[2024-01-24 14:14:46,979] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:14:46,982] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:14:46,982] [INFO] DQC Reference Directory: /var/lib/cwl/stg83ff54eb-45c3-47ee-bcc3-f9713cc18ef1/dqc_reference
[2024-01-24 14:14:49,420] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:14:49,421] [INFO] Task started: Prodigal
[2024-01-24 14:14:49,421] [INFO] Running command: gunzip -c /var/lib/cwl/stg367972b6-dfa9-4e37-9023-e613b2b5f61c/GCF_900706845.1_30316_B01_genomic.fna.gz | prodigal -d GCF_900706845.1_30316_B01_genomic.fna/cds.fna -a GCF_900706845.1_30316_B01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:15:00,784] [INFO] Task succeeded: Prodigal
[2024-01-24 14:15:00,784] [INFO] Task started: HMMsearch
[2024-01-24 14:15:00,784] [INFO] Running command: hmmsearch --tblout GCF_900706845.1_30316_B01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg83ff54eb-45c3-47ee-bcc3-f9713cc18ef1/dqc_reference/reference_markers.hmm GCF_900706845.1_30316_B01_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:15:01,082] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:15:01,083] [INFO] Found 6/6 markers.
[2024-01-24 14:15:01,122] [INFO] Query marker FASTA was written to GCF_900706845.1_30316_B01_genomic.fna/markers.fasta
[2024-01-24 14:15:01,123] [INFO] Task started: Blastn
[2024-01-24 14:15:01,123] [INFO] Running command: blastn -query GCF_900706845.1_30316_B01_genomic.fna/markers.fasta -db /var/lib/cwl/stg83ff54eb-45c3-47ee-bcc3-f9713cc18ef1/dqc_reference/reference_markers.fasta -out GCF_900706845.1_30316_B01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:01,985] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:01,990] [INFO] Selected 11 target genomes.
[2024-01-24 14:15:01,990] [INFO] Target genome list was writen to GCF_900706845.1_30316_B01_genomic.fna/target_genomes.txt
[2024-01-24 14:15:02,000] [INFO] Task started: fastANI
[2024-01-24 14:15:02,000] [INFO] Running command: fastANI --query /var/lib/cwl/stg367972b6-dfa9-4e37-9023-e613b2b5f61c/GCF_900706845.1_30316_B01_genomic.fna.gz --refList GCF_900706845.1_30316_B01_genomic.fna/target_genomes.txt --output GCF_900706845.1_30316_B01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:15:12,639] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:12,640] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg83ff54eb-45c3-47ee-bcc3-f9713cc18ef1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:15:12,640] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg83ff54eb-45c3-47ee-bcc3-f9713cc18ef1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:15:12,652] [INFO] Found 11 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 14:15:12,653] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:15:12,653] [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
Leminorella grimontii	strain=NCTC12152	GCA_900706845.1	82981	82981	type	True	100.0	1437	1438	95	conclusive
Leminorella grimontii	strain=JCM 5902	GCA_024343555.1	82981	82981	type	True	99.9689	1397	1438	95	conclusive
Leminorella grimontii	strain=DSM 5078	GCA_000439085.1	82981	82981	type	True	99.9638	1385	1438	95	conclusive
Leminorella grimontii	strain=ATCC 33999	GCA_000735425.1	82981	82981	type	True	99.9549	1388	1438	95	conclusive
Leminorella richardii	strain=NCTC12151	GCA_900478135.1	158841	158841	type	True	82.9528	945	1438	95	below_threshold
Serratia entomophila	strain=A1	GCA_021462285.1	42906	42906	type	True	78.672	341	1438	95	below_threshold
Jinshanibacter zhutongyuii	strain=CF-458	GCA_004295645.1	2498113	2498113	type	True	78.6524	385	1438	95	below_threshold
Serratia nevei	strain=S15	GCA_008364245.1	2703794	2703794	type	True	78.2875	359	1438	95	below_threshold
Pantoea deleyi	strain=LMG24200	GCA_022647325.1	470932	470932	type	True	77.9224	226	1438	95	below_threshold
Cronobacter sakazakii	strain=ATCC 29544	GCA_001971035.1	28141	28141	type	True	77.8801	231	1438	95	below_threshold
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	77.6856	274	1438	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:15:12,654] [INFO] DFAST Taxonomy check result was written to GCF_900706845.1_30316_B01_genomic.fna/tc_result.tsv
[2024-01-24 14:15:12,655] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:15:12,655] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:15:12,655] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg83ff54eb-45c3-47ee-bcc3-f9713cc18ef1/dqc_reference/checkm_data
[2024-01-24 14:15:12,656] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:15:12,699] [INFO] Task started: CheckM
[2024-01-24 14:15:12,699] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900706845.1_30316_B01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900706845.1_30316_B01_genomic.fna/checkm_input GCF_900706845.1_30316_B01_genomic.fna/checkm_result
[2024-01-24 14:15:48,559] [INFO] Task succeeded: CheckM
[2024-01-24 14:15:48,561] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.44%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:15:48,582] [INFO] ===== Completeness check finished =====
[2024-01-24 14:15:48,582] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:15:48,583] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900706845.1_30316_B01_genomic.fna/markers.fasta)
[2024-01-24 14:15:48,583] [INFO] Task started: Blastn
[2024-01-24 14:15:48,583] [INFO] Running command: blastn -query GCF_900706845.1_30316_B01_genomic.fna/markers.fasta -db /var/lib/cwl/stg83ff54eb-45c3-47ee-bcc3-f9713cc18ef1/dqc_reference/reference_markers_gtdb.fasta -out GCF_900706845.1_30316_B01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:49,648] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:49,657] [INFO] Selected 24 target genomes.
