[2024-01-24 14:30:47,276] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:30:47,278] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:30:47,278] [INFO] DQC Reference Directory: /var/lib/cwl/stg7a48b16b-c75b-4d9d-bdda-312aa040cc18/dqc_reference
[2024-01-24 14:30:48,577] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:30:48,578] [INFO] Task started: Prodigal
[2024-01-24 14:30:48,578] [INFO] Running command: gunzip -c /var/lib/cwl/stgded51d50-8c11-45b2-b0b6-a25e5b982d87/GCF_003605385.1_ASM360538v2_genomic.fna.gz | prodigal -d GCF_003605385.1_ASM360538v2_genomic.fna/cds.fna -a GCF_003605385.1_ASM360538v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:30:59,439] [INFO] Task succeeded: Prodigal
[2024-01-24 14:30:59,439] [INFO] Task started: HMMsearch
[2024-01-24 14:30:59,440] [INFO] Running command: hmmsearch --tblout GCF_003605385.1_ASM360538v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7a48b16b-c75b-4d9d-bdda-312aa040cc18/dqc_reference/reference_markers.hmm GCF_003605385.1_ASM360538v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:30:59,797] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:30:59,798] [INFO] Found 6/6 markers.
[2024-01-24 14:30:59,835] [INFO] Query marker FASTA was written to GCF_003605385.1_ASM360538v2_genomic.fna/markers.fasta
[2024-01-24 14:30:59,836] [INFO] Task started: Blastn
[2024-01-24 14:30:59,836] [INFO] Running command: blastn -query GCF_003605385.1_ASM360538v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg7a48b16b-c75b-4d9d-bdda-312aa040cc18/dqc_reference/reference_markers.fasta -out GCF_003605385.1_ASM360538v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:00,431] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:00,434] [INFO] Selected 17 target genomes.
[2024-01-24 14:31:00,434] [INFO] Target genome list was writen to GCF_003605385.1_ASM360538v2_genomic.fna/target_genomes.txt
[2024-01-24 14:31:00,507] [INFO] Task started: fastANI
[2024-01-24 14:31:00,507] [INFO] Running command: fastANI --query /var/lib/cwl/stgded51d50-8c11-45b2-b0b6-a25e5b982d87/GCF_003605385.1_ASM360538v2_genomic.fna.gz --refList GCF_003605385.1_ASM360538v2_genomic.fna/target_genomes.txt --output GCF_003605385.1_ASM360538v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:31:14,268] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:14,269] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7a48b16b-c75b-4d9d-bdda-312aa040cc18/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:31:14,269] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7a48b16b-c75b-4d9d-bdda-312aa040cc18/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:31:14,276] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:31:14,276] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:31:14,276] [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
Siminovitchia acidinfaciens	strain=3-2-2	GCA_003605385.2	2321395	2321395	type	True	100.0	1422	1425	95	conclusive
Siminovitchia fortis	strain=DSM 16012	GCA_003605365.2	254758	254758	type	True	81.0787	700	1425	95	below_threshold
Siminovitchia fordii	strain=DSM 16014	GCA_000374565.1	254759	254759	type	True	80.7764	799	1425	95	below_threshold
Siminovitchia thermophila	strain=DSM 105453	GCA_016909185.1	1245522	1245522	type	True	77.2986	228	1425	95	below_threshold
Cytobacillus firmus	strain=NCTC10335	GCA_900445365.1	1399	1399	suspected-type	True	77.0163	57	1425	95	below_threshold
Lederbergia galactosidilytica	strain=DSM 15595	GCA_017873565.1	217031	217031	type	True	76.8422	80	1425	95	below_threshold
Cytobacillus firmus	strain=NBRC 15306	GCA_001591465.1	1399	1399	suspected-type	True	76.0057	51	1425	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:31:14,278] [INFO] DFAST Taxonomy check result was written to GCF_003605385.1_ASM360538v2_genomic.fna/tc_result.tsv
[2024-01-24 14:31:14,279] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:31:14,279] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:31:14,279] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7a48b16b-c75b-4d9d-bdda-312aa040cc18/dqc_reference/checkm_data
[2024-01-24 14:31:14,280] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:31:14,325] [INFO] Task started: CheckM
[2024-01-24 14:31:14,325] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003605385.1_ASM360538v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003605385.1_ASM360538v2_genomic.fna/checkm_input GCF_003605385.1_ASM360538v2_genomic.fna/checkm_result
[2024-01-24 14:31:52,072] [INFO] Task succeeded: CheckM
[2024-01-24 14:31:52,074] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:31:52,092] [INFO] ===== Completeness check finished =====
[2024-01-24 14:31:52,093] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:31:52,093] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003605385.1_ASM360538v2_genomic.fna/markers.fasta)
[2024-01-24 14:31:52,094] [INFO] Task started: Blastn
[2024-01-24 14:31:52,094] [INFO] Running command: blastn -query GCF_003605385.1_ASM360538v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg7a48b16b-c75b-4d9d-bdda-312aa040cc18/dqc_reference/reference_markers_gtdb.fasta -out GCF_003605385.1_ASM360538v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:52,932] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:52,937] [INFO] Selected 12 target genomes.
[2024-01-24 14:31:52,937] [INFO] Target genome list was writen to GCF_003605385.1_ASM360538v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:31:52,947] [INFO] Task started: fastANI
[2024-01-24 14:31:52,948] [INFO] Running command: fastANI --query /var/lib/cwl/stgded51d50-8c11-45b2-b0b6-a25e5b982d87/GCF_003605385.1_ASM360538v2_genomic.fna.gz --refList GCF_003605385.1_ASM360538v2_genomic.fna/target_genomes_gtdb.txt --output GCF_003605385.1_ASM360538v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:32:05,437] [INFO] Task succeeded: fastANI
[2024-01-24 14:32:05,445] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:32:05,446] [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_003605385.1	s__Siminovitchia acidinfaciens	100.0	1422	1425	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Siminovitchia	95.0	96.47	96.47	0.87	0.87	2	conclusive
GCF_003605365.2	s__Siminovitchia fortis	81.0488	702	1425	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Siminovitchia	95.0	98.09	98.04	0.87	0.87	16	-
GCF_000374565.1	s__Siminovitchia fordii	80.7883	797	1425	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Siminovitchia	95.0	98.95	97.34	0.95	0.89	4	-
GCF_003605405.2	s__Siminovitchia terrae	80.7527	758	1425	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Siminovitchia	95.0	99.14	99.09	0.90	0.90	3	-
GCF_014836955.1	s__Siminovitchia sp014836955	79.9592	665	1425	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Siminovitchia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009928435.1	s__Siminovitchia sp009928435	79.9104	602	1425	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Siminovitchia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013248975.1	s__Neobacillus endophyticus	76.8952	51	1425	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008764245.1	s__Lederbergia ruris	76.6935	88	1425	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Lederbergia	95.0	98.48	98.48	0.86	0.86	2	-
GCA_017656295.1	s__JACDOC01 sp017656295	76.0713	54	1425	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Domibacillaceae;g__JACDOC01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:32:05,447] [INFO] GTDB search result was written to GCF_003605385.1_ASM360538v2_genomic.fna/result_gtdb.tsv
[2024-01-24 14:32:05,453] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:32:05,456] [INFO] DFAST_QC result json was written to GCF_003605385.1_ASM360538v2_genomic.fna/dqc_result.json
[2024-01-24 14:32:05,456] [INFO] DFAST_QC completed!
[2024-01-24 14:32:05,456] [INFO] Total running time: 0h1m18s