/dqc_reference/reference_markers.hmm GCF_001613265.1_ASM161326v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:31:56,761] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:31:56,762] [INFO] Found 6/6 markers.
[2024-01-24 13:31:56,819] [INFO] Query marker FASTA was written to GCF_001613265.1_ASM161326v1_genomic.fna/markers.fasta
[2024-01-24 13:31:56,819] [INFO] Task started: Blastn
[2024-01-24 13:31:56,819] [INFO] Running command: blastn -query GCF_001613265.1_ASM161326v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd1b1e8a0-60ea-4d2e-a5fd-84b6aac7ef47/dqc_reference/reference_markers.fasta -out GCF_001613265.1_ASM161326v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:31:57,956] [INFO] Task succeeded: Blastn
[2024-01-24 13:31:57,959] [INFO] Selected 16 target genomes.
[2024-01-24 13:31:57,959] [INFO] Target genome list was writen to GCF_001613265.1_ASM161326v1_genomic.fna/target_genomes.txt
[2024-01-24 13:31:57,966] [INFO] Task started: fastANI
[2024-01-24 13:31:57,966] [INFO] Running command: fastANI --query /var/lib/cwl/stg8c9600ca-9b4c-4690-b254-d69639d85279/GCF_001613265.1_ASM161326v1_genomic.fna.gz --refList GCF_001613265.1_ASM161326v1_genomic.fna/target_genomes.txt --output GCF_001613265.1_ASM161326v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:25,171] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:25,172] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd1b1e8a0-60ea-4d2e-a5fd-84b6aac7ef47/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:25,172] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd1b1e8a0-60ea-4d2e-a5fd-84b6aac7ef47/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:25,185] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:32:25,185] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:32:25,185] [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 vermiculata	strain=NBRC 100427	GCA_001613265.1	257274	257274	type	True	100.0	2180	2187	95	conclusive
Nocardia vermiculata	strain=JCM 12354	GCA_012396005.1	257274	257274	type	True	99.9939	2181	2187	95	conclusive
Nocardia aobensis	strain=NBRC 100429	GCA_000308375.1	257277	257277	type	True	83.4259	1362	2187	95	below_threshold
Nocardia elegans	strain=NBRC 108235	GCA_001612845.1	300029	300029	type	True	83.3328	1374	2187	95	below_threshold
Nocardia africana	strain=NBRC 100379	GCA_001612635.1	134964	134964	type	True	83.2413	1380	2187	95	below_threshold
Nocardia kruczakiae	strain=NBRC 101016	GCA_001612965.1	261477	261477	type	True	83.2357	1397	2187	95	below_threshold
Nocardia nova	strain=NBRC 15556	GCA_001613005.1	37330	37330	type	True	83.2277	1374	2187	95	below_threshold
Nocardia cerradoensis	strain=NBRC 101014	GCA_000308535.1	85688	85688	type	True	83.2152	1350	2187	95	below_threshold
Nocardia africana	strain=FDAARGOS_1597	GCA_020731565.1	134964	134964	type	True	83.1978	1359	2187	95	below_threshold
Nocardia mikamii	strain=NBRC 108933	GCA_001613505.1	508464	508464	type	True	83.111	1409	2187	95	below_threshold
Nocardia veterana	strain=NBRC 100344	GCA_000308855.1	132249	132249	type	True	82.8619	1277	2187	95	below_threshold
Nocardia veterana	strain=DSM 44445	GCA_012396305.1	132249	132249	type	True	82.8528	1310	2187	95	below_threshold
Nocardia mexicana	strain=NBRC 108244	GCA_001613165.1	279262	279262	type	True	80.3825	1067	2187	95	below_threshold
Nocardia miyunensis	strain=NBRC 108239	GCA_001613065.1	282684	282684	type	True	80.0903	1001	2187	95	below_threshold
Nocardia coffeae	strain=CA2R105	GCA_019890715.1	2873381	2873381	type	True	80.0218	1058	2187	95	below_threshold
Nocardia stercoris	strain=NEAU-LL90	GCA_003696265.1	2483361	2483361	type	True	79.3755	842	2187	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:25,186] [INFO] DFAST Taxonomy check result was written to GCF_001613265.1_ASM161326v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:25,187] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:25,187] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:25,187] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd1b1e8a0-60ea-4d2e-a5fd-84b6aac7ef47/dqc_reference/checkm_data
