[2024-01-25 20:06:35,518] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:06:35,522] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:06:35,522] [INFO] DQC Reference Directory: /var/lib/cwl/stg2bd62957-875e-41fc-963a-65b5eee7b2c7/dqc_reference
[2024-01-25 20:06:36,712] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:06:36,713] [INFO] Task started: Prodigal
[2024-01-25 20:06:36,713] [INFO] Running command: gunzip -c /var/lib/cwl/stg483d628f-45a5-426c-894f-7a389d94420f/GCF_025234655.1_ASM2523465v1_genomic.fna.gz | prodigal -d GCF_025234655.1_ASM2523465v1_genomic.fna/cds.fna -a GCF_025234655.1_ASM2523465v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:06:42,786] [INFO] Task succeeded: Prodigal
[2024-01-25 20:06:42,787] [INFO] Task started: HMMsearch
[2024-01-25 20:06:42,787] [INFO] Running command: hmmsearch --tblout GCF_025234655.1_ASM2523465v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2bd62957-875e-41fc-963a-65b5eee7b2c7/dqc_reference/reference_markers.hmm GCF_025234655.1_ASM2523465v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:06:42,998] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:06:42,999] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg483d628f-45a5-426c-894f-7a389d94420f/GCF_025234655.1_ASM2523465v1_genomic.fna.gz]
[2024-01-25 20:06:43,026] [INFO] Query marker FASTA was written to GCF_025234655.1_ASM2523465v1_genomic.fna/markers.fasta
[2024-01-25 20:06:43,026] [INFO] Task started: Blastn
[2024-01-25 20:06:43,026] [INFO] Running command: blastn -query GCF_025234655.1_ASM2523465v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2bd62957-875e-41fc-963a-65b5eee7b2c7/dqc_reference/reference_markers.fasta -out GCF_025234655.1_ASM2523465v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:06:43,630] [INFO] Task succeeded: Blastn
[2024-01-25 20:06:43,633] [INFO] Selected 9 target genomes.
[2024-01-25 20:06:43,633] [INFO] Target genome list was writen to GCF_025234655.1_ASM2523465v1_genomic.fna/target_genomes.txt
[2024-01-25 20:06:43,643] [INFO] Task started: fastANI
[2024-01-25 20:06:43,643] [INFO] Running command: fastANI --query /var/lib/cwl/stg483d628f-45a5-426c-894f-7a389d94420f/GCF_025234655.1_ASM2523465v1_genomic.fna.gz --refList GCF_025234655.1_ASM2523465v1_genomic.fna/target_genomes.txt --output GCF_025234655.1_ASM2523465v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:06:49,408] [INFO] Task succeeded: fastANI
[2024-01-25 20:06:49,409] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2bd62957-875e-41fc-963a-65b5eee7b2c7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:06:49,409] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2bd62957-875e-41fc-963a-65b5eee7b2c7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:06:49,416] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 20:06:49,416] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 20:06:49,416] [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
Exiguobacterium undae	strain=DSM 14481	GCA_000620805.1	169177	169177	type	True	87.1063	792	879	95	below_threshold
Exiguobacterium artemiae	strain=9AN	GCA_025234645.1	340145	340145	type	True	85.6254	675	879	95	below_threshold
Exiguobacterium sibiricum	strain=255-15	GCA_000019905.1	332410	332410	type	True	85.473	761	879	95	below_threshold
Exiguobacterium oxidotolerans	strain=JCM 12280	GCA_000702625.1	223958	223958	type	True	82.347	597	879	95	below_threshold
Exiguobacterium enclense	strain=NIO-1109	GCA_900096925.1	1017277	1017277	type	True	80.9563	501	879	95	below_threshold
Exiguobacterium enclense	strain=NIO-1109	GCA_001456895.1	1017277	1017277	type	True	80.9563	501	879	95	below_threshold
Exiguobacterium acetylicum	strain=DSM 20416	GCA_000702605.1	41170	41170	suspected-type	True	80.9099	509	879	95	below_threshold
Exiguobacterium indicum	strain=HHS 31	GCA_001939065.1	296995	296995	type	True	80.842	485	879	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:06:49,418] [INFO] DFAST Taxonomy check result was written to GCF_025234655.1_ASM2523465v1_genomic.fna/tc_result.tsv
[2024-01-25 20:06:49,418] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:06:49,418] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:06:49,419] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2bd62957-875e-41fc-963a-65b5eee7b2c7/dqc_reference/checkm_data
[2024-01-25 20:06:49,419] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:06:49,451] [INFO] Task started: CheckM
[2024-01-25 20:06:49,452] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025234655.1_ASM2523465v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025234655.1_ASM2523465v1_genomic.fna/checkm_input GCF_025234655.1_ASM2523465v1_genomic.fna/checkm_result
[2024-01-25 20:07:12,974] [INFO] Task succeeded: CheckM
[2024-01-25 20:07:12,975] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:07:12,991] [INFO] ===== Completeness check finished =====
[2024-01-25 20:07:12,991] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:07:12,991] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025234655.1_ASM2523465v1_genomic.fna/markers.fasta)
[2024-01-25 20:07:12,991] [INFO] Task started: Blastn
[2024-01-25 20:07:12,991] [INFO] Running command: blastn -query GCF_025234655.1_ASM2523465v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2bd62957-875e-41fc-963a-65b5eee7b2c7/dqc_reference/reference_markers_gtdb.fasta -out GCF_025234655.1_ASM2523465v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:07:13,881] [INFO] Task succeeded: Blastn
[2024-01-25 20:07:13,883] [INFO] Selected 9 target genomes.
