[2024-01-24 15:02:37,298] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:02:37,313] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:02:37,314] [INFO] DQC Reference Directory: /var/lib/cwl/stgcfff54b7-4150-49cc-bc0e-a521dd7d6a2e/dqc_reference
[2024-01-24 15:02:38,725] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:02:38,726] [INFO] Task started: Prodigal
[2024-01-24 15:02:38,726] [INFO] Running command: gunzip -c /var/lib/cwl/stg1cd0981d-2260-45d6-8057-e4d38e935818/GCF_001613065.1_ASM161306v1_genomic.fna.gz | prodigal -d GCF_001613065.1_ASM161306v1_genomic.fna/cds.fna -a GCF_001613065.1_ASM161306v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:03:24,855] [INFO] Task succeeded: Prodigal
[2024-01-24 15:03:24,856] [INFO] Task started: HMMsearch
[2024-01-24 15:03:24,856] [INFO] Running command: hmmsearch --tblout GCF_001613065.1_ASM161306v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcfff54b7-4150-49cc-bc0e-a521dd7d6a2e/dqc_reference/reference_markers.hmm GCF_001613065.1_ASM161306v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:03:25,303] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:03:25,304] [INFO] Found 6/6 markers.
[2024-01-24 15:03:25,404] [INFO] Query marker FASTA was written to GCF_001613065.1_ASM161306v1_genomic.fna/markers.fasta
[2024-01-24 15:03:25,405] [INFO] Task started: Blastn
[2024-01-24 15:03:25,405] [INFO] Running command: blastn -query GCF_001613065.1_ASM161306v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcfff54b7-4150-49cc-bc0e-a521dd7d6a2e/dqc_reference/reference_markers.fasta -out GCF_001613065.1_ASM161306v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:03:26,759] [INFO] Task succeeded: Blastn
[2024-01-24 15:03:26,762] [INFO] Selected 8 target genomes.
[2024-01-24 15:03:26,763] [INFO] Target genome list was writen to GCF_001613065.1_ASM161306v1_genomic.fna/target_genomes.txt
[2024-01-24 15:03:26,765] [INFO] Task started: fastANI
[2024-01-24 15:03:26,765] [INFO] Running command: fastANI --query /var/lib/cwl/stg1cd0981d-2260-45d6-8057-e4d38e935818/GCF_001613065.1_ASM161306v1_genomic.fna.gz --refList GCF_001613065.1_ASM161306v1_genomic.fna/target_genomes.txt --output GCF_001613065.1_ASM161306v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:03:47,103] [INFO] Task succeeded: fastANI
[2024-01-24 15:03:47,103] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcfff54b7-4150-49cc-bc0e-a521dd7d6a2e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:03:47,104] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcfff54b7-4150-49cc-bc0e-a521dd7d6a2e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:03:47,111] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:03:47,111] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:03:47,111] [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 miyunensis	strain=NBRC 108239	GCA_001613065.1	282684	282684	type	True	100.0	3396	3407	95	conclusive
Nocardia jiangxiensis	strain=NBRC 101359	GCA_000308615.1	282685	282685	type	True	90.1405	2447	3407	95	below_threshold
Nocardia coffeae	strain=CA2R105	GCA_019890715.1	2873381	2873381	type	True	89.519	2325	3407	95	below_threshold
Nocardia vaccinii	strain=NBRC 15922	GCA_001613305.1	1822	1822	type	True	88.6939	2023	3407	95	below_threshold
Nocardia macrotermitis	strain=RB20	GCA_009604405.1	2585198	2585198	type	True	87.6629	2024	3407	95	below_threshold
Nocardia albiluteola	strain=NEAU-G5	GCA_018860155.1	2842303	2842303	type	True	82.8661	1623	3407	95	below_threshold
Nocardia mexicana	strain=NBRC 108244	GCA_001613165.1	279262	279262	type	True	81.1618	1344	3407	95	below_threshold
Nocardia mexicana	strain=DSM 44952	GCA_003350525.1	279262	279262	type	True	81.1458	1373	3407	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:03:47,114] [INFO] DFAST Taxonomy check result was written to GCF_001613065.1_ASM161306v1_genomic.fna/tc_result.tsv
[2024-01-24 15:03:47,115] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:03:47,115] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:03:47,115] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcfff54b7-4150-49cc-bc0e-a521dd7d6a2e/dqc_reference/checkm_data
[2024-01-24 15:03:47,116] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:03:47,218] [INFO] Task started: CheckM
[2024-01-24 15:03:47,219] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001613065.1_ASM161306v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001613065.1_ASM161306v1_genomic.fna/checkm_input GCF_001613065.1_ASM161306v1_genomic.fna/checkm_result
[2024-01-24 15:05:54,996] [INFO] Task succeeded: CheckM
[2024-01-24 15:05:54,997] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 2.23%
Strain heterogeneity: 20.00%
--------------------------------------------------------------------------------
[2024-01-24 15:05:55,035] [INFO] ===== Completeness check finished =====
[2024-01-24 15:05:55,035] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:05:55,035] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001613065.1_ASM161306v1_genomic.fna/markers.fasta)
[2024-01-24 15:05:55,036] [INFO] Task started: Blastn
[2024-01-24 15:05:55,036] [INFO] Running command: blastn -query GCF_001613065.1_ASM161306v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcfff54b7-4150-49cc-bc0e-a521dd7d6a2e/dqc_reference/reference_markers_gtdb.fasta -out GCF_001613065.1_ASM161306v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:05:56,901] [INFO] Task succeeded: Blastn
[2024-01-24 15:05:56,904] [INFO] Selected 11 target genomes.
[2024-01-24 15:05:56,904] [INFO] Target genome list was writen to GCF_001613065.1_ASM161306v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:05:56,907] [INFO] Task started: fastANI
[2024-01-24 15:05:56,907] [INFO] Running command: fastANI --query /var/lib/cwl/stg1cd0981d-2260-45d6-8057-e4d38e935818/GCF_001613065.1_ASM161306v1_genomic.fna.gz --refList GCF_001613065.1_ASM161306v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001613065.1_ASM161306v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:06:21,243] [INFO] Task succeeded: fastANI
[2024-01-24 15:06:21,257] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:06:21,257] [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_001613065.1	s__Nocardia miyunensis	100.0	3396	3407	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_000308615.1	s__Nocardia jiangxiensis	90.1117	2453	3407	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	88.7047	2022	3407	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009604405.1	s__Nocardia sp009604405	87.6446	2027	3407	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860155.1	s__Nocardia sp018860155	82.8559	1626	3407	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	81.3577	1370	3407	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001613165.1	s__Nocardia mexicana	81.1543	1344	3407	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002933465.1	s__Nocardia nova_B	80.9716	1210	3407	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	99.92	99.92	0.99	0.99	2	-
GCF_001613105.1	s__Nocardia pseudobrasiliensis	80.8471	1264	3407	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	100.00	100.00	0.99	0.99	2	-
GCF_001613505.1	s__Nocardia mikamii	80.7515	1299	3407	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000523235.1	s__Nocardia nova_A	80.6671	1316	3407	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 15:06:21,259] [INFO] GTDB search result was written to GCF_001613065.1_ASM161306v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:06:21,259] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:06:21,263] [INFO] DFAST_QC result json was written to GCF_001613065.1_ASM161306v1_genomic.fna/dqc_result.json
[2024-01-24 15:06:21,263] [INFO] DFAST_QC completed!
[2024-01-24 15:06:21,263] [INFO] Total running time: 0h3m44s