[2024-01-24 13:32:25,189] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:25,249] [INFO] Task started: CheckM
[2024-01-24 13:32:25,250] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001613265.1_ASM161326v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001613265.1_ASM161326v1_genomic.fna/checkm_input GCF_001613265.1_ASM161326v1_genomic.fna/checkm_result
[2024-01-24 13:33:38,285] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:38,287] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:38,308] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:38,308] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:38,308] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001613265.1_ASM161326v1_genomic.fna/markers.fasta)
[2024-01-24 13:33:38,309] [INFO] Task started: Blastn
[2024-01-24 13:33:38,309] [INFO] Running command: blastn -query GCF_001613265.1_ASM161326v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd1b1e8a0-60ea-4d2e-a5fd-84b6aac7ef47/dqc_reference/reference_markers_gtdb.fasta -out GCF_001613265.1_ASM161326v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:39,976] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:39,979] [INFO] Selected 15 target genomes.
[2024-01-24 13:33:39,979] [INFO] Target genome list was writen to GCF_001613265.1_ASM161326v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:40,014] [INFO] Task started: fastANI
[2024-01-24 13:33:40,014] [INFO] Running command: fastANI --query /var/lib/cwl/stg8c9600ca-9b4c-4690-b254-d69639d85279/GCF_001613265.1_ASM161326v1_genomic.fna.gz --refList GCF_001613265.1_ASM161326v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001613265.1_ASM161326v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:34:03,373] [INFO] Task succeeded: fastANI
[2024-01-24 13:34:03,388] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:34:03,388] [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_001613265.1	s__Nocardia vermiculata	100.0	2180	2187	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_000308375.1	s__Nocardia aobensis	83.4361	1361	2187	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	83.3389	1373	2187	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	96.9334	99.79	99.59	0.97	0.94	3	-
GCF_001613005.1	s__Nocardia nova	83.2782	1365	2187	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	96.9334	98.75	97.55	0.88	0.84	13	-
GCF_001612635.1	s__Nocardia africana	83.2408	1380	2187	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	99.93	99.93	0.99	0.99	2	-
GCF_001612965.1	s__Nocardia kruczakiae	83.225	1399	2187	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.6988	N/A	N/A	N/A	N/A	1	-
GCF_000308535.1	s__Nocardia cerradoensis	83.2078	1351	2187	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0231	99.71	99.43	1.00	0.99	3	-
GCF_015354405.1	s__Nocardia sp015354405	83.1812	1369	2187	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001613505.1	s__Nocardia mikamii	83.1184	1407	2187	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	83.0404	1280	2187	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	82.9851	1405	2187	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000308855.1	s__Nocardia veterana	82.8583	1277	2187	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	100.00	100.00	1.00	1.00	2	-
GCA_017354515.1	s__Nocardia sp017354515	81.0347	730	2187	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015477355.1	s__Nocardia blacklockiae	80.5041	1125	2187	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001613065.1	s__Nocardia miyunensis	80.0932	1002	2187	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 13:34:03,390] [INFO] GTDB search result was written to GCF_001613265.1_ASM161326v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:34:03,390] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:34:03,394] [INFO] DFAST_QC result json was written to GCF_001613265.1_ASM161326v1_genomic.fna/dqc_result.json
[2024-01-24 13:34:03,394] [INFO] DFAST_QC completed!
[2024-01-24 13:34:03,394] [INFO] Total running time: 0h2m36s