[2024-01-24 11:09:50,718] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:09:50,721] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:09:50,721] [INFO] DQC Reference Directory: /var/lib/cwl/stgc20ce0b5-25a3-41c4-ad6d-3f0465491b7a/dqc_reference
[2024-01-24 11:09:53,300] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:09:53,301] [INFO] Task started: Prodigal
[2024-01-24 11:09:53,302] [INFO] Running command: gunzip -c /var/lib/cwl/stg0807e58e-21fd-4329-a2a4-36fd68594db6/GCF_023746535.1_ASM2374653v1_genomic.fna.gz | prodigal -d GCF_023746535.1_ASM2374653v1_genomic.fna/cds.fna -a GCF_023746535.1_ASM2374653v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:10:04,931] [INFO] Task succeeded: Prodigal
[2024-01-24 11:10:04,932] [INFO] Task started: HMMsearch
[2024-01-24 11:10:04,932] [INFO] Running command: hmmsearch --tblout GCF_023746535.1_ASM2374653v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc20ce0b5-25a3-41c4-ad6d-3f0465491b7a/dqc_reference/reference_markers.hmm GCF_023746535.1_ASM2374653v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:10:05,206] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:10:05,207] [INFO] Found 6/6 markers.
[2024-01-24 11:10:05,242] [INFO] Query marker FASTA was written to GCF_023746535.1_ASM2374653v1_genomic.fna/markers.fasta
[2024-01-24 11:10:05,242] [INFO] Task started: Blastn
[2024-01-24 11:10:05,243] [INFO] Running command: blastn -query GCF_023746535.1_ASM2374653v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc20ce0b5-25a3-41c4-ad6d-3f0465491b7a/dqc_reference/reference_markers.fasta -out GCF_023746535.1_ASM2374653v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:10:05,889] [INFO] Task succeeded: Blastn
[2024-01-24 11:10:05,893] [INFO] Selected 26 target genomes.
[2024-01-24 11:10:05,893] [INFO] Target genome list was writen to GCF_023746535.1_ASM2374653v1_genomic.fna/target_genomes.txt
[2024-01-24 11:10:05,932] [INFO] Task started: fastANI
[2024-01-24 11:10:05,932] [INFO] Running command: fastANI --query /var/lib/cwl/stg0807e58e-21fd-4329-a2a4-36fd68594db6/GCF_023746535.1_ASM2374653v1_genomic.fna.gz --refList GCF_023746535.1_ASM2374653v1_genomic.fna/target_genomes.txt --output GCF_023746535.1_ASM2374653v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:10:21,013] [INFO] Task succeeded: fastANI
[2024-01-24 11:10:21,014] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc20ce0b5-25a3-41c4-ad6d-3f0465491b7a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:10:21,014] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc20ce0b5-25a3-41c4-ad6d-3f0465491b7a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:10:21,020] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:10:21,021] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:10:21,021] [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 sedimenti	strain=CAU 1612	GCA_017313765.1	2816034	2816034	type	True	76.9825	169	1355	95	below_threshold
Sneathiella chungangensis	strain=KCTC 32476	GCA_009882935.1	1418234	1418234	type	True	76.9005	189	1355	95	below_threshold
Sneathiella chungangensis	strain=KCTC32476	GCA_012720125.1	1418234	1418234	type	True	76.7594	183	1355	95	below_threshold
Sneathiella litorea	strain=DP05	GCA_009882915.1	2606216	2606216	type	True	76.6632	151	1355	95	below_threshold
Sneathiella aquimaris	strain=216LB-ZA1-12	GCA_012720095.1	2599305	2599305	type	True	76.5629	86	1355	95	below_threshold
Sneathiella glossodoripedis	strain=JCM 23214	GCA_000616095.1	418853	418853	type	True	76.4352	78	1355	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:10:21,022] [INFO] DFAST Taxonomy check result was written to GCF_023746535.1_ASM2374653v1_genomic.fna/tc_result.tsv
[2024-01-24 11:10:21,023] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:10:21,023] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:10:21,023] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc20ce0b5-25a3-41c4-ad6d-3f0465491b7a/dqc_reference/checkm_data
[2024-01-24 11:10:21,025] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:10:21,067] [INFO] Task started: CheckM
[2024-01-24 11:10:21,067] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_023746535.1_ASM2374653v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_023746535.1_ASM2374653v1_genomic.fna/checkm_input GCF_023746535.1_ASM2374653v1_genomic.fna/checkm_result
[2024-01-24 11:10:59,133] [INFO] Task succeeded: CheckM
[2024-01-24 11:10:59,134] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:10:59,154] [INFO] ===== Completeness check finished =====
[2024-01-24 11:10:59,155] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:10:59,155] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_023746535.1_ASM2374653v1_genomic.fna/markers.fasta)
[2024-01-24 11:10:59,156] [INFO] Task started: Blastn
[2024-01-24 11:10:59,156] [INFO] Running command: blastn -query GCF_023746535.1_ASM2374653v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc20ce0b5-25a3-41c4-ad6d-3f0465491b7a/dqc_reference/reference_markers_gtdb.fasta -out GCF_023746535.1_ASM2374653v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:11:00,279] [INFO] Task succeeded: Blastn
[2024-01-24 11:11:00,284] [INFO] Selected 25 target genomes.
[2024-01-24 11:11:00,284] [INFO] Target genome list was writen to GCF_023746535.1_ASM2374653v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:11:00,416] [INFO] Task started: fastANI
[2024-01-24 11:11:00,417] [INFO] Running command: fastANI --query /var/lib/cwl/stg0807e58e-21fd-4329-a2a4-36fd68594db6/GCF_023746535.1_ASM2374653v1_genomic.fna.gz --refList GCF_023746535.1_ASM2374653v1_genomic.fna/target_genomes_gtdb.txt --output GCF_023746535.1_ASM2374653v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:11:18,047] [INFO] Task succeeded: fastANI
[2024-01-24 11:11:18,058] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:11:18,059] [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
GCA_002706985.1	s__Sneathiella sp002706985	77.1449	149	1355	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sneathiellales;f__Sneathiellaceae;g__Sneathiella	95.0	99.70	99.70	0.85	0.85	2	-
GCA_002732675.1	s__Sneathiella sp002732675	76.995	151	1355	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sneathiellales;f__Sneathiellaceae;g__Sneathiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017313765.1	s__Sneathiella sp017313765	76.9825	169	1355	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sneathiellales;f__Sneathiellaceae;g__Sneathiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009882935.1	s__Sneathiella chungangensis	76.9137	188	1355	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sneathiellales;f__Sneathiellaceae;g__Sneathiella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_009882915.1	s__Sneathiella litorea	76.6632	151	1355	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	76.5629	86	1355	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sneathiellales;f__Sneathiellaceae;g__Sneathiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000616095.1	s__Sneathiella glossodoripedis	76.4352	78	1355	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	76.1227	70	1355	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	76.1023	72	1355	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	76.0959	57	1355	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 11:11:18,060] [INFO] GTDB search result was written to GCF_023746535.1_ASM2374653v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:11:18,061] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:11:18,064] [INFO] DFAST_QC result json was written to GCF_023746535.1_ASM2374653v1_genomic.fna/dqc_result.json
[2024-01-24 11:11:18,064] [INFO] DFAST_QC completed!
[2024-01-24 11:11:18,064] [INFO] Total running time: 0h1m27s