[2024-01-25 17:58:50,561] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:58:50,564] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:58:50,564] [INFO] DQC Reference Directory: /var/lib/cwl/stgee5c2ab0-2d29-4d9d-a60d-57b06da18786/dqc_reference
[2024-01-25 17:58:51,697] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:58:51,697] [INFO] Task started: Prodigal
[2024-01-25 17:58:51,698] [INFO] Running command: gunzip -c /var/lib/cwl/stg0d6d9060-e410-47aa-b94e-fae7d068d6d5/GCF_000374565.1_ASM37456v1_genomic.fna.gz | prodigal -d GCF_000374565.1_ASM37456v1_genomic.fna/cds.fna -a GCF_000374565.1_ASM37456v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:59:01,284] [INFO] Task succeeded: Prodigal
[2024-01-25 17:59:01,285] [INFO] Task started: HMMsearch
[2024-01-25 17:59:01,285] [INFO] Running command: hmmsearch --tblout GCF_000374565.1_ASM37456v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgee5c2ab0-2d29-4d9d-a60d-57b06da18786/dqc_reference/reference_markers.hmm GCF_000374565.1_ASM37456v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:59:01,532] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:59:01,533] [INFO] Found 6/6 markers.
[2024-01-25 17:59:01,567] [INFO] Query marker FASTA was written to GCF_000374565.1_ASM37456v1_genomic.fna/markers.fasta
[2024-01-25 17:59:01,568] [INFO] Task started: Blastn
[2024-01-25 17:59:01,568] [INFO] Running command: blastn -query GCF_000374565.1_ASM37456v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgee5c2ab0-2d29-4d9d-a60d-57b06da18786/dqc_reference/reference_markers.fasta -out GCF_000374565.1_ASM37456v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:59:02,101] [INFO] Task succeeded: Blastn
[2024-01-25 17:59:02,104] [INFO] Selected 18 target genomes.
[2024-01-25 17:59:02,105] [INFO] Target genome list was writen to GCF_000374565.1_ASM37456v1_genomic.fna/target_genomes.txt
[2024-01-25 17:59:02,116] [INFO] Task started: fastANI
[2024-01-25 17:59:02,116] [INFO] Running command: fastANI --query /var/lib/cwl/stg0d6d9060-e410-47aa-b94e-fae7d068d6d5/GCF_000374565.1_ASM37456v1_genomic.fna.gz --refList GCF_000374565.1_ASM37456v1_genomic.fna/target_genomes.txt --output GCF_000374565.1_ASM37456v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:59:15,510] [INFO] Task succeeded: fastANI
[2024-01-25 17:59:15,511] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgee5c2ab0-2d29-4d9d-a60d-57b06da18786/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:59:15,511] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgee5c2ab0-2d29-4d9d-a60d-57b06da18786/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:59:15,519] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:59:15,519] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:59:15,519] [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 fordii	strain=DSM 16014	GCA_000374565.1	254759	254759	type	True	100.0	1481	1483	95	conclusive
Siminovitchia fortis	strain=DSM 16012	GCA_003605365.2	254758	254758	type	True	84.5502	889	1483	95	below_threshold
Siminovitchia acidinfaciens	strain=3-2-2	GCA_003605385.2	2321395	2321395	type	True	80.776	791	1483	95	below_threshold
Siminovitchia thermophila	strain=DSM 105453	GCA_016909185.1	1245522	1245522	type	True	79.1104	260	1483	95	below_threshold
Lederbergia citri	strain=FJAT-49780	GCA_018343625.1	2833580	2833580	type	True	77.6446	120	1483	95	below_threshold
Lederbergia panacisoli	strain=KACC 17503	GCA_024626525.1	1255251	1255251	type	True	77.43	100	1483	95	below_threshold
Lederbergia citrisecundus	strain=FJAT-49732	GCA_018343695.1	2833583	2833583	type	True	77.061	110	1483	95	below_threshold
Cytobacillus solani	strain=FJAT-18043	GCA_001420595.1	1637975	1637975	type	True	76.7626	71	1483	95	below_threshold
Cytobacillus firmus	strain=NCTC10335	GCA_900445365.1	1399	1399	suspected-type	True	76.6073	61	1483	95	below_threshold
Cytobacillus firmus	strain=NBRC 15306	GCA_001591465.1	1399	1399	suspected-type	True	75.7373	54	1483	95	below_threshold
Bacillus badius	strain=NBRC 15713	GCA_001591605.1	1455	1455	type	True	75.6454	57	1483	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:59:15,520] [INFO] DFAST Taxonomy check result was written to GCF_000374565.1_ASM37456v1_genomic.fna/tc_result.tsv
[2024-01-25 17:59:15,521] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:59:15,521] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:59:15,521] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgee5c2ab0-2d29-4d9d-a60d-57b06da18786/dqc_reference/checkm_data
[2024-01-25 17:59:15,522] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:59:15,568] [INFO] Task started: CheckM
[2024-01-25 17:59:15,568] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000374565.1_ASM37456v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000374565.1_ASM37456v1_genomic.fna/checkm_input GCF_000374565.1_ASM37456v1_genomic.fna/checkm_result
[2024-01-25 17:59:47,576] [INFO] Task succeeded: CheckM
[2024-01-25 17:59:47,577] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:59:47,591] [INFO] ===== Completeness check finished =====
[2024-01-25 17:59:47,592] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:59:47,592] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000374565.1_ASM37456v1_genomic.fna/markers.fasta)
[2024-01-25 17:59:47,592] [INFO] Task started: Blastn
[2024-01-25 17:59:47,592] [INFO] Running command: blastn -query GCF_000374565.1_ASM37456v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgee5c2ab0-2d29-4d9d-a60d-57b06da18786/dqc_reference/reference_markers_gtdb.fasta -out GCF_000374565.1_ASM37456v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:59:48,335] [INFO] Task succeeded: Blastn
[2024-01-25 17:59:48,338] [INFO] Selected 6 target genomes.
[2024-01-25 17:59:48,338] [INFO] Target genome list was writen to GCF_000374565.1_ASM37456v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:59:48,343] [INFO] Task started: fastANI
[2024-01-25 17:59:48,343] [INFO] Running command: fastANI --query /var/lib/cwl/stg0d6d9060-e410-47aa-b94e-fae7d068d6d5/GCF_000374565.1_ASM37456v1_genomic.fna.gz --refList GCF_000374565.1_ASM37456v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000374565.1_ASM37456v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:59:54,874] [INFO] Task succeeded: fastANI
[2024-01-25 17:59:54,879] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:59:54,879] [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_000374565.1	s__Siminovitchia fordii	100.0	1481	1483	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	conclusive
GCF_003605365.2	s__Siminovitchia fortis	84.5502	889	1483	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_003605405.2	s__Siminovitchia terrae	83.2765	1019	1483	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	82.143	905	1483	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	81.8929	758	1483	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_003605385.1	s__Siminovitchia acidinfaciens	80.776	791	1483	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	-
--------------------------------------------------------------------------------
[2024-01-25 17:59:54,882] [INFO] GTDB search result was written to GCF_000374565.1_ASM37456v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:59:54,883] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:59:54,885] [INFO] DFAST_QC result json was written to GCF_000374565.1_ASM37456v1_genomic.fna/dqc_result.json
[2024-01-25 17:59:54,885] [INFO] DFAST_QC completed!
[2024-01-25 17:59:54,885] [INFO] Total running time: 0h1m4s