[2024-01-24 10:57:38,340] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:38,342] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:38,342] [INFO] DQC Reference Directory: /var/lib/cwl/stgf3f180b8-f71c-4f98-aae6-6f858f580333/dqc_reference
[2024-01-24 10:57:39,630] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:39,632] [INFO] Task started: Prodigal
[2024-01-24 10:57:39,632] [INFO] Running command: gunzip -c /var/lib/cwl/stgfc15f41f-5725-460a-8fc9-dd5d7578e205/GCF_024721565.1_ASM2472156v1_genomic.fna.gz | prodigal -d GCF_024721565.1_ASM2472156v1_genomic.fna/cds.fna -a GCF_024721565.1_ASM2472156v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:45,589] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:45,590] [INFO] Task started: HMMsearch
[2024-01-24 10:57:45,590] [INFO] Running command: hmmsearch --tblout GCF_024721565.1_ASM2472156v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf3f180b8-f71c-4f98-aae6-6f858f580333/dqc_reference/reference_markers.hmm GCF_024721565.1_ASM2472156v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:45,862] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:45,864] [INFO] Found 6/6 markers.
[2024-01-24 10:57:45,891] [INFO] Query marker FASTA was written to GCF_024721565.1_ASM2472156v1_genomic.fna/markers.fasta
[2024-01-24 10:57:45,891] [INFO] Task started: Blastn
[2024-01-24 10:57:45,891] [INFO] Running command: blastn -query GCF_024721565.1_ASM2472156v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf3f180b8-f71c-4f98-aae6-6f858f580333/dqc_reference/reference_markers.fasta -out GCF_024721565.1_ASM2472156v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:46,530] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:46,535] [INFO] Selected 8 target genomes.
[2024-01-24 10:57:46,535] [INFO] Target genome list was writen to GCF_024721565.1_ASM2472156v1_genomic.fna/target_genomes.txt
[2024-01-24 10:57:46,541] [INFO] Task started: fastANI
[2024-01-24 10:57:46,542] [INFO] Running command: fastANI --query /var/lib/cwl/stgfc15f41f-5725-460a-8fc9-dd5d7578e205/GCF_024721565.1_ASM2472156v1_genomic.fna.gz --refList GCF_024721565.1_ASM2472156v1_genomic.fna/target_genomes.txt --output GCF_024721565.1_ASM2472156v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:57:52,106] [INFO] Task succeeded: fastANI
[2024-01-24 10:57:52,106] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf3f180b8-f71c-4f98-aae6-6f858f580333/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:57:52,107] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf3f180b8-f71c-4f98-aae6-6f858f580333/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:57:52,119] [INFO] Found 8 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 10:57:52,120] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:57:52,120] [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
Listeria innocua	strain=F4078	GCA_024721565.1	1642	1642	type	True	100.0	959	961	95	conclusive
Listeria innocua	strain=F4078	GCA_014527425.1	1642	1642	type	True	99.9757	947	961	95	conclusive
Listeria innocua	strain=H0996	GCA_017363655.2	1642	1642	claderef	True	98.8528	896	961	95	conclusive
Listeria innocua	strain=2010L-2059	GCA_017363615.2	1642	1642	claderef	True	96.6046	860	961	95	conclusive
Listeria farberi	strain=FSL L7-0091	GCA_014229245.1	2713500	2713500	type	True	92.4446	828	961	95	below_threshold
Listeria monocytogenes	strain=G4599	GCA_001466295.1	1639	1639	claderef	True	89.4274	821	961	95	below_threshold
Listeria monocytogenes	strain=J0099	GCA_013625995.1	1639	1639	claderef	True	89.3211	844	961	95	below_threshold
Listeria swaminathanii	strain=FSL L7-0020	GCA_014229645.1	2713501	2713501	type	True	88.2995	823	961	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:57:52,121] [INFO] DFAST Taxonomy check result was written to GCF_024721565.1_ASM2472156v1_genomic.fna/tc_result.tsv
[2024-01-24 10:57:52,122] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:57:52,122] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:57:52,122] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf3f180b8-f71c-4f98-aae6-6f858f580333/dqc_reference/checkm_data
[2024-01-24 10:57:52,123] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:57:52,155] [INFO] Task started: CheckM
[2024-01-24 10:57:52,155] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024721565.1_ASM2472156v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024721565.1_ASM2472156v1_genomic.fna/checkm_input GCF_024721565.1_ASM2472156v1_genomic.fna/checkm_result
[2024-01-24 10:58:16,328] [INFO] Task succeeded: CheckM
[2024-01-24 10:58:16,329] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:58:16,352] [INFO] ===== Completeness check finished =====
[2024-01-24 10:58:16,353] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:58:16,353] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024721565.1_ASM2472156v1_genomic.fna/markers.fasta)
[2024-01-24 10:58:16,354] [INFO] Task started: Blastn
[2024-01-24 10:58:16,354] [INFO] Running command: blastn -query GCF_024721565.1_ASM2472156v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf3f180b8-f71c-4f98-aae6-6f858f580333/dqc_reference/reference_markers_gtdb.fasta -out GCF_024721565.1_ASM2472156v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:17,210] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:17,213] [INFO] Selected 10 target genomes.
[2024-01-24 10:58:17,214] [INFO] Target genome list was writen to GCF_024721565.1_ASM2472156v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:58:17,222] [INFO] Task started: fastANI
[2024-01-24 10:58:17,222] [INFO] Running command: fastANI --query /var/lib/cwl/stgfc15f41f-5725-460a-8fc9-dd5d7578e205/GCF_024721565.1_ASM2472156v1_genomic.fna.gz --refList GCF_024721565.1_ASM2472156v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024721565.1_ASM2472156v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:58:24,443] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:24,453] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:58:24,453] [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_015276835.1	s__Listeria innocua	98.8228	882	961	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria	95.0	98.16	96.24	0.95	0.92	107	conclusive
GCF_014229245.1	s__Listeria farberi	92.4446	828	961	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria	95.0	99.35	99.31	0.93	0.92	5	-
GCF_000307025.1	s__Listeria monocytogenes_B	89.6533	823	961	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria	95.0	99.46	95.21	0.96	0.90	1699	-
GCF_900187225.1	s__Listeria monocytogenes	89.0736	832	961	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria	95.0	99.04	95.98	0.97	0.89	1977	-
GCF_013282665.1	s__Listeria monocytogenes_C	88.7865	814	961	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria	95.0	95.79	95.20	0.93	0.91	176	-
GCF_014224155.1	s__Listeria cossartiae	88.3298	811	961	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria	95.0	98.01	97.44	0.96	0.94	9	-
GCF_014229645.1	s__Listeria sp014229645	88.2911	824	961	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014229095.1	s__Listeria cayugensis	88.1969	803	961	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria	95.0	97.39	97.39	0.93	0.93	2	-
GCF_000060285.1	s__Listeria welshimeri	87.721	784	961	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria	95.0	98.96	98.73	0.93	0.90	49	-
GCF_014322765.1	s__Listeria immobilis	83.5652	694	961	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria	95.0	99.35	97.95	0.95	0.87	9	-
--------------------------------------------------------------------------------
[2024-01-24 10:58:24,456] [INFO] GTDB search result was written to GCF_024721565.1_ASM2472156v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:58:24,456] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:58:24,461] [INFO] DFAST_QC result json was written to GCF_024721565.1_ASM2472156v1_genomic.fna/dqc_result.json
[2024-01-24 10:58:24,461] [INFO] DFAST_QC completed!
[2024-01-24 10:58:24,462] [INFO] Total running time: 0h0m46s