[2024-01-24 11:44:38,165] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:44:38,174] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:44:38,175] [INFO] DQC Reference Directory: /var/lib/cwl/stg296a530a-4bf6-4a77-8183-8d8dbd98649a/dqc_reference
[2024-01-24 11:44:41,493] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:44:41,494] [INFO] Task started: Prodigal
[2024-01-24 11:44:41,495] [INFO] Running command: gunzip -c /var/lib/cwl/stg27272633-e346-4ef9-8180-8b4e60173072/GCF_006494375.1_ASM649437v1_genomic.fna.gz | prodigal -d GCF_006494375.1_ASM649437v1_genomic.fna/cds.fna -a GCF_006494375.1_ASM649437v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:44:54,086] [INFO] Task succeeded: Prodigal
[2024-01-24 11:44:54,087] [INFO] Task started: HMMsearch
[2024-01-24 11:44:54,087] [INFO] Running command: hmmsearch --tblout GCF_006494375.1_ASM649437v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg296a530a-4bf6-4a77-8183-8d8dbd98649a/dqc_reference/reference_markers.hmm GCF_006494375.1_ASM649437v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:44:54,367] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:44:54,369] [INFO] Found 6/6 markers.
[2024-01-24 11:44:54,412] [INFO] Query marker FASTA was written to GCF_006494375.1_ASM649437v1_genomic.fna/markers.fasta
[2024-01-24 11:44:54,413] [INFO] Task started: Blastn
[2024-01-24 11:44:54,413] [INFO] Running command: blastn -query GCF_006494375.1_ASM649437v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg296a530a-4bf6-4a77-8183-8d8dbd98649a/dqc_reference/reference_markers.fasta -out GCF_006494375.1_ASM649437v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:55,287] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:55,291] [INFO] Selected 12 target genomes.
[2024-01-24 11:44:55,292] [INFO] Target genome list was writen to GCF_006494375.1_ASM649437v1_genomic.fna/target_genomes.txt
[2024-01-24 11:44:55,340] [INFO] Task started: fastANI
[2024-01-24 11:44:55,340] [INFO] Running command: fastANI --query /var/lib/cwl/stg27272633-e346-4ef9-8180-8b4e60173072/GCF_006494375.1_ASM649437v1_genomic.fna.gz --refList GCF_006494375.1_ASM649437v1_genomic.fna/target_genomes.txt --output GCF_006494375.1_ASM649437v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:45:07,301] [INFO] Task succeeded: fastANI
[2024-01-24 11:45:07,302] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg296a530a-4bf6-4a77-8183-8d8dbd98649a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:45:07,302] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg296a530a-4bf6-4a77-8183-8d8dbd98649a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:45:07,316] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:45:07,317] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:45:07,317] [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
Pantoea agglomerans	strain=FDAARGOS 1447	GCA_019048385.1	549	549	suspected-type	True	88.6125	1287	1537	95	below_threshold
Pantoea agglomerans	strain=NBRC 102470	GCA_001598475.1	549	549	suspected-type	True	88.6033	1288	1537	95	below_threshold
Pantoea deleyi	strain=LMG 24200	GCA_006494415.1	470932	470932	type	True	87.6937	1243	1537	95	below_threshold
Pantoea deleyi	strain=LMG 24200	GCA_002095375.1	470932	470932	type	True	87.6844	1114	1537	95	below_threshold
Pantoea deleyi	strain=LMG24200	GCA_022647325.1	470932	470932	type	True	87.5716	1267	1537	95	below_threshold
Pantoea eucalypti	strain=LMG 24197	GCA_006494355.1	470933	470933	type	True	87.4699	1262	1537	95	below_threshold
Pantoea eucalypti	strain=LMG 24197	GCA_009646115.1	470933	470933	type	True	87.4402	1279	1537	95	below_threshold
Pantoea conspicua	strain=LMG 24534	GCA_002095315.1	472705	472705	type	True	85.5888	1096	1537	95	below_threshold
Pantoea stewartii subsp. indologenes	strain=LMG 2632	GCA_000757405.2	66270	66269	type	True	81.0848	835	1537	95	below_threshold
Erwinia aphidicola	strain=X001	GCA_024169515.1	68334	68334	type	True	79.7795	732	1537	95	below_threshold
Erwinia phyllosphaerae	strain=CMYE1	GCA_019132875.1	2853256	2853256	type	True	79.207	634	1537	95	below_threshold
