[2024-01-24 11:58:53,413] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:58:53,416] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:58:53,416] [INFO] DQC Reference Directory: /var/lib/cwl/stg5b35dbf2-9d7f-4b07-bc22-6031deaf7da3/dqc_reference
[2024-01-24 11:58:54,594] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:58:54,595] [INFO] Task started: Prodigal
[2024-01-24 11:58:54,595] [INFO] Running command: gunzip -c /var/lib/cwl/stg4f5ea555-5f39-4430-97d9-6e35fa3bd814/GCF_012932565.1_ASM1293256v1_genomic.fna.gz | prodigal -d GCF_012932565.1_ASM1293256v1_genomic.fna/cds.fna -a GCF_012932565.1_ASM1293256v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:59:04,674] [INFO] Task succeeded: Prodigal
[2024-01-24 11:59:04,675] [INFO] Task started: HMMsearch
[2024-01-24 11:59:04,675] [INFO] Running command: hmmsearch --tblout GCF_012932565.1_ASM1293256v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5b35dbf2-9d7f-4b07-bc22-6031deaf7da3/dqc_reference/reference_markers.hmm GCF_012932565.1_ASM1293256v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:59:04,983] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:59:04,985] [INFO] Found 6/6 markers.
[2024-01-24 11:59:05,029] [INFO] Query marker FASTA was written to GCF_012932565.1_ASM1293256v1_genomic.fna/markers.fasta
[2024-01-24 11:59:05,030] [INFO] Task started: Blastn
[2024-01-24 11:59:05,030] [INFO] Running command: blastn -query GCF_012932565.1_ASM1293256v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5b35dbf2-9d7f-4b07-bc22-6031deaf7da3/dqc_reference/reference_markers.fasta -out GCF_012932565.1_ASM1293256v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:05,785] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:05,789] [INFO] Selected 19 target genomes.
[2024-01-24 11:59:05,789] [INFO] Target genome list was writen to GCF_012932565.1_ASM1293256v1_genomic.fna/target_genomes.txt
[2024-01-24 11:59:05,830] [INFO] Task started: fastANI
[2024-01-24 11:59:05,830] [INFO] Running command: fastANI --query /var/lib/cwl/stg4f5ea555-5f39-4430-97d9-6e35fa3bd814/GCF_012932565.1_ASM1293256v1_genomic.fna.gz --refList GCF_012932565.1_ASM1293256v1_genomic.fna/target_genomes.txt --output GCF_012932565.1_ASM1293256v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:59:17,432] [INFO] Task succeeded: fastANI
[2024-01-24 11:59:17,433] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5b35dbf2-9d7f-4b07-bc22-6031deaf7da3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:59:17,433] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5b35dbf2-9d7f-4b07-bc22-6031deaf7da3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:59:17,440] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:59:17,441] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:59:17,441] [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
Sneathiella limimaris	strain=KCTC 52846	GCA_012932565.1	1964213	1964213	type	True	100.0	1218	1218	95	conclusive
Sneathiella glossodoripedis	strain=JCM 23214	GCA_000616095.1	418853	418853	type	True	77.8636	220	1218	95	below_threshold
Sneathiella aquimaris	strain=216LB-ZA1-12	GCA_012720095.1	2599305	2599305	type	True	77.0345	168	1218	95	below_threshold
Sneathiella chinensis	strain=LMG23452	GCA_012720115.1	349750	349750	type	True	76.9432	150	1218	95	below_threshold
Sneathiella litorea	strain=DP05	GCA_009882915.1	2606216	2606216	type	True	76.8977	71	1218	95	below_threshold
Sneathiella chungangensis	strain=KCTC 32476	GCA_009882935.1	1418234	1418234	type	True	76.7751	77	1218	95	below_threshold
Sneathiella chungangensis	strain=KCTC32476	GCA_012720125.1	1418234	1418234	type	True	76.7313	77	1218	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:59:17,442] [INFO] DFAST Taxonomy check result was written to GCF_012932565.1_ASM1293256v1_genomic.fna/tc_result.tsv
[2024-01-24 11:59:17,443] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:59:17,443] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:59:17,443] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5b35dbf2-9d7f-4b07-bc22-6031deaf7da3/dqc_reference/checkm_data
[2024-01-24 11:59:17,444] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:59:17,481] [INFO] Task started: CheckM