[2024-01-25 20:07:13,884] [INFO] Target genome list was writen to GCF_025234655.1_ASM2523465v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:07:13,892] [INFO] Task started: fastANI
[2024-01-25 20:07:13,893] [INFO] Running command: fastANI --query /var/lib/cwl/stg483d628f-45a5-426c-894f-7a389d94420f/GCF_025234655.1_ASM2523465v1_genomic.fna.gz --refList GCF_025234655.1_ASM2523465v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025234655.1_ASM2523465v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:07:20,350] [INFO] Task succeeded: fastANI
[2024-01-25 20:07:20,357] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:07:20,357] [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_000685865.1	s__Exiguobacterium_A antarcticum	98.6038	861	879	d__Bacteria;p__Firmicutes;c__Bacilli;o__Exiguobacterales;f__Exiguobacteraceae;g__Exiguobacterium_A	95.0	98.55	98.18	0.96	0.96	5	conclusive
GCF_001870785.1	s__Exiguobacterium_A sp001870785	94.7265	805	879	d__Bacteria;p__Firmicutes;c__Bacilli;o__Exiguobacterales;f__Exiguobacteraceae;g__Exiguobacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000620805.1	s__Exiguobacterium_A undae	87.0909	794	879	d__Bacteria;p__Firmicutes;c__Bacilli;o__Exiguobacterales;f__Exiguobacteraceae;g__Exiguobacterium_A	95.0	97.90	97.06	0.95	0.92	5	-
GCF_000620865.1	s__Exiguobacterium_A sibiricum_A	86.5228	770	879	d__Bacteria;p__Firmicutes;c__Bacilli;o__Exiguobacterales;f__Exiguobacteraceae;g__Exiguobacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003339585.1	s__Exiguobacterium_A sp003339585	86.0239	771	879	d__Bacteria;p__Firmicutes;c__Bacilli;o__Exiguobacterales;f__Exiguobacteraceae;g__Exiguobacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014524545.1	s__Exiguobacterium_A sp004339505	85.7997	773	879	d__Bacteria;p__Firmicutes;c__Bacilli;o__Exiguobacterales;f__Exiguobacteraceae;g__Exiguobacterium_A	95.0	98.54	98.54	0.96	0.96	3	-
GCF_000019905.1	s__Exiguobacterium_A sibiricum	85.4544	763	879	d__Bacteria;p__Firmicutes;c__Bacilli;o__Exiguobacterales;f__Exiguobacteraceae;g__Exiguobacterium_A	95.0	96.48	95.46	0.93	0.90	4	-
GCF_000702625.1	s__Exiguobacterium_A oxidotolerans	82.3382	598	879	d__Bacteria;p__Firmicutes;c__Bacilli;o__Exiguobacterales;f__Exiguobacteraceae;g__Exiguobacterium_A	95.0	95.91	95.68	0.90	0.87	15	-
GCF_018618755.1	s__Exiguobacterium_A sp018618755	82.2912	621	879	d__Bacteria;p__Firmicutes;c__Bacilli;o__Exiguobacterales;f__Exiguobacteraceae;g__Exiguobacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:07:20,358] [INFO] GTDB search result was written to GCF_025234655.1_ASM2523465v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:07:20,359] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:07:20,368] [INFO] DFAST_QC result json was written to GCF_025234655.1_ASM2523465v1_genomic.fna/dqc_result.json
[2024-01-25 20:07:20,369] [INFO] DFAST_QC completed!
[2024-01-25 20:07:20,369] [INFO] Total running time: 0h0m45s