[2024-01-24 15:02:36,109] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:02:36,111] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:02:36,112] [INFO] DQC Reference Directory: /var/lib/cwl/stg445548d4-6d9e-4054-af91-f91dfa120e02/dqc_reference
[2024-01-24 15:02:38,275] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:02:38,277] [INFO] Task started: Prodigal
[2024-01-24 15:02:38,278] [INFO] Running command: gunzip -c /var/lib/cwl/stgb443e523-4cad-4b01-bf35-936915fc453f/GCF_014225985.1_ASM1422598v1_genomic.fna.gz | prodigal -d GCF_014225985.1_ASM1422598v1_genomic.fna/cds.fna -a GCF_014225985.1_ASM1422598v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:02:44,809] [INFO] Task succeeded: Prodigal
[2024-01-24 15:02:44,809] [INFO] Task started: HMMsearch
[2024-01-24 15:02:44,810] [INFO] Running command: hmmsearch --tblout GCF_014225985.1_ASM1422598v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg445548d4-6d9e-4054-af91-f91dfa120e02/dqc_reference/reference_markers.hmm GCF_014225985.1_ASM1422598v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:02:45,133] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:02:45,134] [INFO] Found 6/6 markers.
[2024-01-24 15:02:45,165] [INFO] Query marker FASTA was written to GCF_014225985.1_ASM1422598v1_genomic.fna/markers.fasta
[2024-01-24 15:02:45,166] [INFO] Task started: Blastn
[2024-01-24 15:02:45,166] [INFO] Running command: blastn -query GCF_014225985.1_ASM1422598v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg445548d4-6d9e-4054-af91-f91dfa120e02/dqc_reference/reference_markers.fasta -out GCF_014225985.1_ASM1422598v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:02:47,986] [INFO] Task succeeded: Blastn
[2024-01-24 15:02:47,990] [INFO] Selected 8 target genomes.
[2024-01-24 15:02:47,990] [INFO] Target genome list was writen to GCF_014225985.1_ASM1422598v1_genomic.fna/target_genomes.txt
[2024-01-24 15:02:47,996] [INFO] Task started: fastANI
[2024-01-24 15:02:47,996] [INFO] Running command: fastANI --query /var/lib/cwl/stgb443e523-4cad-4b01-bf35-936915fc453f/GCF_014225985.1_ASM1422598v1_genomic.fna.gz --refList GCF_014225985.1_ASM1422598v1_genomic.fna/target_genomes.txt --output GCF_014225985.1_ASM1422598v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:02:53,804] [INFO] Task succeeded: fastANI
[2024-01-24 15:02:53,805] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg445548d4-6d9e-4054-af91-f91dfa120e02/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:02:53,806] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg445548d4-6d9e-4054-af91-f91dfa120e02/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:02:53,852] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 15:02:53,852] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 15:02:53,852] [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	93.2533	861	922	95	below_threshold
Listeria monocytogenes	strain=NCTC10357	GCA_900187225.1	1639	1639	type	True	90.2637	804	922	95	below_threshold
Listeria monocytogenes	strain=J0099	GCA_013625995.1	1639	1639	claderef	True	90.2435	820	922	95	below_threshold
Listeria monocytogenes	strain=FSL F6-684	GCA_000743465.1	1639	1639	type	True	90.2222	805	922	95	below_threshold
Listeria monocytogenes	strain=2014L-6393	GCA_013626145.1	1639	1639	claderef	True	90.0811	804	922	95	below_threshold
Listeria monocytogenes	strain=G4599	GCA_001466295.1	1639	1639	claderef	True	89.7999	809	922	95	below_threshold
Listeria monocytogenes	strain=2014L-6256	GCA_013625895.1	1639	1639	claderef	True	89.5974	817	922	95	below_threshold
Listeria welshimeri	strain=NCTC11857	GCA_900187315.1	1643	1643	type	True	86.9137	733	922	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:02:53,854] [INFO] DFAST Taxonomy check result was written to GCF_014225985.1_ASM1422598v1_genomic.fna/tc_result.tsv
[2024-01-24 15:02:53,854] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:02:53,854] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:02:53,854] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg445548d4-6d9e-4054-af91-f91dfa120e02/dqc_reference/checkm_data
[2024-01-24 15:02:53,861] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:02:53,891] [INFO] Task started: CheckM
[2024-01-24 15:02:53,892] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014225985.1_ASM1422598v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014225985.1_ASM1422598v1_genomic.fna/checkm_input GCF_014225985.1_ASM1422598v1_genomic.fna/checkm_result
[2024-01-24 15:03:24,510] [INFO] Task succeeded: CheckM
[2024-01-24 15:03:24,511] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:03:24,558] [INFO] ===== Completeness check finished =====
[2024-01-24 15:03:24,559] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:03:24,559] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014225985.1_ASM1422598v1_genomic.fna/markers.fasta)
[2024-01-24 15:03:24,560] [INFO] Task started: Blastn
[2024-01-24 15:03:24,560] [INFO] Running command: blastn -query GCF_014225985.1_ASM1422598v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg445548d4-6d9e-4054-af91-f91dfa120e02/dqc_reference/reference_markers_gtdb.fasta -out GCF_014225985.1_ASM1422598v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:03:25,987] [INFO] Task succeeded: Blastn
[2024-01-24 15:03:25,991] [INFO] Selected 7 target genomes.
[2024-01-24 15:03:25,991] [INFO] Target genome list was writen to GCF_014225985.1_ASM1422598v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:03:26,008] [INFO] Task started: fastANI
[2024-01-24 15:03:26,008] [INFO] Running command: fastANI --query /var/lib/cwl/stgb443e523-4cad-4b01-bf35-936915fc453f/GCF_014225985.1_ASM1422598v1_genomic.fna.gz --refList GCF_014225985.1_ASM1422598v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014225985.1_ASM1422598v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:03:31,450] [INFO] Task succeeded: fastANI
[2024-01-24 15:03:31,485] [INFO] Found 7 fastANI hits (2 hits with ANI > circumscription radius)
[2024-01-24 15:03:31,486] [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_014229095.1	s__Listeria cayugensis	97.3855	857	922	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria	95.0	97.39	97.39	0.93	0.93	2	inconclusive
GCF_014224155.1	s__Listeria cossartiae	95.3163	865	922	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria	95.0	98.01	97.44	0.96	0.94	9	inconclusive
GCA_000183865.1	s__Listeria marthii	94.9982	861	922	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria	95.0	98.26	98.03	0.95	0.91	34	-
GCF_014229645.1	s__Listeria sp014229645	93.2533	861	922	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900187225.1	s__Listeria monocytogenes	90.2833	803	922	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	89.8927	806	922	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	89.5377	819	922	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria	95.0	95.79	95.20	0.93	0.91	176	-
--------------------------------------------------------------------------------
[2024-01-24 15:03:31,487] [INFO] GTDB search result was written to GCF_014225985.1_ASM1422598v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:03:31,488] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:03:31,491] [INFO] DFAST_QC result json was written to GCF_014225985.1_ASM1422598v1_genomic.fna/dqc_result.json
[2024-01-24 15:03:31,491] [INFO] DFAST_QC completed!
[2024-01-24 15:03:31,491] [INFO] Total running time: 0h0m55s