[2024-01-25 18:33:21,167] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:33:21,169] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:33:21,169] [INFO] DQC Reference Directory: /var/lib/cwl/stgb8b3ba41-eedc-4d05-a559-bb4c40902015/dqc_reference
[2024-01-25 18:33:22,334] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:33:22,335] [INFO] Task started: Prodigal
[2024-01-25 18:33:22,335] [INFO] Running command: gunzip -c /var/lib/cwl/stg375c0a58-0e62-4816-8009-6167d21b2c9d/GCF_013820765.1_ASM1382076v1_genomic.fna.gz | prodigal -d GCF_013820765.1_ASM1382076v1_genomic.fna/cds.fna -a GCF_013820765.1_ASM1382076v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:33:29,553] [INFO] Task succeeded: Prodigal
[2024-01-25 18:33:29,553] [INFO] Task started: HMMsearch
[2024-01-25 18:33:29,553] [INFO] Running command: hmmsearch --tblout GCF_013820765.1_ASM1382076v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb8b3ba41-eedc-4d05-a559-bb4c40902015/dqc_reference/reference_markers.hmm GCF_013820765.1_ASM1382076v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:33:29,769] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:33:29,770] [INFO] Found 6/6 markers.
[2024-01-25 18:33:29,798] [INFO] Query marker FASTA was written to GCF_013820765.1_ASM1382076v1_genomic.fna/markers.fasta
[2024-01-25 18:33:29,798] [INFO] Task started: Blastn
[2024-01-25 18:33:29,798] [INFO] Running command: blastn -query GCF_013820765.1_ASM1382076v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb8b3ba41-eedc-4d05-a559-bb4c40902015/dqc_reference/reference_markers.fasta -out GCF_013820765.1_ASM1382076v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:33:30,339] [INFO] Task succeeded: Blastn
[2024-01-25 18:33:30,341] [INFO] Selected 11 target genomes.
[2024-01-25 18:33:30,341] [INFO] Target genome list was writen to GCF_013820765.1_ASM1382076v1_genomic.fna/target_genomes.txt
[2024-01-25 18:33:30,373] [INFO] Task started: fastANI
[2024-01-25 18:33:30,373] [INFO] Running command: fastANI --query /var/lib/cwl/stg375c0a58-0e62-4816-8009-6167d21b2c9d/GCF_013820765.1_ASM1382076v1_genomic.fna.gz --refList GCF_013820765.1_ASM1382076v1_genomic.fna/target_genomes.txt --output GCF_013820765.1_ASM1382076v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:33:38,099] [INFO] Task succeeded: fastANI
[2024-01-25 18:33:38,099] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb8b3ba41-eedc-4d05-a559-bb4c40902015/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:33:38,099] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb8b3ba41-eedc-4d05-a559-bb4c40902015/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:33:38,107] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:33:38,107] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:33:38,107] [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 rustica	strain=FSL W9-0585	GCA_013820765.1	2713503	2713503	type	True	100.0	1135	1139	95	conclusive
Listeria portnoyi	strain=FSL L7-1582	GCA_014322795.1	2713504	2713504	type	True	94.4593	874	1139	95	below_threshold
Listeria newyorkensis	strain=FSL M6-0635	GCA_000766145.1	1497681	1497681	type	True	89.6955	882	1139	95	below_threshold
Listeria newyorkensis	strain=NCTC13937	GCA_900461625.1	1497681	1497681	type	True	89.5999	889	1139	95	below_threshold
Listeria cornellensis	strain=FSL F6-0969	GCA_000525855.1	1494961	1494961	type	True	89.4276	846	1139	95	below_threshold
Listeria rocourtiae	strain=FSL F6-920	GCA_000525975.1	647910	647910	type	True	84.0047	738	1139	95	below_threshold
Listeria monocytogenes	strain=2014L-6393	GCA_013626145.1	1639	1639	claderef	True	77.7233	153	1139	95	below_threshold
Listeria monocytogenes	strain=J0099	GCA_013625995.1	1639	1639	claderef	True	77.7083	155	1139	95	below_threshold
Listeria innocua	strain=H0996	GCA_017363655.2	1642	1642	claderef	True	77.6902	163	1139	95	below_threshold
Listeria swaminathanii	strain=FSL L7-0020	GCA_014229645.1	2713501	2713501	type	True	77.6392	181	1139	95	below_threshold
Listeria monocytogenes	strain=2014L-6256	GCA_013625895.1	1639	1639	claderef	True	77.5886	177	1139	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:33:38,109] [INFO] DFAST Taxonomy check result was written to GCF_013820765.1_ASM1382076v1_genomic.fna/tc_result.tsv
[2024-01-25 18:33:38,109] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:33:38,110] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:33:38,110] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb8b3ba41-eedc-4d05-a559-bb4c40902015/dqc_reference/checkm_data
[2024-01-25 18:33:38,110] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:33:38,147] [INFO] Task started: CheckM
[2024-01-25 18:33:38,148] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013820765.1_ASM1382076v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013820765.1_ASM1382076v1_genomic.fna/checkm_input GCF_013820765.1_ASM1382076v1_genomic.fna/checkm_result
[2024-01-25 18:34:04,307] [INFO] Task succeeded: CheckM
[2024-01-25 18:34:04,308] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:34:04,325] [INFO] ===== Completeness check finished =====
[2024-01-25 18:34:04,325] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:34:04,326] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013820765.1_ASM1382076v1_genomic.fna/markers.fasta)
[2024-01-25 18:34:04,326] [INFO] Task started: Blastn
[2024-01-25 18:34:04,326] [INFO] Running command: blastn -query GCF_013820765.1_ASM1382076v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb8b3ba41-eedc-4d05-a559-bb4c40902015/dqc_reference/reference_markers_gtdb.fasta -out GCF_013820765.1_ASM1382076v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:34:05,148] [INFO] Task succeeded: Blastn
[2024-01-25 18:34:05,150] [INFO] Selected 7 target genomes.
[2024-01-25 18:34:05,151] [INFO] Target genome list was writen to GCF_013820765.1_ASM1382076v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:34:05,176] [INFO] Task started: fastANI
[2024-01-25 18:34:05,176] [INFO] Running command: fastANI --query /var/lib/cwl/stg375c0a58-0e62-4816-8009-6167d21b2c9d/GCF_013820765.1_ASM1382076v1_genomic.fna.gz --refList GCF_013820765.1_ASM1382076v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013820765.1_ASM1382076v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:34:11,603] [INFO] Task succeeded: fastANI
[2024-01-25 18:34:11,608] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:34:11,609] [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_013820765.1	s__Listeria_A rustica	100.0	1135	1139	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014322795.1	s__Listeria_A portnoyi	94.4687	873	1139	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	89.683	883	1139	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	89.4049	848	1139	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_003534205.1	s__Listeria_A weihenstephanensis	86.3338	801	1139	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_000525835.1	s__Listeria_A grandensis	84.6186	759	1139	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_000525975.1	s__Listeria_A rocourtiae	84.0146	737	1139	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria_A	95.0	99.32	98.60	0.93	0.89	4	-
--------------------------------------------------------------------------------
[2024-01-25 18:34:11,610] [INFO] GTDB search result was written to GCF_013820765.1_ASM1382076v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:34:11,610] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:34:11,613] [INFO] DFAST_QC result json was written to GCF_013820765.1_ASM1382076v1_genomic.fna/dqc_result.json
[2024-01-25 18:34:11,613] [INFO] DFAST_QC completed!
[2024-01-25 18:34:11,613] [INFO] Total running time: 0h0m50s