[2024-01-24 14:13:16,539] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:13:16,542] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:13:16,542] [INFO] DQC Reference Directory: /var/lib/cwl/stg854023f4-49cb-4062-9fa6-5891b29ea122/dqc_reference
[2024-01-24 14:13:17,884] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:13:17,886] [INFO] Task started: Prodigal
[2024-01-24 14:13:17,886] [INFO] Running command: gunzip -c /var/lib/cwl/stg1dcac25f-368a-4f46-be14-5b2c74991662/GCF_007991215.1_ASM799121v1_genomic.fna.gz | prodigal -d GCF_007991215.1_ASM799121v1_genomic.fna/cds.fna -a GCF_007991215.1_ASM799121v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:13:29,023] [INFO] Task succeeded: Prodigal
[2024-01-24 14:13:29,023] [INFO] Task started: HMMsearch
[2024-01-24 14:13:29,023] [INFO] Running command: hmmsearch --tblout GCF_007991215.1_ASM799121v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg854023f4-49cb-4062-9fa6-5891b29ea122/dqc_reference/reference_markers.hmm GCF_007991215.1_ASM799121v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:13:29,346] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:13:29,348] [INFO] Found 6/6 markers.
[2024-01-24 14:13:29,410] [INFO] Query marker FASTA was written to GCF_007991215.1_ASM799121v1_genomic.fna/markers.fasta
[2024-01-24 14:13:29,411] [INFO] Task started: Blastn
[2024-01-24 14:13:29,411] [INFO] Running command: blastn -query GCF_007991215.1_ASM799121v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg854023f4-49cb-4062-9fa6-5891b29ea122/dqc_reference/reference_markers.fasta -out GCF_007991215.1_ASM799121v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:13:30,095] [INFO] Task succeeded: Blastn
[2024-01-24 14:13:30,099] [INFO] Selected 11 target genomes.
[2024-01-24 14:13:30,100] [INFO] Target genome list was writen to GCF_007991215.1_ASM799121v1_genomic.fna/target_genomes.txt
[2024-01-24 14:13:30,110] [INFO] Task started: fastANI
[2024-01-24 14:13:30,110] [INFO] Running command: fastANI --query /var/lib/cwl/stg1dcac25f-368a-4f46-be14-5b2c74991662/GCF_007991215.1_ASM799121v1_genomic.fna.gz --refList GCF_007991215.1_ASM799121v1_genomic.fna/target_genomes.txt --output GCF_007991215.1_ASM799121v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:13:40,856] [INFO] Task succeeded: fastANI
[2024-01-24 14:13:40,857] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg854023f4-49cb-4062-9fa6-5891b29ea122/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:13:40,857] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg854023f4-49cb-4062-9fa6-5891b29ea122/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:13:40,864] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:13:40,864] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:13:40,864] [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
Aneurinibacillus danicus	strain=NBRC 102444	GCA_007991215.1	267746	267746	type	True	100.0	1316	1332	95	conclusive
Aneurinibacillus migulanus	strain=NBRC 15520	GCA_006539965.1	47500	47500	type	True	79.5453	511	1332	95	below_threshold
Aneurinibacillus migulanus	strain=DSM 2895	GCA_900100065.1	47500	47500	type	True	79.5238	520	1332	95	below_threshold
Aneurinibacillus migulanus	strain=NCTC 7096	GCA_000878905.1	47500	47500	type	True	79.4652	526	1332	95	below_threshold
Aneurinibacillus migulanus	strain=DSM 2895	GCA_001274715.1	47500	47500	type	True	79.4595	525	1332	95	below_threshold
Aneurinibacillus aneurinilyticus	strain=ATCC 12856	GCA_000466385.1	1391	1391	type	True	79.3155	490	1332	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:13:40,866] [INFO] DFAST Taxonomy check result was written to GCF_007991215.1_ASM799121v1_genomic.fna/tc_result.tsv
[2024-01-24 14:13:40,867] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:13:40,867] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:13:40,867] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg854023f4-49cb-4062-9fa6-5891b29ea122/dqc_reference/checkm_data
[2024-01-24 14:13:40,869] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:13:40,920] [INFO] Task started: CheckM
[2024-01-24 14:13:40,920] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007991215.1_ASM799121v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007991215.1_ASM799121v1_genomic.fna/checkm_input GCF_007991215.1_ASM799121v1_genomic.fna/checkm_result
[2024-01-24 14:14:16,780] [INFO] Task succeeded: CheckM
[2024-01-24 14:14:16,781] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:14:16,804] [INFO] ===== Completeness check finished =====
[2024-01-24 14:14:16,804] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:14:16,805] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007991215.1_ASM799121v1_genomic.fna/markers.fasta)
[2024-01-24 14:14:16,805] [INFO] Task started: Blastn
[2024-01-24 14:14:16,805] [INFO] Running command: blastn -query GCF_007991215.1_ASM799121v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg854023f4-49cb-4062-9fa6-5891b29ea122/dqc_reference/reference_markers_gtdb.fasta -out GCF_007991215.1_ASM799121v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:17,610] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:17,613] [INFO] Selected 17 target genomes.
