[2024-01-25 19:42:20,614] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:42:20,615] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:42:20,615] [INFO] DQC Reference Directory: /var/lib/cwl/stgafd11720-e69f-48c8-a5b5-1b236b92ee99/dqc_reference
[2024-01-25 19:42:21,758] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:42:21,760] [INFO] Task started: Prodigal
[2024-01-25 19:42:21,760] [INFO] Running command: gunzip -c /var/lib/cwl/stg5eb4abf3-67d5-4527-9729-46d21a481e9b/GCF_900453065.1_58116_F02_genomic.fna.gz | prodigal -d GCF_900453065.1_58116_F02_genomic.fna/cds.fna -a GCF_900453065.1_58116_F02_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:42:29,334] [INFO] Task succeeded: Prodigal
[2024-01-25 19:42:29,334] [INFO] Task started: HMMsearch
[2024-01-25 19:42:29,335] [INFO] Running command: hmmsearch --tblout GCF_900453065.1_58116_F02_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgafd11720-e69f-48c8-a5b5-1b236b92ee99/dqc_reference/reference_markers.hmm GCF_900453065.1_58116_F02_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:42:29,594] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:42:29,595] [INFO] Found 6/6 markers.
[2024-01-25 19:42:29,623] [INFO] Query marker FASTA was written to GCF_900453065.1_58116_F02_genomic.fna/markers.fasta
[2024-01-25 19:42:29,623] [INFO] Task started: Blastn
[2024-01-25 19:42:29,623] [INFO] Running command: blastn -query GCF_900453065.1_58116_F02_genomic.fna/markers.fasta -db /var/lib/cwl/stgafd11720-e69f-48c8-a5b5-1b236b92ee99/dqc_reference/reference_markers.fasta -out GCF_900453065.1_58116_F02_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:42:30,200] [INFO] Task succeeded: Blastn
[2024-01-25 19:42:30,203] [INFO] Selected 15 target genomes.
[2024-01-25 19:42:30,203] [INFO] Target genome list was writen to GCF_900453065.1_58116_F02_genomic.fna/target_genomes.txt
[2024-01-25 19:42:30,213] [INFO] Task started: fastANI
[2024-01-25 19:42:30,213] [INFO] Running command: fastANI --query /var/lib/cwl/stg5eb4abf3-67d5-4527-9729-46d21a481e9b/GCF_900453065.1_58116_F02_genomic.fna.gz --refList GCF_900453065.1_58116_F02_genomic.fna/target_genomes.txt --output GCF_900453065.1_58116_F02_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:42:42,016] [INFO] Task succeeded: fastANI
[2024-01-25 19:42:42,017] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgafd11720-e69f-48c8-a5b5-1b236b92ee99/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:42:42,017] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgafd11720-e69f-48c8-a5b5-1b236b92ee99/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:42:42,025] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:42:42,025] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:42:42,025] [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 booriae	strain=NCTC13936	GCA_900453065.1	1552123	1552123	type	True	100.0	1160	1160	95	conclusive
Listeria booriae	strain=FSL A5-0281	GCA_000766865.1	1552123	1552123	type	True	99.9864	1129	1160	95	conclusive
Listeria riparia	strain=FSL S10-1204	GCA_000525995.1	1494964	1494964	type	True	92.4111	901	1160	95	below_threshold
Listeria newyorkensis	strain=NCTC13937	GCA_900461625.1	1497681	1497681	type	True	82.1677	729	1160	95	below_threshold
Listeria newyorkensis	strain=FSL M6-0635	GCA_000766145.1	1497681	1497681	type	True	82.0708	703	1160	95	below_threshold
Listeria cornellensis	strain=FSL F6-0969	GCA_000525855.1	1494961	1494961	type	True	81.942	654	1160	95	below_threshold
Listeria portnoyi	strain=FSL L7-1582	GCA_014322795.1	2713504	2713504	type	True	81.8558	643	1160	95	below_threshold
Listeria rustica	strain=FSL W9-0585	GCA_013820765.1	2713503	2713503	type	True	81.7851	694	1160	95	below_threshold
Listeria weihenstephanensis	strain=FSL R9-0317	GCA_000525955.1	1006155	1006155	type	True	81.2996	675	1160	95	below_threshold
Listeria grayi	strain=DSM 20601	GCA_000148995.1	1641	1641	type	True	78.1275	96	1160	95	below_threshold
Listeria monocytogenes	strain=2014L-6256	GCA_013625895.1	1639	1639	claderef	True	78.0793	177	1160	95	below_threshold
