[2024-01-24 12:44:43,696] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:44:43,697] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:44:43,698] [INFO] DQC Reference Directory: /var/lib/cwl/stgd9885b2a-3770-4108-9c1e-4e7b10d31426/dqc_reference
[2024-01-24 12:44:45,190] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:44:45,191] [INFO] Task started: Prodigal
[2024-01-24 12:44:45,191] [INFO] Running command: gunzip -c /var/lib/cwl/stg725972d6-c770-4d58-9977-28d60818683e/GCF_000744115.1_ASM74411v1_genomic.fna.gz | prodigal -d GCF_000744115.1_ASM74411v1_genomic.fna/cds.fna -a GCF_000744115.1_ASM74411v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:44:50,618] [INFO] Task succeeded: Prodigal
[2024-01-24 12:44:50,618] [INFO] Task started: HMMsearch
[2024-01-24 12:44:50,619] [INFO] Running command: hmmsearch --tblout GCF_000744115.1_ASM74411v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd9885b2a-3770-4108-9c1e-4e7b10d31426/dqc_reference/reference_markers.hmm GCF_000744115.1_ASM74411v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:44:50,928] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:44:50,929] [INFO] Found 6/6 markers.
[2024-01-24 12:44:50,957] [INFO] Query marker FASTA was written to GCF_000744115.1_ASM74411v1_genomic.fna/markers.fasta
[2024-01-24 12:44:50,958] [INFO] Task started: Blastn
[2024-01-24 12:44:50,958] [INFO] Running command: blastn -query GCF_000744115.1_ASM74411v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd9885b2a-3770-4108-9c1e-4e7b10d31426/dqc_reference/reference_markers.fasta -out GCF_000744115.1_ASM74411v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:44:51,554] [INFO] Task succeeded: Blastn
[2024-01-24 12:44:51,557] [INFO] Selected 12 target genomes.
[2024-01-24 12:44:51,558] [INFO] Target genome list was writen to GCF_000744115.1_ASM74411v1_genomic.fna/target_genomes.txt
[2024-01-24 12:44:51,573] [INFO] Task started: fastANI
[2024-01-24 12:44:51,573] [INFO] Running command: fastANI --query /var/lib/cwl/stg725972d6-c770-4d58-9977-28d60818683e/GCF_000744115.1_ASM74411v1_genomic.fna.gz --refList GCF_000744115.1_ASM74411v1_genomic.fna/target_genomes.txt --output GCF_000744115.1_ASM74411v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:44:58,480] [INFO] Task succeeded: fastANI
[2024-01-24 12:44:58,481] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd9885b2a-3770-4108-9c1e-4e7b10d31426/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:44:58,481] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd9885b2a-3770-4108-9c1e-4e7b10d31426/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:44:58,488] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:44:58,488] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:44:58,488] [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
Carnobacterium alterfunditum	strain=pf4	GCA_000744115.1	28230	28230	type	True	100.0	862	870	95	conclusive
Carnobacterium pleistocenium	strain=FTR1	GCA_000744285.1	181073	181073	type	True	87.0708	664	870	95	below_threshold
Carnobacterium jeotgali	strain=MS3	GCA_000745125.1	545534	545534	type	True	83.4087	557	870	95	below_threshold
Carnobacterium jeotgali	strain=MS3	GCA_000708655.1	545534	545534	type	True	83.0925	507	870	95	below_threshold
Carnobacterium viridans	strain=MPL-11	GCA_900102725.1	174587	174587	type	True	82.5756	536	870	95	below_threshold
Carnobacterium inhibens subsp. gilichinskyi	strain=WN1359	GCA_000493735.1	1266845	147709	type	True	82.1275	514	870	95	below_threshold
Carnobacterium inhibens subsp. inhibens	strain=K1	GCA_000746825.1	1758721	147709	type	True	82.1264	516	870	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:44:58,490] [INFO] DFAST Taxonomy check result was written to GCF_000744115.1_ASM74411v1_genomic.fna/tc_result.tsv
[2024-01-24 12:44:58,490] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:44:58,491] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:44:58,491] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd9885b2a-3770-4108-9c1e-4e7b10d31426/dqc_reference/checkm_data
[2024-01-24 12:44:58,492] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:44:58,523] [INFO] Task started: CheckM
[2024-01-24 12:44:58,524] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000744115.1_ASM74411v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000744115.1_ASM74411v1_genomic.fna/checkm_input GCF_000744115.1_ASM74411v1_genomic.fna/checkm_result
[2024-01-24 12:45:22,154] [INFO] Task succeeded: CheckM
[2024-01-24 12:45:22,155] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:45:22,177] [INFO] ===== Completeness check finished =====
[2024-01-24 12:45:22,178] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:45:22,178] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000744115.1_ASM74411v1_genomic.fna/markers.fasta)
[2024-01-24 12:45:22,179] [INFO] Task started: Blastn
[2024-01-24 12:45:22,179] [INFO] Running command: blastn -query GCF_000744115.1_ASM74411v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd9885b2a-3770-4108-9c1e-4e7b10d31426/dqc_reference/reference_markers_gtdb.fasta -out GCF_000744115.1_ASM74411v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:22,932] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:22,936] [INFO] Selected 6 target genomes.
[2024-01-24 12:45:22,936] [INFO] Target genome list was writen to GCF_000744115.1_ASM74411v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:45:22,970] [INFO] Task started: fastANI
[2024-01-24 12:45:22,971] [INFO] Running command: fastANI --query /var/lib/cwl/stg725972d6-c770-4d58-9977-28d60818683e/GCF_000744115.1_ASM74411v1_genomic.fna.gz --refList GCF_000744115.1_ASM74411v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000744115.1_ASM74411v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:45:27,866] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:27,877] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:45:27,878] [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_000744115.1	s__Carnobacterium_A alterfunditum	100.0	865	870	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Carnobacterium_A	95.0	98.24	96.49	0.94	0.89	3	conclusive
GCF_000744285.1	s__Carnobacterium_A pleistocenium	87.0826	664	870	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Carnobacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000745125.1	s__Carnobacterium_A jeotgali	83.4081	557	870	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Carnobacterium_A	95.0	99.33	98.67	0.94	0.87	3	-
GCF_900102725.1	s__Carnobacterium_A viridans	82.627	534	870	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Carnobacterium_A	95.0	98.44	98.44	0.88	0.88	2	-
GCF_000195575.1	s__Carnobacterium_A sp000195575	82.5697	559	870	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Carnobacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000746825.1	s__Carnobacterium_A inhibens	82.1426	518	870	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Carnobacterium_A	95.0	98.16	98.07	0.90	0.88	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:45:27,880] [INFO] GTDB search result was written to GCF_000744115.1_ASM74411v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:45:27,880] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:45:27,884] [INFO] DFAST_QC result json was written to GCF_000744115.1_ASM74411v1_genomic.fna/dqc_result.json
[2024-01-24 12:45:27,884] [INFO] DFAST_QC completed!
[2024-01-24 12:45:27,884] [INFO] Total running time: 0h0m44s