[2023-06-19 10:05:48,615] [INFO] DFAST_QC pipeline started.
[2023-06-19 10:05:48,619] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 10:05:48,619] [INFO] DQC Reference Directory: /var/lib/cwl/stgf22686f1-8f94-4520-82f3-ece3bd5b0e47/dqc_reference
[2023-06-19 10:05:50,175] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 10:05:50,176] [INFO] Task started: Prodigal
[2023-06-19 10:05:50,176] [INFO] Running command: gunzip -c /var/lib/cwl/stg5aa97be4-68f4-467b-8e9f-eca802c9f3da/GCA_018371335.1_ASM1837133v1_genomic.fna.gz | prodigal -d GCA_018371335.1_ASM1837133v1_genomic.fna/cds.fna -a GCA_018371335.1_ASM1837133v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 10:05:55,672] [INFO] Task succeeded: Prodigal
[2023-06-19 10:05:55,673] [INFO] Task started: HMMsearch
[2023-06-19 10:05:55,673] [INFO] Running command: hmmsearch --tblout GCA_018371335.1_ASM1837133v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf22686f1-8f94-4520-82f3-ece3bd5b0e47/dqc_reference/reference_markers.hmm GCA_018371335.1_ASM1837133v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 10:05:55,937] [INFO] Task succeeded: HMMsearch
[2023-06-19 10:05:55,938] [INFO] Found 6/6 markers.
[2023-06-19 10:05:55,973] [INFO] Query marker FASTA was written to GCA_018371335.1_ASM1837133v1_genomic.fna/markers.fasta
[2023-06-19 10:05:55,974] [INFO] Task started: Blastn
[2023-06-19 10:05:55,974] [INFO] Running command: blastn -query GCA_018371335.1_ASM1837133v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf22686f1-8f94-4520-82f3-ece3bd5b0e47/dqc_reference/reference_markers.fasta -out GCA_018371335.1_ASM1837133v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 10:05:56,644] [INFO] Task succeeded: Blastn
[2023-06-19 10:05:56,649] [INFO] Selected 27 target genomes.
[2023-06-19 10:05:56,649] [INFO] Target genome list was writen to GCA_018371335.1_ASM1837133v1_genomic.fna/target_genomes.txt
[2023-06-19 10:05:56,658] [INFO] Task started: fastANI
[2023-06-19 10:05:56,658] [INFO] Running command: fastANI --query /var/lib/cwl/stg5aa97be4-68f4-467b-8e9f-eca802c9f3da/GCA_018371335.1_ASM1837133v1_genomic.fna.gz --refList GCA_018371335.1_ASM1837133v1_genomic.fna/target_genomes.txt --output GCA_018371335.1_ASM1837133v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 10:06:16,298] [INFO] Task succeeded: fastANI
[2023-06-19 10:06:16,298] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf22686f1-8f94-4520-82f3-ece3bd5b0e47/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 10:06:16,299] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf22686f1-8f94-4520-82f3-ece3bd5b0e47/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 10:06:16,307] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2023-06-19 10:06:16,307] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-19 10:06:16,307] [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
Duodenibacillus massiliensis	strain=Marseille-P2968	GCA_900128485.1	1852381	1852381	type	True	98.7054	593	642	95	conclusive
Sutterella parvirubra	strain=YIT 11816	GCA_000250875.1	437898	437898	type	True	77.7063	95	642	95	below_threshold
Sutterella megalosphaeroides	strain=6FBBBH3	GCA_003609995.1	2494234	2494234	type	True	77.4769	113	642	95	below_threshold
Sutterella faecalis	strain=KGMB03119	GCA_006337085.1	2584944	2584944	type	True	77.4208	110	642	95	below_threshold
Sutterella wadsworthensis	strain=DSM 14016	GCA_003315195.1	40545	40545	type	True	77.2542	72	642	95	below_threshold
Sutterella wadsworthensis	strain=FDAARGOS_1159	GCA_016724805.1	40545	40545	type	True	77.2197	73	642	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 10:06:16,309] [INFO] DFAST Taxonomy check result was written to GCA_018371335.1_ASM1837133v1_genomic.fna/tc_result.tsv
[2023-06-19 10:06:16,310] [INFO] ===== Taxonomy check completed =====
[2023-06-19 10:06:16,310] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 10:06:16,311] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf22686f1-8f94-4520-82f3-ece3bd5b0e47/dqc_reference/checkm_data
[2023-06-19 10:06:16,312] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 10:06:16,342] [INFO] Task started: CheckM
[2023-06-19 10:06:16,343] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018371335.1_ASM1837133v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018371335.1_ASM1837133v1_genomic.fna/checkm_input GCA_018371335.1_ASM1837133v1_genomic.fna/checkm_result
[2023-06-19 10:06:39,751] [INFO] Task succeeded: CheckM
[2023-06-19 10:06:39,752] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 10:06:39,774] [INFO] ===== Completeness check finished =====
[2023-06-19 10:06:39,774] [INFO] ===== Start GTDB Search =====
[2023-06-19 10:06:39,775] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018371335.1_ASM1837133v1_genomic.fna/markers.fasta)
[2023-06-19 10:06:39,775] [INFO] Task started: Blastn
[2023-06-19 10:06:39,775] [INFO] Running command: blastn -query GCA_018371335.1_ASM1837133v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf22686f1-8f94-4520-82f3-ece3bd5b0e47/dqc_reference/reference_markers_gtdb.fasta -out GCA_018371335.1_ASM1837133v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 10:06:40,745] [INFO] Task succeeded: Blastn
[2023-06-19 10:06:40,749] [INFO] Selected 17 target genomes.