Listeria monocytogenes	strain=2014L-6393	GCA_013626145.1	1639	1639	claderef	True	77.9372	179	1160	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:42:42,027] [INFO] DFAST Taxonomy check result was written to GCF_900453065.1_58116_F02_genomic.fna/tc_result.tsv
[2024-01-25 19:42:42,027] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:42:42,027] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:42:42,028] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgafd11720-e69f-48c8-a5b5-1b236b92ee99/dqc_reference/checkm_data
[2024-01-25 19:42:42,028] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:42:42,063] [INFO] Task started: CheckM
[2024-01-25 19:42:42,063] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900453065.1_58116_F02_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900453065.1_58116_F02_genomic.fna/checkm_input GCF_900453065.1_58116_F02_genomic.fna/checkm_result
[2024-01-25 19:43:08,188] [INFO] Task succeeded: CheckM
[2024-01-25 19:43:08,189] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:43:08,206] [INFO] ===== Completeness check finished =====
[2024-01-25 19:43:08,206] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:43:08,206] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900453065.1_58116_F02_genomic.fna/markers.fasta)
[2024-01-25 19:43:08,206] [INFO] Task started: Blastn
[2024-01-25 19:43:08,206] [INFO] Running command: blastn -query GCF_900453065.1_58116_F02_genomic.fna/markers.fasta -db /var/lib/cwl/stgafd11720-e69f-48c8-a5b5-1b236b92ee99/dqc_reference/reference_markers_gtdb.fasta -out GCF_900453065.1_58116_F02_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:43:08,969] [INFO] Task succeeded: Blastn
[2024-01-25 19:43:08,972] [INFO] Selected 9 target genomes.
[2024-01-25 19:43:08,972] [INFO] Target genome list was writen to GCF_900453065.1_58116_F02_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:43:08,982] [INFO] Task started: fastANI
[2024-01-25 19:43:08,982] [INFO] Running command: fastANI --query /var/lib/cwl/stg5eb4abf3-67d5-4527-9729-46d21a481e9b/GCF_900453065.1_58116_F02_genomic.fna.gz --refList GCF_900453065.1_58116_F02_genomic.fna/target_genomes_gtdb.txt --output GCF_900453065.1_58116_F02_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:43:16,013] [INFO] Task succeeded: fastANI
[2024-01-25 19:43:16,019] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:43:16,020] [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_000766865.1	s__Listeria_A booriae	99.9864	1129	1160	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria_A	95.0	97.10	95.37	0.89	0.81	92	conclusive
GCF_000525995.1	s__Listeria_A riparia	92.394	902	1160	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000766145.1	s__Listeria_A newyorkensis	82.0477	707	1160	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria_A	95.0	98.92	95.80	0.93	0.85	8	-
GCF_000525855.1	s__Listeria_A cornellensis	81.9676	650	1160	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014322795.1	s__Listeria_A portnoyi	81.844	645	1160	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013820765.1	s__Listeria_A rustica	81.809	691	1160	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000525835.1	s__Listeria_A grandensis	81.6758	653	1160	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria_A	95.0	97.47	97.36	0.88	0.88	4	-
GCF_003534205.1	s__Listeria_A weihenstephanensis	81.5785	692	1160	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria_A	95.0	99.01	98.05	0.93	0.87	3	-
GCF_000148995.1	s__Listeria grayi	78.1275	96	1160	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria	95.0	99.08	98.48	0.95	0.92	6	-
--------------------------------------------------------------------------------
[2024-01-25 19:43:16,021] [INFO] GTDB search result was written to GCF_900453065.1_58116_F02_genomic.fna/result_gtdb.tsv
[2024-01-25 19:43:16,021] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:43:16,024] [INFO] DFAST_QC result json was written to GCF_900453065.1_58116_F02_genomic.fna/dqc_result.json
[2024-01-25 19:43:16,024] [INFO] DFAST_QC completed!
[2024-01-25 19:43:16,024] [INFO] Total running time: 0h0m55s