[2024-01-24 11:51:11,130] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:11,132] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:11,132] [INFO] DQC Reference Directory: /var/lib/cwl/stga2f76ea0-0071-44cd-ab14-ec2c92ee528a/dqc_reference
[2024-01-24 11:51:12,505] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:12,506] [INFO] Task started: Prodigal
[2024-01-24 11:51:12,506] [INFO] Running command: gunzip -c /var/lib/cwl/stg82125e86-12e0-40e6-80e4-1756c4e302b6/GCF_014229645.1_ASM1422964v1_genomic.fna.gz | prodigal -d GCF_014229645.1_ASM1422964v1_genomic.fna/cds.fna -a GCF_014229645.1_ASM1422964v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:18,447] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:18,448] [INFO] Task started: HMMsearch
[2024-01-24 11:51:18,448] [INFO] Running command: hmmsearch --tblout GCF_014229645.1_ASM1422964v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga2f76ea0-0071-44cd-ab14-ec2c92ee528a/dqc_reference/reference_markers.hmm GCF_014229645.1_ASM1422964v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:18,752] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:18,754] [INFO] Found 6/6 markers.
[2024-01-24 11:51:18,790] [INFO] Query marker FASTA was written to GCF_014229645.1_ASM1422964v1_genomic.fna/markers.fasta
[2024-01-24 11:51:18,791] [INFO] Task started: Blastn
[2024-01-24 11:51:18,791] [INFO] Running command: blastn -query GCF_014229645.1_ASM1422964v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga2f76ea0-0071-44cd-ab14-ec2c92ee528a/dqc_reference/reference_markers.fasta -out GCF_014229645.1_ASM1422964v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:19,397] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:19,403] [INFO] Selected 8 target genomes.
[2024-01-24 11:51:19,404] [INFO] Target genome list was writen to GCF_014229645.1_ASM1422964v1_genomic.fna/target_genomes.txt
[2024-01-24 11:51:19,420] [INFO] Task started: fastANI
[2024-01-24 11:51:19,420] [INFO] Running command: fastANI --query /var/lib/cwl/stg82125e86-12e0-40e6-80e4-1756c4e302b6/GCF_014229645.1_ASM1422964v1_genomic.fna.gz --refList GCF_014229645.1_ASM1422964v1_genomic.fna/target_genomes.txt --output GCF_014229645.1_ASM1422964v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:51:24,936] [INFO] Task succeeded: fastANI
[2024-01-24 11:51:24,937] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga2f76ea0-0071-44cd-ab14-ec2c92ee528a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:51:24,937] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga2f76ea0-0071-44cd-ab14-ec2c92ee528a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:51:24,945] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:51:24,945] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:51:24,946] [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 swaminathanii	strain=FSL L7-0020	GCA_014229645.1	2713501	2713501	type	True	100.0	927	928	95	conclusive
Listeria monocytogenes	strain=NCTC10357	GCA_900187225.1	1639	1639	type	True	90.3768	830	928	95	below_threshold
Listeria monocytogenes	strain=FSL F6-684	GCA_000743465.1	1639	1639	type	True	90.3253	832	928	95	below_threshold
Listeria monocytogenes	strain=J0099	GCA_013625995.1	1639	1639	claderef	True	90.0292	844	928	95	below_threshold
Listeria monocytogenes	strain=2014L-6393	GCA_013626145.1	1639	1639	claderef	True	89.8912	814	928	95	below_threshold
Listeria monocytogenes	strain=G4599	GCA_001466295.1	1639	1639	claderef	True	89.7904	826	928	95	below_threshold
Listeria monocytogenes	strain=2014L-6256	GCA_013625895.1	1639	1639	claderef	True	89.4077	791	928	95	below_threshold
Listeria innocua	strain=F4078	GCA_024721565.1	1642	1642	type	True	88.2884	819	928	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:51:24,947] [INFO] DFAST Taxonomy check result was written to GCF_014229645.1_ASM1422964v1_genomic.fna/tc_result.tsv
[2024-01-24 11:51:24,948] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:51:24,948] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:51:24,948] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga2f76ea0-0071-44cd-ab14-ec2c92ee528a/dqc_reference/checkm_data
[2024-01-24 11:51:24,949] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:51:24,976] [INFO] Task started: CheckM
[2024-01-24 11:51:24,977] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014229645.1_ASM1422964v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014229645.1_ASM1422964v1_genomic.fna/checkm_input GCF_014229645.1_ASM1422964v1_genomic.fna/checkm_result
[2024-01-24 11:51:48,354] [INFO] Task succeeded: CheckM
[2024-01-24 11:51:48,355] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:51:48,372] [INFO] ===== Completeness check finished =====
[2024-01-24 11:51:48,372] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:51:48,372] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014229645.1_ASM1422964v1_genomic.fna/markers.fasta)
[2024-01-24 11:51:48,373] [INFO] Task started: Blastn
[2024-01-24 11:51:48,373] [INFO] Running command: blastn -query GCF_014229645.1_ASM1422964v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga2f76ea0-0071-44cd-ab14-ec2c92ee528a/dqc_reference/reference_markers_gtdb.fasta -out GCF_014229645.1_ASM1422964v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:49,187] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:49,190] [INFO] Selected 8 target genomes.
[2024-01-24 11:51:49,190] [INFO] Target genome list was writen to GCF_014229645.1_ASM1422964v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:51:49,198] [INFO] Task started: fastANI
[2024-01-24 11:51:49,198] [INFO] Running command: fastANI --query /var/lib/cwl/stg82125e86-12e0-40e6-80e4-1756c4e302b6/GCF_014229645.1_ASM1422964v1_genomic.fna.gz --refList GCF_014229645.1_ASM1422964v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014229645.1_ASM1422964v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:51:55,113] [INFO] Task succeeded: fastANI
[2024-01-24 11:51:55,121] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:51:55,121] [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_014229645.1	s__Listeria sp014229645	100.0	927	928	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_000183865.1	s__Listeria marthii	94.3818	866	928	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria	95.0	98.26	98.03	0.95	0.91	34	-
GCF_014229095.1	s__Listeria cayugensis	92.8954	862	928	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria	95.0	97.39	97.39	0.93	0.93	2	-
GCF_014224155.1	s__Listeria cossartiae	92.5271	848	928	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria	95.0	98.01	97.44	0.96	0.94	9	-
GCF_900187225.1	s__Listeria monocytogenes	90.3768	830	928	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria	95.0	99.04	95.98	0.97	0.89	1977	-
GCF_000307025.1	s__Listeria monocytogenes_B	89.7313	829	928	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria	95.0	99.46	95.21	0.96	0.90	1699	-
GCF_013282665.1	s__Listeria monocytogenes_C	89.5006	808	928	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria	95.0	95.79	95.20	0.93	0.91	176	-
GCF_015276835.1	s__Listeria innocua	88.3951	802	928	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria	95.0	98.16	96.24	0.95	0.92	107	-
--------------------------------------------------------------------------------
[2024-01-24 11:51:55,123] [INFO] GTDB search result was written to GCF_014229645.1_ASM1422964v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:51:55,124] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:51:55,126] [INFO] DFAST_QC result json was written to GCF_014229645.1_ASM1422964v1_genomic.fna/dqc_result.json
[2024-01-24 11:51:55,126] [INFO] DFAST_QC completed!
[2024-01-24 11:51:55,127] [INFO] Total running time: 0h0m44s