[2024-01-25 20:20:35,614] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:20:35,616] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:20:35,616] [INFO] DQC Reference Directory: /var/lib/cwl/stg976e593c-cfea-4d19-832f-393a3d12e6d0/dqc_reference
[2024-01-25 20:20:36,719] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:20:36,719] [INFO] Task started: Prodigal
[2024-01-25 20:20:36,720] [INFO] Running command: gunzip -c /var/lib/cwl/stg914528b5-1ed5-4b63-b9f2-67999bef2f60/GCF_900453005.1_52363_F01_genomic.fna.gz | prodigal -d GCF_900453005.1_52363_F01_genomic.fna/cds.fna -a GCF_900453005.1_52363_F01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:20:42,329] [INFO] Task succeeded: Prodigal
[2024-01-25 20:20:42,329] [INFO] Task started: HMMsearch
[2024-01-25 20:20:42,329] [INFO] Running command: hmmsearch --tblout GCF_900453005.1_52363_F01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg976e593c-cfea-4d19-832f-393a3d12e6d0/dqc_reference/reference_markers.hmm GCF_900453005.1_52363_F01_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:20:42,572] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:20:42,573] [INFO] Found 6/6 markers.
[2024-01-25 20:20:42,596] [INFO] Query marker FASTA was written to GCF_900453005.1_52363_F01_genomic.fna/markers.fasta
[2024-01-25 20:20:42,597] [INFO] Task started: Blastn
[2024-01-25 20:20:42,597] [INFO] Running command: blastn -query GCF_900453005.1_52363_F01_genomic.fna/markers.fasta -db /var/lib/cwl/stg976e593c-cfea-4d19-832f-393a3d12e6d0/dqc_reference/reference_markers.fasta -out GCF_900453005.1_52363_F01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:20:43,148] [INFO] Task succeeded: Blastn
[2024-01-25 20:20:43,151] [INFO] Selected 20 target genomes.
[2024-01-25 20:20:43,151] [INFO] Target genome list was writen to GCF_900453005.1_52363_F01_genomic.fna/target_genomes.txt
[2024-01-25 20:20:43,160] [INFO] Task started: fastANI
[2024-01-25 20:20:43,160] [INFO] Running command: fastANI --query /var/lib/cwl/stg914528b5-1ed5-4b63-b9f2-67999bef2f60/GCF_900453005.1_52363_F01_genomic.fna.gz --refList GCF_900453005.1_52363_F01_genomic.fna/target_genomes.txt --output GCF_900453005.1_52363_F01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:20:53,098] [INFO] Task succeeded: fastANI
[2024-01-25 20:20:53,099] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg976e593c-cfea-4d19-832f-393a3d12e6d0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:20:53,099] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg976e593c-cfea-4d19-832f-393a3d12e6d0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:20:53,108] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 20:20:53,108] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:20:53,108] [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 grayi	strain=NCTC 10815	GCA_900453005.1	1641	1641	type	True	100.0	864	866	95	conclusive
Listeria grayi	strain=DSM 20601	GCA_000148995.1	1641	1641	type	True	99.5581	825	866	95	conclusive
Listeria innocua	strain=F4078	GCA_024721565.1	1642	1642	type	True	79.2665	161	866	95	below_threshold
Listeria booriae	strain=NCTC13936	GCA_900453065.1	1552123	1552123	type	True	78.9374	94	866	95	below_threshold
Listeria monocytogenes	strain=NCTC10357	GCA_900187225.1	1639	1639	type	True	78.7301	142	866	95	below_threshold
Listeria monocytogenes	strain=FSL F6-684	GCA_000743465.1	1639	1639	type	True	78.5652	143	866	95	below_threshold
Listeria innocua	strain=F4078	GCA_014527425.1	1642	1642	type	True	78.3901	150	866	95	below_threshold
Listeria farberi	strain=FSL L7-0091	GCA_014229245.1	2713500	2713500	type	True	78.2038	127	866	95	below_threshold
Listeria swaminathanii	strain=FSL L7-0020	GCA_014229645.1	2713501	2713501	type	True	78.0861	143	866	95	below_threshold
Listeria booriae	strain=FSL A5-0281	GCA_000766865.1	1552123	1552123	type	True	77.9196	89	866	95	below_threshold
Listeria monocytogenes	strain=J0099	GCA_013625995.1	1639	1639	claderef	True	77.8345	138	866	95	below_threshold
Listeria monocytogenes	strain=2014L-6393	GCA_013626145.1	1639	1639	claderef	True	77.7727	136	866	95	below_threshold
Listeria monocytogenes	strain=2014L-6256	GCA_013625895.1	1639	1639	claderef	True	77.5827	145	866	95	below_threshold
Listeria valentina	strain=CLIP 2019/00642	GCA_011800755.1	2705293	2705293	type	True	77.538	103	866	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:20:53,110] [INFO] DFAST Taxonomy check result was written to GCF_900453005.1_52363_F01_genomic.fna/tc_result.tsv
