[2024-01-25 18:46:37,043] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:46:37,045] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:46:37,045] [INFO] DQC Reference Directory: /var/lib/cwl/stgd0ac41d9-734d-4095-9805-e6f0a6ac35a4/dqc_reference
[2024-01-25 18:46:38,131] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:46:38,131] [INFO] Task started: Prodigal
[2024-01-25 18:46:38,131] [INFO] Running command: gunzip -c /var/lib/cwl/stg2c8076e7-c40f-4262-bd49-b0fa7c9e5212/GCF_900187025.1_49923_F01_genomic.fna.gz | prodigal -d GCF_900187025.1_49923_F01_genomic.fna/cds.fna -a GCF_900187025.1_49923_F01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:46:43,461] [INFO] Task succeeded: Prodigal
[2024-01-25 18:46:43,461] [INFO] Task started: HMMsearch
[2024-01-25 18:46:43,461] [INFO] Running command: hmmsearch --tblout GCF_900187025.1_49923_F01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd0ac41d9-734d-4095-9805-e6f0a6ac35a4/dqc_reference/reference_markers.hmm GCF_900187025.1_49923_F01_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:46:43,667] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:46:43,668] [INFO] Found 6/6 markers.
[2024-01-25 18:46:43,691] [INFO] Query marker FASTA was written to GCF_900187025.1_49923_F01_genomic.fna/markers.fasta
[2024-01-25 18:46:43,692] [INFO] Task started: Blastn
[2024-01-25 18:46:43,692] [INFO] Running command: blastn -query GCF_900187025.1_49923_F01_genomic.fna/markers.fasta -db /var/lib/cwl/stgd0ac41d9-734d-4095-9805-e6f0a6ac35a4/dqc_reference/reference_markers.fasta -out GCF_900187025.1_49923_F01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:46:44,234] [INFO] Task succeeded: Blastn
[2024-01-25 18:46:44,236] [INFO] Selected 11 target genomes.
[2024-01-25 18:46:44,237] [INFO] Target genome list was writen to GCF_900187025.1_49923_F01_genomic.fna/target_genomes.txt
[2024-01-25 18:46:44,243] [INFO] Task started: fastANI
[2024-01-25 18:46:44,244] [INFO] Running command: fastANI --query /var/lib/cwl/stg2c8076e7-c40f-4262-bd49-b0fa7c9e5212/GCF_900187025.1_49923_F01_genomic.fna.gz --refList GCF_900187025.1_49923_F01_genomic.fna/target_genomes.txt --output GCF_900187025.1_49923_F01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:46:51,617] [INFO] Task succeeded: fastANI
[2024-01-25 18:46:51,618] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd0ac41d9-734d-4095-9805-e6f0a6ac35a4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:46:51,618] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd0ac41d9-734d-4095-9805-e6f0a6ac35a4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:46:51,626] [INFO] Found 11 fastANI hits (4 hits with ANI > threshold)
[2024-01-25 18:46:51,626] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:46:51,626] [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 ivanovii subsp. ivanovii	strain=NCTC11846	GCA_900187025.1	202751	1638	type	True	100.0	972	973	95	conclusive
Listeria ivanovii subsp. ivanovii	strain=NCTC11007	GCA_900187195.1	202751	1638	type	True	99.9998	971	973	95	conclusive
Listeria ivanovii subsp. ivanovii	strain=WSLC 3010	GCA_000763515.1	202751	1638	type	True	99.9998	972	973	95	conclusive
Listeria ivanovii subsp. ivanovii	strain=PAM 55	GCA_000252975.1	202751	1638	claderef	True	99.9625	971	973	95	conclusive
Listeria seeligeri	strain=SLCC3954	GCA_000027145.1	1640	1640	type	True	88.148	792	973	95	below_threshold
Listeria immobilis	strain=FSL L7-1519	GCA_014322765.1	2713502	2713502	type	True	86.6519	764	973	95	below_threshold
Listeria innocua	strain=F4078	GCA_024721565.1	1642	1642	type	True	84.3483	718	973	95	below_threshold
Listeria innocua	strain=2010L-2059	GCA_017363615.2	1642	1642	claderef	True	84.1494	727	973	95	below_threshold
Listeria monocytogenes	strain=G4599	GCA_001466295.1	1639	1639	claderef	True	83.885	736	973	95	below_threshold
Listeria monocytogenes	strain=J0099	GCA_013625995.1	1639	1639	claderef	True	83.8802	730	973	95	below_threshold