[2024-01-24 14:15:49,658] [INFO] Target genome list was writen to GCF_900706845.1_30316_B01_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:15:49,687] [INFO] Task started: fastANI
[2024-01-24 14:15:49,687] [INFO] Running command: fastANI --query /var/lib/cwl/stg367972b6-dfa9-4e37-9023-e613b2b5f61c/GCF_900706845.1_30316_B01_genomic.fna.gz --refList GCF_900706845.1_30316_B01_genomic.fna/target_genomes_gtdb.txt --output GCF_900706845.1_30316_B01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:16:08,751] [INFO] Task succeeded: fastANI
[2024-01-24 14:16:08,769] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:16:08,769] [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_000439085.1	s__Leminorella grimontii	99.9638	1385	1438	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Leminorella	95.0	99.99	99.98	1.00	0.99	4	conclusive
GCF_900478135.1	s__Leminorella richardii	82.9742	946	1438	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Leminorella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000513215.1	s__Serratia bockelmannii	78.9358	332	1438	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	96.0065	98.98	98.60	0.94	0.92	42	-
GCF_900187015.1	s__Serratia ficaria	78.8879	371	1438	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.0	99.70	99.56	0.95	0.92	5	-
GCF_003096015.2	s__Limnobaculum parvum	78.8204	320	1438	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Limnobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013394855.1	s__Limnobaculum xujianqingii	78.7272	365	1438	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Limnobaculum	95.0	98.42	97.65	0.92	0.89	4	-
GCF_002220655.1	s__Serratia marcescens_K	78.7146	362	1438	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	96.0833	98.79	98.10	0.94	0.88	411	-
GCF_004295645.1	s__Limnobaculum zhutongyuii	78.6749	387	1438	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Limnobaculum	95.0	100.00	100.00	1.00	1.00	2	-
GCF_006715005.1	s__Serratia marcescens_J	78.5716	353	1438	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	96.1913	98.92	98.92	0.95	0.95	2	-
GCF_003812745.1	s__Serratia sp003812745	78.5162	362	1438	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.8367	N/A	N/A	N/A	N/A	1	-
GCF_003363015.1	s__Enterobacillus tribolii	78.3819	312	1438	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016649425.1	s__Limnobaculum allomyrinae	78.3452	352	1438	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Limnobaculum	95.0	99.99	99.99	0.99	0.99	2	-
GCF_001642805.2	s__Serratia surfactantfaciens	78.2779	360	1438	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.0	98.81	97.95	0.93	0.91	10	-
GCF_013375155.1	s__Serratia ureilytica	78.2187	351	1438	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.3985	98.73	97.62	0.94	0.88	142	-
GCF_001517405.1	s__Erwinia_B gerundensis	78.1937	215	1438	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia_B	95.0	98.84	98.67	0.95	0.94	8	-
GCF_001598855.1	s__Pluralibacter gergoviae	78.1925	330	1438	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pluralibacter	95.0	98.81	98.03	0.90	0.85	23	-
GCF_001902635.1	s__Serratia marcescens_F	78.1327	341	1438	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112475.1	s__Pragia fontium	78.0905	328	1438	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pragia	95.0	99.20	98.63	0.97	0.95	5	-
GCF_003612015.1	s__Pantoea piersonii	77.8346	262	1438	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	99.15	96.25	0.97	0.92	11	-
GCF_004342285.1	s__Klebsiella sp004342285	77.8049	258	1438	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001922585.1	s__1-19 sp001922585	77.7775	214	1438	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__1-19	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009800925.1	s__Budvicia diplopodorum	77.7688	314	1438	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Budvicia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000427805.1	s__Budvicia aquatica	77.7407	285	1438	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Budvicia	95.0	99.94	99.91	1.00	1.00	3	-
--------------------------------------------------------------------------------
[2024-01-24 14:16:08,771] [INFO] GTDB search result was written to GCF_900706845.1_30316_B01_genomic.fna/result_gtdb.tsv
[2024-01-24 14:16:08,771] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:16:08,775] [INFO] DFAST_QC result json was written to GCF_900706845.1_30316_B01_genomic.fna/dqc_result.json
[2024-01-24 14:16:08,775] [INFO] DFAST_QC completed!
[2024-01-24 14:16:08,775] [INFO] Total running time: 0h1m22s