[2024-01-25 20:14:05,808] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:14:05,810] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:14:05,810] [INFO] DQC Reference Directory: /var/lib/cwl/stgaab77b81-d635-4b6d-a8a2-3499e62e2c7f/dqc_reference
[2024-01-25 20:14:06,933] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:14:06,934] [INFO] Task started: Prodigal
[2024-01-25 20:14:06,934] [INFO] Running command: gunzip -c /var/lib/cwl/stg8e608ba6-62ce-4d06-9c38-7464d8c43d2a/GCF_023556335.1_ASM2355633v1_genomic.fna.gz | prodigal -d GCF_023556335.1_ASM2355633v1_genomic.fna/cds.fna -a GCF_023556335.1_ASM2355633v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:14:16,588] [INFO] Task succeeded: Prodigal
[2024-01-25 20:14:16,588] [INFO] Task started: HMMsearch
[2024-01-25 20:14:16,589] [INFO] Running command: hmmsearch --tblout GCF_023556335.1_ASM2355633v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaab77b81-d635-4b6d-a8a2-3499e62e2c7f/dqc_reference/reference_markers.hmm GCF_023556335.1_ASM2355633v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:14:16,782] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:14:16,783] [INFO] Found 6/6 markers.
[2024-01-25 20:14:16,810] [INFO] Query marker FASTA was written to GCF_023556335.1_ASM2355633v1_genomic.fna/markers.fasta
[2024-01-25 20:14:16,811] [INFO] Task started: Blastn
[2024-01-25 20:14:16,811] [INFO] Running command: blastn -query GCF_023556335.1_ASM2355633v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaab77b81-d635-4b6d-a8a2-3499e62e2c7f/dqc_reference/reference_markers.fasta -out GCF_023556335.1_ASM2355633v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:14:17,786] [INFO] Task succeeded: Blastn
[2024-01-25 20:14:17,790] [INFO] Selected 12 target genomes.
[2024-01-25 20:14:17,790] [INFO] Target genome list was writen to GCF_023556335.1_ASM2355633v1_genomic.fna/target_genomes.txt
[2024-01-25 20:14:17,794] [INFO] Task started: fastANI
[2024-01-25 20:14:17,795] [INFO] Running command: fastANI --query /var/lib/cwl/stg8e608ba6-62ce-4d06-9c38-7464d8c43d2a/GCF_023556335.1_ASM2355633v1_genomic.fna.gz --refList GCF_023556335.1_ASM2355633v1_genomic.fna/target_genomes.txt --output GCF_023556335.1_ASM2355633v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:14:28,310] [INFO] Task succeeded: fastANI
[2024-01-25 20:14:28,310] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaab77b81-d635-4b6d-a8a2-3499e62e2c7f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:14:28,311] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaab77b81-d635-4b6d-a8a2-3499e62e2c7f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:14:28,319] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 20:14:28,319] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 20:14:28,319] [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
Stenotrophomonas nitritireducens	strain=DSM 12575	GCA_001431425.1	83617	83617	type	True	88.1624	859	1123	95	below_threshold
Stenotrophomonas acidaminiphila	strain=JCM 13310	GCA_001431595.1	128780	128780	type	True	87.77	825	1123	95	below_threshold
Stenotrophomonas acidaminiphila	strain=DSM 13117	GCA_024221815.1	128780	128780	type	True	87.7421	877	1123	95	below_threshold
Stenotrophomonas daejeonensis	strain=JCM 16244	GCA_001431505.1	659018	659018	type	True	86.9222	758	1123	95	below_threshold
Stenotrophomonas pictorum	strain=JCM 9942	GCA_001310775.1	86184	86184	type	True	84.4524	490	1123	95	below_threshold
Stenotrophomonas bentonitica	strain=DSM 103927	GCA_013185915.1	1450134	1450134	type	True	83.2278	702	1123	95	below_threshold
Stenotrophomonas humi	strain=DSM 18929	GCA_001431415.1	405444	405444	type	True	83.2209	766	1123	95	below_threshold
Xanthomonas massiliensis	strain=SN8	GCA_900018785.1	1720302	1720302	type	True	82.8521	710	1123	95	below_threshold
Pseudoxanthomonas jiangsuensis	strain=DSM 22398	GCA_010093185.1	619688	619688	type	True	82.6304	675	1123	95	below_threshold
Stenotrophomonas pennii	strain=Sa5BUN4	GCA_014836545.1	2762239	2762239	type	True	82.0809	676	1123	95	below_threshold
Xanthomonas hydrangeae	strain=LMG 31884	GCA_905142475.1	2775159	2775159	type	True	80.6238	633	1123	95	below_threshold