Cronobacter sakazakii	strain=ATCC 29544	GCA_001971035.1	28141	28141	type	True	78.539	488	1537	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:45:07,318] [INFO] DFAST Taxonomy check result was written to GCF_006494375.1_ASM649437v1_genomic.fna/tc_result.tsv
[2024-01-24 11:45:07,319] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:45:07,319] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:45:07,320] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg296a530a-4bf6-4a77-8183-8d8dbd98649a/dqc_reference/checkm_data
[2024-01-24 11:45:07,321] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:45:07,368] [INFO] Task started: CheckM
[2024-01-24 11:45:07,369] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006494375.1_ASM649437v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006494375.1_ASM649437v1_genomic.fna/checkm_input GCF_006494375.1_ASM649437v1_genomic.fna/checkm_result
[2024-01-24 11:45:48,026] [INFO] Task succeeded: CheckM
[2024-01-24 11:45:48,027] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:45:48,048] [INFO] ===== Completeness check finished =====
[2024-01-24 11:45:48,049] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:45:48,050] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006494375.1_ASM649437v1_genomic.fna/markers.fasta)
[2024-01-24 11:45:48,050] [INFO] Task started: Blastn
[2024-01-24 11:45:48,050] [INFO] Running command: blastn -query GCF_006494375.1_ASM649437v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg296a530a-4bf6-4a77-8183-8d8dbd98649a/dqc_reference/reference_markers_gtdb.fasta -out GCF_006494375.1_ASM649437v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:45:49,237] [INFO] Task succeeded: Blastn
[2024-01-24 11:45:49,241] [INFO] Selected 12 target genomes.
[2024-01-24 11:45:49,241] [INFO] Target genome list was writen to GCF_006494375.1_ASM649437v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:45:49,274] [INFO] Task started: fastANI
[2024-01-24 11:45:49,274] [INFO] Running command: fastANI --query /var/lib/cwl/stg27272633-e346-4ef9-8180-8b4e60173072/GCF_006494375.1_ASM649437v1_genomic.fna.gz --refList GCF_006494375.1_ASM649437v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006494375.1_ASM649437v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:46:01,008] [INFO] Task succeeded: fastANI
[2024-01-24 11:46:01,028] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:46:01,028] [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_006494375.1	s__Pantoea anthophila	100.0	1535	1537	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	98.39	98.21	0.92	0.90	16	conclusive
GCF_001598475.1	s__Pantoea agglomerans	88.6033	1288	1537	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	98.21	96.93	0.94	0.88	124	-
GCF_008632075.1	s__Pantoea sp008632075	88.4452	1276	1537	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	99.47	99.36	0.95	0.94	34	-
GCF_004792415.1	s__Pantoea vagans	88.4443	1307	1537	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	97.00	95.86	0.91	0.88	14	-
GCF_009905795.1	s__Pantoea sp003512445	88.1223	1265	1537	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	99.25	99.25	0.92	0.92	2	-
GCF_900115075.1	s__Pantoea sp900115075	88.1084	1309	1537	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	96.06	96.06	0.92	0.92	2	-
GCF_006494415.1	s__Pantoea deleyi	87.6883	1244	1537	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	99.95	99.95	0.98	0.98	2	-
GCF_009646115.1	s__Pantoea eucalypti	87.4492	1278	1537	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	99.21	98.96	0.95	0.93	16	-
GCF_003236715.1	s__Pantoea sp003236715	87.3213	1165	1537	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000196615.1	s__Erwinia billingiae	79.6796	733	1537	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	97.77	97.43	0.91	0.82	7	-
--------------------------------------------------------------------------------
[2024-01-24 11:46:01,030] [INFO] GTDB search result was written to GCF_006494375.1_ASM649437v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:46:01,031] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:46:01,037] [INFO] DFAST_QC result json was written to GCF_006494375.1_ASM649437v1_genomic.fna/dqc_result.json
[2024-01-24 11:46:01,037] [INFO] DFAST_QC completed!
[2024-01-24 11:46:01,037] [INFO] Total running time: 0h1m23s