Listeria monocytogenes	strain=2014L-6256	GCA_013625895.1	1639	1639	claderef	True	83.8357	706	973	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:46:51,627] [INFO] DFAST Taxonomy check result was written to GCF_900187025.1_49923_F01_genomic.fna/tc_result.tsv
[2024-01-25 18:46:51,628] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:46:51,628] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:46:51,629] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd0ac41d9-734d-4095-9805-e6f0a6ac35a4/dqc_reference/checkm_data
[2024-01-25 18:46:51,630] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:46:51,668] [INFO] Task started: CheckM
[2024-01-25 18:46:51,669] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900187025.1_49923_F01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900187025.1_49923_F01_genomic.fna/checkm_input GCF_900187025.1_49923_F01_genomic.fna/checkm_result
[2024-01-25 18:47:12,717] [INFO] Task succeeded: CheckM
[2024-01-25 18:47:12,718] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:47:12,735] [INFO] ===== Completeness check finished =====
[2024-01-25 18:47:12,735] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:47:12,735] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900187025.1_49923_F01_genomic.fna/markers.fasta)
[2024-01-25 18:47:12,735] [INFO] Task started: Blastn
[2024-01-25 18:47:12,735] [INFO] Running command: blastn -query GCF_900187025.1_49923_F01_genomic.fna/markers.fasta -db /var/lib/cwl/stgd0ac41d9-734d-4095-9805-e6f0a6ac35a4/dqc_reference/reference_markers_gtdb.fasta -out GCF_900187025.1_49923_F01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:47:13,503] [INFO] Task succeeded: Blastn
[2024-01-25 18:47:13,506] [INFO] Selected 9 target genomes.
[2024-01-25 18:47:13,507] [INFO] Target genome list was writen to GCF_900187025.1_49923_F01_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:47:13,512] [INFO] Task started: fastANI
[2024-01-25 18:47:13,512] [INFO] Running command: fastANI --query /var/lib/cwl/stg2c8076e7-c40f-4262-bd49-b0fa7c9e5212/GCF_900187025.1_49923_F01_genomic.fna.gz --refList GCF_900187025.1_49923_F01_genomic.fna/target_genomes_gtdb.txt --output GCF_900187025.1_49923_F01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:47:19,874] [INFO] Task succeeded: fastANI
[2024-01-25 18:47:19,880] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:47:19,881] [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_900187025.1	s__Listeria ivanovii	100.0	973	973	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria	95.0	99.75	99.44	0.99	0.97	26	conclusive
GCF_000763495.1	s__Listeria londoniensis	93.3694	864	973	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria	95.0	99.36	98.73	0.96	0.94	17	-
GCF_000027145.1	s__Listeria seeligeri	88.148	792	973	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria	95.0	97.08	96.23	0.92	0.88	167	-
GCF_014322765.1	s__Listeria immobilis	86.6607	763	973	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria	95.0	99.35	97.95	0.95	0.87	9	-
GCF_015276835.1	s__Listeria innocua	84.2223	722	973	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria	95.0	98.16	96.24	0.95	0.92	107	-
GCF_000307025.1	s__Listeria monocytogenes_B	84.1139	739	973	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	84.0965	742	973	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	83.9422	714	973	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014224155.1	s__Listeria cossartiae	83.8967	713	973	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria	95.0	98.01	97.44	0.96	0.94	9	-
--------------------------------------------------------------------------------
[2024-01-25 18:47:19,882] [INFO] GTDB search result was written to GCF_900187025.1_49923_F01_genomic.fna/result_gtdb.tsv
[2024-01-25 18:47:19,882] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:47:19,885] [INFO] DFAST_QC result json was written to GCF_900187025.1_49923_F01_genomic.fna/dqc_result.json
[2024-01-25 18:47:19,885] [INFO] DFAST_QC completed!
[2024-01-25 18:47:19,885] [INFO] Total running time: 0h0m43s