[2023-06-29 09:02:15,136] [INFO] DFAST_QC pipeline started.
[2023-06-29 09:02:15,140] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 09:02:15,140] [INFO] DQC Reference Directory: /var/lib/cwl/stgb651da5e-dceb-41c7-9ac2-1b095a0c627d/dqc_reference
[2023-06-29 09:02:16,480] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 09:02:16,481] [INFO] Task started: Prodigal
[2023-06-29 09:02:16,481] [INFO] Running command: gunzip -c /var/lib/cwl/stga7c04280-3866-4f5a-9e9a-935fbd726158/GCA_020285445.1_ASM2028544v1_genomic.fna.gz | prodigal -d GCA_020285445.1_ASM2028544v1_genomic.fna/cds.fna -a GCA_020285445.1_ASM2028544v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 09:02:35,673] [INFO] Task succeeded: Prodigal
[2023-06-29 09:02:35,673] [INFO] Task started: HMMsearch
[2023-06-29 09:02:35,673] [INFO] Running command: hmmsearch --tblout GCA_020285445.1_ASM2028544v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb651da5e-dceb-41c7-9ac2-1b095a0c627d/dqc_reference/reference_markers.hmm GCA_020285445.1_ASM2028544v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 09:02:35,946] [INFO] Task succeeded: HMMsearch
[2023-06-29 09:02:35,948] [INFO] Found 6/6 markers.
[2023-06-29 09:02:35,999] [INFO] Query marker FASTA was written to GCA_020285445.1_ASM2028544v1_genomic.fna/markers.fasta
[2023-06-29 09:02:35,999] [INFO] Task started: Blastn
[2023-06-29 09:02:36,000] [INFO] Running command: blastn -query GCA_020285445.1_ASM2028544v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb651da5e-dceb-41c7-9ac2-1b095a0c627d/dqc_reference/reference_markers.fasta -out GCA_020285445.1_ASM2028544v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 09:02:36,617] [INFO] Task succeeded: Blastn
[2023-06-29 09:02:36,639] [INFO] Selected 25 target genomes.
[2023-06-29 09:02:36,639] [INFO] Target genome list was writen to GCA_020285445.1_ASM2028544v1_genomic.fna/target_genomes.txt
[2023-06-29 09:02:36,641] [INFO] Task started: fastANI
[2023-06-29 09:02:36,641] [INFO] Running command: fastANI --query /var/lib/cwl/stga7c04280-3866-4f5a-9e9a-935fbd726158/GCA_020285445.1_ASM2028544v1_genomic.fna.gz --refList GCA_020285445.1_ASM2028544v1_genomic.fna/target_genomes.txt --output GCA_020285445.1_ASM2028544v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 09:02:57,215] [INFO] Task succeeded: fastANI
[2023-06-29 09:02:57,216] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb651da5e-dceb-41c7-9ac2-1b095a0c627d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 09:02:57,217] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb651da5e-dceb-41c7-9ac2-1b095a0c627d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 09:02:57,221] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 09:02:57,222] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 09:02:57,222] [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
Chryseotalea sanaruensis	strain=Ys	GCA_003990915.1	2482724	2482724	type	True	75.5344	53	1297	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 09:02:57,224] [INFO] DFAST Taxonomy check result was written to GCA_020285445.1_ASM2028544v1_genomic.fna/tc_result.tsv
[2023-06-29 09:02:57,225] [INFO] ===== Taxonomy check completed =====
[2023-06-29 09:02:57,225] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 09:02:57,225] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb651da5e-dceb-41c7-9ac2-1b095a0c627d/dqc_reference/checkm_data
[2023-06-29 09:02:57,227] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 09:02:57,267] [INFO] Task started: CheckM
[2023-06-29 09:02:57,268] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020285445.1_ASM2028544v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020285445.1_ASM2028544v1_genomic.fna/checkm_input GCA_020285445.1_ASM2028544v1_genomic.fna/checkm_result
[2023-06-29 09:03:53,926] [INFO] Task succeeded: CheckM
[2023-06-29 09:03:53,928] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 09:03:53,951] [INFO] ===== Completeness check finished =====
[2023-06-29 09:03:53,951] [INFO] ===== Start GTDB Search =====
[2023-06-29 09:03:53,952] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020285445.1_ASM2028544v1_genomic.fna/markers.fasta)
[2023-06-29 09:03:53,952] [INFO] Task started: Blastn
[2023-06-29 09:03:53,952] [INFO] Running command: blastn -query GCA_020285445.1_ASM2028544v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb651da5e-dceb-41c7-9ac2-1b095a0c627d/dqc_reference/reference_markers_gtdb.fasta -out GCA_020285445.1_ASM2028544v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 09:03:54,714] [INFO] Task succeeded: Blastn
[2023-06-29 09:03:54,719] [INFO] Selected 22 target genomes.
[2023-06-29 09:03:54,719] [INFO] Target genome list was writen to GCA_020285445.1_ASM2028544v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 09:03:54,720] [INFO] Task started: fastANI
[2023-06-29 09:03:54,720] [INFO] Running command: fastANI --query /var/lib/cwl/stga7c04280-3866-4f5a-9e9a-935fbd726158/GCA_020285445.1_ASM2028544v1_genomic.fna.gz --refList GCA_020285445.1_ASM2028544v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020285445.1_ASM2028544v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 09:04:11,019] [INFO] Task succeeded: fastANI
[2023-06-29 09:04:11,035] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 09:04:11,035] [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_013140395.1	s__ELB16-189 sp013140395	88.4659	551	1297	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__ELB16-189	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013298505.1	s__ELB16-189 sp013298505	78.6112	260	1297	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__ELB16-189	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018267275.1	s__ELB16-189 sp018267275	78.2046	152	1297	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__ELB16-189	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016191555.1	s__ELB16-189 sp016191555	77.1608	168	1297	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__ELB16-189	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013140555.1	s__ELB16-189 sp013140555	77.0623	174	1297	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__ELB16-189	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002398365.1	s__ELB16-189 sp002398365	76.9112	217	1297	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__ELB16-189	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013414665.1	s__ELB16-189 sp013414665	76.0813	88	1297	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__ELB16-189	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018266435.1	s__ELB16-189 sp018266435	76.0483	70	1297	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__ELB16-189	95.0	99.94	99.94	0.96	0.96	2	-
GCA_015472025.1	s__ELB16-189 sp015472025	76.0209	63	1297	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__ELB16-189	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018267285.1	s__ELB16-189 sp018267285	75.9286	65	1297	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__ELB16-189	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001567185.1	s__ELB16-189 sp001567185	75.8249	88	1297	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__ELB16-189	95.0	98.67	98.67	0.88	0.88	2	-
GCA_018267215.1	s__ELB16-189 sp018267215	75.75	71	1297	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__ELB16-189	95.0	99.99	99.99	0.96	0.96	2	-
GCA_018266055.1	s__ELB16-189 sp018266055	75.6806	76	1297	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__ELB16-189	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003990915.1	s__Chryseotalea sanaruensis	75.5524	52	1297	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Chryseotalea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 09:04:11,037] [INFO] GTDB search result was written to GCA_020285445.1_ASM2028544v1_genomic.fna/result_gtdb.tsv
[2023-06-29 09:04:11,037] [INFO] ===== GTDB Search completed =====
[2023-06-29 09:04:11,041] [INFO] DFAST_QC result json was written to GCA_020285445.1_ASM2028544v1_genomic.fna/dqc_result.json
[2023-06-29 09:04:11,041] [INFO] DFAST_QC completed!
[2023-06-29 09:04:11,041] [INFO] Total running time: 0h1m56s