[2023-06-05 07:09:43,815] [INFO] DFAST_QC pipeline started.
[2023-06-05 07:09:43,818] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 07:09:43,818] [INFO] DQC Reference Directory: /var/lib/cwl/stg803250d2-a417-4625-a860-cdcd5c7e462d/dqc_reference
[2023-06-05 07:09:45,229] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 07:09:45,230] [INFO] Task started: Prodigal
[2023-06-05 07:09:45,231] [INFO] Running command: gunzip -c /var/lib/cwl/stg747cbb45-df58-4ce2-a1d4-ae64d98f1c94/GCA_004294095.1_ASM429409v1_genomic.fna.gz | prodigal -d GCA_004294095.1_ASM429409v1_genomic.fna/cds.fna -a GCA_004294095.1_ASM429409v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 07:10:04,481] [INFO] Task succeeded: Prodigal
[2023-06-05 07:10:04,482] [INFO] Task started: HMMsearch
[2023-06-05 07:10:04,482] [INFO] Running command: hmmsearch --tblout GCA_004294095.1_ASM429409v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg803250d2-a417-4625-a860-cdcd5c7e462d/dqc_reference/reference_markers.hmm GCA_004294095.1_ASM429409v1_genomic.fna/protein.faa > /dev/null
[2023-06-05 07:10:04,722] [INFO] Task succeeded: HMMsearch
[2023-06-05 07:10:04,723] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg747cbb45-df58-4ce2-a1d4-ae64d98f1c94/GCA_004294095.1_ASM429409v1_genomic.fna.gz]
[2023-06-05 07:10:04,754] [INFO] Query marker FASTA was written to GCA_004294095.1_ASM429409v1_genomic.fna/markers.fasta
[2023-06-05 07:10:04,755] [INFO] Task started: Blastn
[2023-06-05 07:10:04,755] [INFO] Running command: blastn -query GCA_004294095.1_ASM429409v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg803250d2-a417-4625-a860-cdcd5c7e462d/dqc_reference/reference_markers.fasta -out GCA_004294095.1_ASM429409v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 07:10:05,405] [INFO] Task succeeded: Blastn
[2023-06-05 07:10:05,434] [INFO] Selected 16 target genomes.
[2023-06-05 07:10:05,435] [INFO] Target genome list was writen to GCA_004294095.1_ASM429409v1_genomic.fna/target_genomes.txt
[2023-06-05 07:10:05,438] [INFO] Task started: fastANI
[2023-06-05 07:10:05,438] [INFO] Running command: fastANI --query /var/lib/cwl/stg747cbb45-df58-4ce2-a1d4-ae64d98f1c94/GCA_004294095.1_ASM429409v1_genomic.fna.gz --refList GCA_004294095.1_ASM429409v1_genomic.fna/target_genomes.txt --output GCA_004294095.1_ASM429409v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 07:10:16,958] [INFO] Task succeeded: fastANI
[2023-06-05 07:10:16,958] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg803250d2-a417-4625-a860-cdcd5c7e462d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 07:10:16,959] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg803250d2-a417-4625-a860-cdcd5c7e462d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 07:10:16,964] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 07:10:16,964] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 07:10:16,964] [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
Luteolibacter yonseiensis	strain=JCM 18052	GCA_016595465.1	1144680	1144680	type	True	77.061	80	941	95	below_threshold
Luteolibacter pohnpeiensis	strain=KCTC 22041	GCA_016595435.1	454153	454153	type	True	76.0788	67	941	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 07:10:16,967] [INFO] DFAST Taxonomy check result was written to GCA_004294095.1_ASM429409v1_genomic.fna/tc_result.tsv
[2023-06-05 07:10:16,967] [INFO] ===== Taxonomy check completed =====
[2023-06-05 07:10:16,968] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 07:10:16,968] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg803250d2-a417-4625-a860-cdcd5c7e462d/dqc_reference/checkm_data
[2023-06-05 07:10:16,970] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 07:10:17,006] [INFO] Task started: CheckM
[2023-06-05 07:10:17,006] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_004294095.1_ASM429409v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_004294095.1_ASM429409v1_genomic.fna/checkm_input GCA_004294095.1_ASM429409v1_genomic.fna/checkm_result
[2023-06-05 07:11:12,740] [INFO] Task succeeded: CheckM
[2023-06-05 07:11:12,742] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 07:11:12,767] [INFO] ===== Completeness check finished =====
[2023-06-05 07:11:12,768] [INFO] ===== Start GTDB Search =====
[2023-06-05 07:11:12,768] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_004294095.1_ASM429409v1_genomic.fna/markers.fasta)
[2023-06-05 07:11:12,769] [INFO] Task started: Blastn
[2023-06-05 07:11:12,769] [INFO] Running command: blastn -query GCA_004294095.1_ASM429409v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg803250d2-a417-4625-a860-cdcd5c7e462d/dqc_reference/reference_markers_gtdb.fasta -out GCA_004294095.1_ASM429409v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 07:11:13,714] [INFO] Task succeeded: Blastn
[2023-06-05 07:11:13,719] [INFO] Selected 17 target genomes.
[2023-06-05 07:11:13,719] [INFO] Target genome list was writen to GCA_004294095.1_ASM429409v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 07:11:13,836] [INFO] Task started: fastANI
[2023-06-05 07:11:13,837] [INFO] Running command: fastANI --query /var/lib/cwl/stg747cbb45-df58-4ce2-a1d4-ae64d98f1c94/GCA_004294095.1_ASM429409v1_genomic.fna.gz --refList GCA_004294095.1_ASM429409v1_genomic.fna/target_genomes_gtdb.txt --output GCA_004294095.1_ASM429409v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 07:11:26,258] [INFO] Task succeeded: fastANI
[2023-06-05 07:11:26,269] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 07:11:26,269] [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_004294095.1	s__Luteolibacter sp004294095	100.0	938	941	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	98.11	98.11	0.89	0.89	2	conclusive
GCF_016595465.1	s__Luteolibacter yonseiensis	77.061	80	941	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903919975.1	s__Luteolibacter sp903919975	76.796	93	941	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	99.90	99.84	0.96	0.96	3	-
GCA_002307065.1	s__Luteolibacter sp002307065	76.6963	71	941	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903906515.1	s__Luteolibacter sp903906515	76.4956	70	941	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	99.85	99.81	0.93	0.92	3	-
GCA_003820635.1	s__Luteolibacter sp003820635	76.3449	91	941	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018402445.1	s__Luteolibacter sp018402445	76.2729	59	941	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903908495.1	s__Luteolibacter sp903908495	76.2666	62	941	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903827375.1	s__Luteolibacter sp903827375	75.9945	57	941	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	99.41	99.23	0.90	0.81	16	-
GCA_903934285.1	s__Luteolibacter sp903934285	75.9843	70	941	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	99.86	99.86	0.92	0.92	3	-
GCA_017301995.1	s__Luteolibacter sp017301995	75.9628	60	941	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 07:11:26,272] [INFO] GTDB search result was written to GCA_004294095.1_ASM429409v1_genomic.fna/result_gtdb.tsv
[2023-06-05 07:11:26,272] [INFO] ===== GTDB Search completed =====
[2023-06-05 07:11:26,275] [INFO] DFAST_QC result json was written to GCA_004294095.1_ASM429409v1_genomic.fna/dqc_result.json
[2023-06-05 07:11:26,275] [INFO] DFAST_QC completed!
[2023-06-05 07:11:26,275] [INFO] Total running time: 0h1m42s