Xanthomonas hortorum	strain=CFBP 2533	GCA_021353095.1	56454	56454	pathovar	True	80.5148	618	1123	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:14:28,320] [INFO] DFAST Taxonomy check result was written to GCF_023556335.1_ASM2355633v1_genomic.fna/tc_result.tsv
[2024-01-25 20:14:28,321] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:14:28,321] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:14:28,321] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaab77b81-d635-4b6d-a8a2-3499e62e2c7f/dqc_reference/checkm_data
[2024-01-25 20:14:28,322] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:14:28,362] [INFO] Task started: CheckM
[2024-01-25 20:14:28,362] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_023556335.1_ASM2355633v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_023556335.1_ASM2355633v1_genomic.fna/checkm_input GCF_023556335.1_ASM2355633v1_genomic.fna/checkm_result
[2024-01-25 20:15:18,862] [INFO] Task succeeded: CheckM
[2024-01-25 20:15:18,864] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:15:18,888] [INFO] ===== Completeness check finished =====
[2024-01-25 20:15:18,888] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:15:18,889] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_023556335.1_ASM2355633v1_genomic.fna/markers.fasta)
[2024-01-25 20:15:18,889] [INFO] Task started: Blastn
[2024-01-25 20:15:18,889] [INFO] Running command: blastn -query GCF_023556335.1_ASM2355633v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaab77b81-d635-4b6d-a8a2-3499e62e2c7f/dqc_reference/reference_markers_gtdb.fasta -out GCF_023556335.1_ASM2355633v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:15:20,940] [INFO] Task succeeded: Blastn
[2024-01-25 20:15:20,943] [INFO] Selected 9 target genomes.
[2024-01-25 20:15:20,943] [INFO] Target genome list was writen to GCF_023556335.1_ASM2355633v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:15:20,948] [INFO] Task started: fastANI
[2024-01-25 20:15:20,948] [INFO] Running command: fastANI --query /var/lib/cwl/stg8e608ba6-62ce-4d06-9c38-7464d8c43d2a/GCF_023556335.1_ASM2355633v1_genomic.fna.gz --refList GCF_023556335.1_ASM2355633v1_genomic.fna/target_genomes_gtdb.txt --output GCF_023556335.1_ASM2355633v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:15:29,347] [INFO] Task succeeded: fastANI
[2024-01-25 20:15:29,353] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 20:15:29,354] [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_009496535.1	s__Stenotrophomonas sp003504055	88.3883	901	1123	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	96.53	96.53	0.92	0.92	2	-
GCF_001431425.1	s__Stenotrophomonas nitritireducens	88.1006	863	1123	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	98.94	98.42	0.92	0.89	3	-
GCF_002951995.1	s__Stenotrophomonas acidaminiphila_A	87.9115	881	1123	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	98.50	98.36	0.92	0.88	13	-
GCF_001431595.1	s__Stenotrophomonas acidaminiphila	87.7806	823	1123	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	98.49	97.05	0.89	0.86	11	-
GCF_001431505.1	s__Stenotrophomonas daejeonensis	86.9684	755	1123	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900078405.1	s__Stenotrophomonas sp900078405	86.3963	783	1123	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002799165.1	s__Stenotrophomonas maltophilia_Q	83.2201	758	1123	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	97.69	95.30	0.93	0.83	9	-
GCF_004216795.1	s__Stenotrophomonas_A sp004216795	83.0109	698	1123	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900018785.1	s__Xanthomonas_B massiliensis	82.8988	706	1123	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas_B	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-25 20:15:29,355] [INFO] GTDB search result was written to GCF_023556335.1_ASM2355633v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:15:29,355] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:15:29,359] [INFO] DFAST_QC result json was written to GCF_023556335.1_ASM2355633v1_genomic.fna/dqc_result.json
[2024-01-25 20:15:29,359] [INFO] DFAST_QC completed!
[2024-01-25 20:15:29,359] [INFO] Total running time: 0h1m24s