[2024-01-24 14:14:17,614] [INFO] Target genome list was writen to GCF_007991215.1_ASM799121v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:14:17,628] [INFO] Task started: fastANI
[2024-01-24 14:14:17,629] [INFO] Running command: fastANI --query /var/lib/cwl/stg1dcac25f-368a-4f46-be14-5b2c74991662/GCF_007991215.1_ASM799121v1_genomic.fna.gz --refList GCF_007991215.1_ASM799121v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007991215.1_ASM799121v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:14:32,202] [INFO] Task succeeded: fastANI
[2024-01-24 14:14:32,212] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:14:32,213] [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_007991215.1	s__Aneurinibacillus danicus	100.0	1316	1332	d__Bacteria;p__Firmicutes;c__Bacilli;o__Aneurinibacillales;f__Aneurinibacillaceae;g__Aneurinibacillus	95.0	99.16	99.16	0.84	0.84	2	conclusive
GCF_001274715.1	s__Aneurinibacillus migulanus	79.4595	525	1332	d__Bacteria;p__Firmicutes;c__Bacilli;o__Aneurinibacillales;f__Aneurinibacillaceae;g__Aneurinibacillus	95.0	99.46	98.76	0.96	0.91	8	-
GCF_000466385.1	s__Aneurinibacillus aneurinilyticus	79.3354	488	1332	d__Bacteria;p__Firmicutes;c__Bacilli;o__Aneurinibacillales;f__Aneurinibacillaceae;g__Aneurinibacillus	95.0	99.57	99.14	0.94	0.88	3	-
GCF_900099925.1	s__Aneurinibacillus thermoaerophilus	79.3129	361	1332	d__Bacteria;p__Firmicutes;c__Bacilli;o__Aneurinibacillales;f__Aneurinibacillaceae;g__Aneurinibacillus	95.0	99.68	99.68	0.95	0.95	2	-
GCF_000430625.1	s__Aneurinibacillus_B terranovensis	78.8034	138	1332	d__Bacteria;p__Firmicutes;c__Bacilli;o__Aneurinibacillales;f__Aneurinibacillaceae;g__Aneurinibacillus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001015055.1	s__Aneurinibacillus_A tyrosinisolvens	77.6662	203	1332	d__Bacteria;p__Firmicutes;c__Bacilli;o__Aneurinibacillales;f__Aneurinibacillaceae;g__Aneurinibacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002355375.1	s__Aneurinibacillus soli	77.399	190	1332	d__Bacteria;p__Firmicutes;c__Bacilli;o__Aneurinibacillales;f__Aneurinibacillaceae;g__Aneurinibacillus	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:14:32,214] [INFO] GTDB search result was written to GCF_007991215.1_ASM799121v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:14:32,215] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:14:32,218] [INFO] DFAST_QC result json was written to GCF_007991215.1_ASM799121v1_genomic.fna/dqc_result.json
[2024-01-24 14:14:32,218] [INFO] DFAST_QC completed!
[2024-01-24 14:14:32,218] [INFO] Total running time: 0h1m16s