[2024-01-25 20:20:53,111] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:20:53,112] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:20:53,112] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg976e593c-cfea-4d19-832f-393a3d12e6d0/dqc_reference/checkm_data
[2024-01-25 20:20:53,112] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:20:53,140] [INFO] Task started: CheckM
[2024-01-25 20:20:53,141] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900453005.1_52363_F01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900453005.1_52363_F01_genomic.fna/checkm_input GCF_900453005.1_52363_F01_genomic.fna/checkm_result
[2024-01-25 20:21:14,820] [INFO] Task succeeded: CheckM
[2024-01-25 20:21:14,821] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:21:14,838] [INFO] ===== Completeness check finished =====
[2024-01-25 20:21:14,838] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:21:14,838] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900453005.1_52363_F01_genomic.fna/markers.fasta)
[2024-01-25 20:21:14,838] [INFO] Task started: Blastn
[2024-01-25 20:21:14,838] [INFO] Running command: blastn -query GCF_900453005.1_52363_F01_genomic.fna/markers.fasta -db /var/lib/cwl/stg976e593c-cfea-4d19-832f-393a3d12e6d0/dqc_reference/reference_markers_gtdb.fasta -out GCF_900453005.1_52363_F01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:21:15,618] [INFO] Task succeeded: Blastn
[2024-01-25 20:21:15,621] [INFO] Selected 25 target genomes.
[2024-01-25 20:21:15,622] [INFO] Target genome list was writen to GCF_900453005.1_52363_F01_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:21:15,678] [INFO] Task started: fastANI
[2024-01-25 20:21:15,678] [INFO] Running command: fastANI --query /var/lib/cwl/stg914528b5-1ed5-4b63-b9f2-67999bef2f60/GCF_900453005.1_52363_F01_genomic.fna.gz --refList GCF_900453005.1_52363_F01_genomic.fna/target_genomes_gtdb.txt --output GCF_900453005.1_52363_F01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:21:28,754] [INFO] Task succeeded: fastANI
[2024-01-25 20:21:28,764] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:21:28,765] [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_000148995.1	s__Listeria grayi	99.5511	826	866	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria	95.0	99.08	98.48	0.95	0.92	6	conclusive
GCF_000060285.1	s__Listeria welshimeri	79.6394	135	866	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria	95.0	98.96	98.73	0.93	0.90	49	-
GCF_900187225.1	s__Listeria monocytogenes	78.856	143	866	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	78.7941	150	866	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria	95.0	95.79	95.20	0.93	0.91	176	-
GCA_000183865.1	s__Listeria marthii	78.328	145	866	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria	95.0	98.26	98.03	0.95	0.91	34	-
GCF_000344175.1	s__Listeria fleischmannii	78.2695	96	866	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria	95.0	96.87	95.72	0.93	0.89	9	-
GCF_014229245.1	s__Listeria farberi	78.2038	127	866	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria	95.0	99.35	99.31	0.93	0.92	5	-
GCF_015276835.1	s__Listeria innocua	78.1486	154	866	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria	95.0	98.16	96.24	0.95	0.92	107	-
GCF_014229095.1	s__Listeria cayugensis	78.054	151	866	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria	95.0	97.39	97.39	0.93	0.93	2	-
GCF_014229645.1	s__Listeria sp014229645	78.0175	142	866	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000766865.1	s__Listeria_A booriae	77.9196	89	866	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria_A	95.0	97.10	95.37	0.89	0.81	92	-
GCF_000525795.1	s__Listeria aquatica	77.8705	96	866	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria	95.0	97.71	97.71	0.93	0.93	2	-
GCF_000525975.1	s__Listeria_A rocourtiae	77.7231	77	866	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria_A	95.0	99.32	98.60	0.93	0.89	4	-
GCF_014224155.1	s__Listeria cossartiae	77.5414	146	866	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria	95.0	98.01	97.44	0.96	0.94	9	-
GCF_011800755.1	s__Listeria valentina	77.538	103	866	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 20:21:28,766] [INFO] GTDB search result was written to GCF_900453005.1_52363_F01_genomic.fna/result_gtdb.tsv
[2024-01-25 20:21:28,766] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:21:28,769] [INFO] DFAST_QC result json was written to GCF_900453005.1_52363_F01_genomic.fna/dqc_result.json
[2024-01-25 20:21:28,769] [INFO] DFAST_QC completed!
[2024-01-25 20:21:28,769] [INFO] Total running time: 0h0m53s