[2024-01-24 11:59:17,482] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_012932565.1_ASM1293256v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_012932565.1_ASM1293256v1_genomic.fna/checkm_input GCF_012932565.1_ASM1293256v1_genomic.fna/checkm_result
[2024-01-24 11:59:52,837] [INFO] Task succeeded: CheckM
[2024-01-24 11:59:52,838] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:59:52,861] [INFO] ===== Completeness check finished =====
[2024-01-24 11:59:52,861] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:59:52,861] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_012932565.1_ASM1293256v1_genomic.fna/markers.fasta)
[2024-01-24 11:59:52,861] [INFO] Task started: Blastn
[2024-01-24 11:59:52,862] [INFO] Running command: blastn -query GCF_012932565.1_ASM1293256v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5b35dbf2-9d7f-4b07-bc22-6031deaf7da3/dqc_reference/reference_markers_gtdb.fasta -out GCF_012932565.1_ASM1293256v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:53,948] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:53,951] [INFO] Selected 18 target genomes.
[2024-01-24 11:59:53,951] [INFO] Target genome list was writen to GCF_012932565.1_ASM1293256v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:59:53,983] [INFO] Task started: fastANI
[2024-01-24 11:59:53,983] [INFO] Running command: fastANI --query /var/lib/cwl/stg4f5ea555-5f39-4430-97d9-6e35fa3bd814/GCF_012932565.1_ASM1293256v1_genomic.fna.gz --refList GCF_012932565.1_ASM1293256v1_genomic.fna/target_genomes_gtdb.txt --output GCF_012932565.1_ASM1293256v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:00:04,604] [INFO] Task succeeded: fastANI
[2024-01-24 12:00:04,612] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:00:04,613] [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_012932565.1	s__Sneathiella limimaris	100.0	1218	1218	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sneathiellales;f__Sneathiellaceae;g__Sneathiella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000616095.1	s__Sneathiella glossodoripedis	77.8636	220	1218	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sneathiellales;f__Sneathiellaceae;g__Sneathiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015143595.1	s__Sneathiella sp015143595	77.3949	182	1218	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sneathiellales;f__Sneathiellaceae;g__Sneathiella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002163135.1	s__Sneathiella sp002163135	77.1786	141	1218	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sneathiellales;f__Sneathiellaceae;g__Sneathiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012720095.1	s__Sneathiella aquimaris	77.0333	168	1218	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sneathiellales;f__Sneathiellaceae;g__Sneathiella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017643685.1	s__Sneathiella sp017643685	76.9825	158	1218	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sneathiellales;f__Sneathiellaceae;g__Sneathiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012720115.1	s__Sneathiella chinensis	76.927	151	1218	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sneathiellales;f__Sneathiellaceae;g__Sneathiella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002428885.1	s__Sneathiella sp002428885	76.5818	128	1218	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sneathiellales;f__Sneathiellaceae;g__Sneathiella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016765515.1	s__Sneathiella sp016765515	76.4691	56	1218	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sneathiellales;f__Sneathiellaceae;g__Sneathiella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:00:04,614] [INFO] GTDB search result was written to GCF_012932565.1_ASM1293256v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:00:04,615] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:00:04,618] [INFO] DFAST_QC result json was written to GCF_012932565.1_ASM1293256v1_genomic.fna/dqc_result.json
[2024-01-24 12:00:04,618] [INFO] DFAST_QC completed!
[2024-01-24 12:00:04,618] [INFO] Total running time: 0h1m11s