[2024-01-25 18:59:50,617] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:59:50,618] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:59:50,618] [INFO] DQC Reference Directory: /var/lib/cwl/stg8754d6cb-6278-4540-bbbd-7bffd5acbb17/dqc_reference
[2024-01-25 18:59:51,768] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:59:51,769] [INFO] Task started: Prodigal
[2024-01-25 18:59:51,769] [INFO] Running command: gunzip -c /var/lib/cwl/stg56d3d478-9729-4e94-818f-cdeade6f7c8c/GCF_000620985.1_ASM62098v1_genomic.fna.gz | prodigal -d GCF_000620985.1_ASM62098v1_genomic.fna/cds.fna -a GCF_000620985.1_ASM62098v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:59:56,193] [INFO] Task succeeded: Prodigal
[2024-01-25 18:59:56,193] [INFO] Task started: HMMsearch
[2024-01-25 18:59:56,193] [INFO] Running command: hmmsearch --tblout GCF_000620985.1_ASM62098v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8754d6cb-6278-4540-bbbd-7bffd5acbb17/dqc_reference/reference_markers.hmm GCF_000620985.1_ASM62098v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:59:56,405] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:59:56,406] [INFO] Found 6/6 markers.
[2024-01-25 18:59:56,426] [INFO] Query marker FASTA was written to GCF_000620985.1_ASM62098v1_genomic.fna/markers.fasta
[2024-01-25 18:59:56,427] [INFO] Task started: Blastn
[2024-01-25 18:59:56,427] [INFO] Running command: blastn -query GCF_000620985.1_ASM62098v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8754d6cb-6278-4540-bbbd-7bffd5acbb17/dqc_reference/reference_markers.fasta -out GCF_000620985.1_ASM62098v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:59:56,984] [INFO] Task succeeded: Blastn
[2024-01-25 18:59:56,987] [INFO] Selected 19 target genomes.
[2024-01-25 18:59:56,987] [INFO] Target genome list was writen to GCF_000620985.1_ASM62098v1_genomic.fna/target_genomes.txt
[2024-01-25 18:59:57,005] [INFO] Task started: fastANI
[2024-01-25 18:59:57,005] [INFO] Running command: fastANI --query /var/lib/cwl/stg56d3d478-9729-4e94-818f-cdeade6f7c8c/GCF_000620985.1_ASM62098v1_genomic.fna.gz --refList GCF_000620985.1_ASM62098v1_genomic.fna/target_genomes.txt --output GCF_000620985.1_ASM62098v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:00:06,888] [INFO] Task succeeded: fastANI
[2024-01-25 19:00:06,888] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8754d6cb-6278-4540-bbbd-7bffd5acbb17/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:00:06,888] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8754d6cb-6278-4540-bbbd-7bffd5acbb17/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:00:06,894] [INFO] Found 6 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:00:06,894] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:00:06,894] [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
Brochothrix thermosphacta	strain=DSM 20171	GCA_000620985.1	2756	2756	type	True	100.0	817	820	95	conclusive
Brochothrix thermosphacta	strain=DSM 20171	GCA_001715655.1	2756	2756	type	True	99.9832	800	820	95	conclusive
Brochothrix campestris	strain=FSL F6-1037	GCA_000525915.1	2757	2757	type	True	79.79	264	820	95	below_threshold
Listeria innocua	strain=H0996	GCA_017363655.2	1642	1642	claderef	True	76.7966	50	820	95	below_threshold
Listeria innocua	strain=F4078	GCA_024721565.1	1642	1642	type	True	76.752	51	820	95	below_threshold
Listeria monocytogenes	strain=J0099	GCA_013625995.1	1639	1639	claderef	True	76.1688	51	820	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:00:06,896] [INFO] DFAST Taxonomy check result was written to GCF_000620985.1_ASM62098v1_genomic.fna/tc_result.tsv
[2024-01-25 19:00:06,896] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:00:06,896] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:00:06,896] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8754d6cb-6278-4540-bbbd-7bffd5acbb17/dqc_reference/checkm_data
[2024-01-25 19:00:06,897] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:00:06,925] [INFO] Task started: CheckM
[2024-01-25 19:00:06,925] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000620985.1_ASM62098v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000620985.1_ASM62098v1_genomic.fna/checkm_input GCF_000620985.1_ASM62098v1_genomic.fna/checkm_result
[2024-01-25 19:00:25,930] [INFO] Task succeeded: CheckM
[2024-01-25 19:00:25,931] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:00:25,950] [INFO] ===== Completeness check finished =====
[2024-01-25 19:00:25,950] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:00:25,951] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000620985.1_ASM62098v1_genomic.fna/markers.fasta)
[2024-01-25 19:00:25,951] [INFO] Task started: Blastn
[2024-01-25 19:00:25,951] [INFO] Running command: blastn -query GCF_000620985.1_ASM62098v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8754d6cb-6278-4540-bbbd-7bffd5acbb17/dqc_reference/reference_markers_gtdb.fasta -out GCF_000620985.1_ASM62098v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:00:26,682] [INFO] Task succeeded: Blastn
[2024-01-25 19:00:26,685] [INFO] Selected 21 target genomes.
[2024-01-25 19:00:26,685] [INFO] Target genome list was writen to GCF_000620985.1_ASM62098v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:00:26,718] [INFO] Task started: fastANI
[2024-01-25 19:00:26,718] [INFO] Running command: fastANI --query /var/lib/cwl/stg56d3d478-9729-4e94-818f-cdeade6f7c8c/GCF_000620985.1_ASM62098v1_genomic.fna.gz --refList GCF_000620985.1_ASM62098v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000620985.1_ASM62098v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:00:39,633] [INFO] Task succeeded: fastANI
[2024-01-25 19:00:39,638] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:00:39,638] [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_000620985.1	s__Brochothrix thermosphacta	100.0	817	820	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Brochothrix	95.0	99.06	98.76	0.94	0.90	27	conclusive
GCF_000525915.1	s__Brochothrix campestris	79.7854	265	820	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Brochothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900187225.1	s__Listeria monocytogenes	76.582	54	820	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria	95.0	99.04	95.98	0.97	0.89	1977	-
GCF_014229645.1	s__Listeria sp014229645	76.3179	54	820	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:00:39,640] [INFO] GTDB search result was written to GCF_000620985.1_ASM62098v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:00:39,640] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:00:39,643] [INFO] DFAST_QC result json was written to GCF_000620985.1_ASM62098v1_genomic.fna/dqc_result.json
[2024-01-25 19:00:39,643] [INFO] DFAST_QC completed!
[2024-01-25 19:00:39,643] [INFO] Total running time: 0h0m49s