[2023-06-19 10:06:40,749] [INFO] Target genome list was writen to GCA_018371335.1_ASM1837133v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 10:06:40,758] [INFO] Task started: fastANI
[2023-06-19 10:06:40,758] [INFO] Running command: fastANI --query /var/lib/cwl/stg5aa97be4-68f4-467b-8e9f-eca802c9f3da/GCA_018371335.1_ASM1837133v1_genomic.fna.gz --refList GCA_018371335.1_ASM1837133v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018371335.1_ASM1837133v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 10:06:48,469] [INFO] Task succeeded: fastANI
[2023-06-19 10:06:48,486] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 10:06:48,486] [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_900128485.1	s__Duodenibacillus massiliensis	98.7054	593	642	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duodenibacillus	95.0	98.71	98.48	0.94	0.92	8	conclusive
GCA_900544255.1	s__Duodenibacillus sp900544255	79.433	234	642	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duodenibacillus	95.0	97.25	96.77	0.84	0.84	3	-
GCA_900762555.1	s__Duodenibacillus sp900762555	79.0564	216	642	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duodenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003472385.1	s__Duodenibacillus intestinigallinarum	78.8672	163	642	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duodenibacillus	95.0	98.80	98.31	0.95	0.93	6	-
GCA_900315045.1	s__Duodenibacillus sp900315045	78.6627	121	642	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duodenibacillus	95.0	98.77	97.52	0.92	0.86	10	-
GCA_900767875.1	s__Duodenibacillus sp900767875	78.6416	190	642	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duodenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900552915.1	s__Duodenibacillus sp900552915	78.5461	142	642	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duodenibacillus	95.0	98.20	98.20	0.77	0.77	2	-
GCA_900538905.1	s__Duodenibacillus intestinavium	78.5272	149	642	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duodenibacillus	95.0	97.77	96.85	0.89	0.87	4	-
GCA_900552545.1	s__Duodenibacillus sp900552545	78.5042	184	642	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duodenibacillus	95.0	98.45	98.39	0.81	0.78	3	-
GCF_009183815.1	s__Sutterella seckii_A	78.1248	119	642	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Sutterella	95.0	98.09	95.34	0.87	0.81	4	-
GCA_900543805.1	s__Sutterella merdavium	77.785	107	642	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Sutterella	95.0	98.29	97.30	0.92	0.87	4	-
GCA_017628205.1	s__Duodenibacillus sp017628205	77.6696	100	642	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duodenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006337085.1	s__Sutterella faecalis	77.4721	108	642	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Sutterella	95.0	99.36	97.93	0.96	0.93	5	-
GCA_900544335.1	s__Duodenibacillus sp900544335	76.831	60	642	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duodenibacillus	95.0	98.18	97.92	0.85	0.85	3	-
--------------------------------------------------------------------------------
[2023-06-19 10:06:48,488] [INFO] GTDB search result was written to GCA_018371335.1_ASM1837133v1_genomic.fna/result_gtdb.tsv
[2023-06-19 10:06:48,489] [INFO] ===== GTDB Search completed =====
[2023-06-19 10:06:48,492] [INFO] DFAST_QC result json was written to GCA_018371335.1_ASM1837133v1_genomic.fna/dqc_result.json
[2023-06-19 10:06:48,492] [INFO] DFAST_QC completed!
[2023-06-19 10:06:48,492] [INFO] Total running time: 0h0m60s