[2024-01-24 12:36:54,752] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:36:54,754] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:36:54,755] [INFO] DQC Reference Directory: /var/lib/cwl/stg3bcb9fdf-91c2-474f-bb90-ddb5fcf1e2f6/dqc_reference
[2024-01-24 12:36:57,086] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:36:57,087] [INFO] Task started: Prodigal
[2024-01-24 12:36:57,088] [INFO] Running command: gunzip -c /var/lib/cwl/stg924061f0-ebb9-4421-9ca4-2051c2425d15/GCF_019048385.1_ASM1904838v1_genomic.fna.gz | prodigal -d GCF_019048385.1_ASM1904838v1_genomic.fna/cds.fna -a GCF_019048385.1_ASM1904838v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:37:09,967] [INFO] Task succeeded: Prodigal
[2024-01-24 12:37:09,967] [INFO] Task started: HMMsearch
[2024-01-24 12:37:09,967] [INFO] Running command: hmmsearch --tblout GCF_019048385.1_ASM1904838v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3bcb9fdf-91c2-474f-bb90-ddb5fcf1e2f6/dqc_reference/reference_markers.hmm GCF_019048385.1_ASM1904838v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:37:10,331] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:37:10,333] [INFO] Found 6/6 markers.
[2024-01-24 12:37:10,376] [INFO] Query marker FASTA was written to GCF_019048385.1_ASM1904838v1_genomic.fna/markers.fasta
[2024-01-24 12:37:10,377] [INFO] Task started: Blastn
[2024-01-24 12:37:10,377] [INFO] Running command: blastn -query GCF_019048385.1_ASM1904838v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3bcb9fdf-91c2-474f-bb90-ddb5fcf1e2f6/dqc_reference/reference_markers.fasta -out GCF_019048385.1_ASM1904838v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:11,373] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:11,376] [INFO] Selected 11 target genomes.
[2024-01-24 12:37:11,377] [INFO] Target genome list was writen to GCF_019048385.1_ASM1904838v1_genomic.fna/target_genomes.txt
[2024-01-24 12:37:12,025] [INFO] Task started: fastANI
[2024-01-24 12:37:12,026] [INFO] Running command: fastANI --query /var/lib/cwl/stg924061f0-ebb9-4421-9ca4-2051c2425d15/GCF_019048385.1_ASM1904838v1_genomic.fna.gz --refList GCF_019048385.1_ASM1904838v1_genomic.fna/target_genomes.txt --output GCF_019048385.1_ASM1904838v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:37:24,042] [INFO] Task succeeded: fastANI
[2024-01-24 12:37:24,042] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3bcb9fdf-91c2-474f-bb90-ddb5fcf1e2f6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:37:24,043] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3bcb9fdf-91c2-474f-bb90-ddb5fcf1e2f6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:37:24,056] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:37:24,057] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:37:24,057] [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	100.0	1563	1563	95	conclusive
Pantoea agglomerans	strain=NBRC 102470	GCA_001598475.1	549	549	suspected-type	True	99.9803	1537	1563	95	conclusive
Pantoea eucalypti	strain=LMG 24197	GCA_009646115.1	470933	470933	type	True	90.6579	1344	1563	95	below_threshold
Pantoea eucalypti	strain=LMG 24197	GCA_006494355.1	470933	470933	type	True	90.6326	1330	1563	95	below_threshold
Pantoea deleyi	strain=LMG 24200	GCA_002095375.1	470932	470932	type	True	88.5322	1131	1563	95	below_threshold
Pantoea deleyi	strain=LMG24200	GCA_022647325.1	470932	470932	type	True	88.5143	1292	1563	95	below_threshold
Pantoea conspicua	strain=LMG 24534	GCA_002095315.1	472705	472705	type	True	86.5109	1131	1563	95	below_threshold
Pantoea stewartii subsp. indologenes	strain=LMG 2632	GCA_000757405.2	66270	66269	type	True	81.0796	857	1563	95	below_threshold
Enterobacter hormaechei	strain=FDAARGOS 1433	GCA_019048245.1	158836	158836	suspected-type	True	79.0053	518	1563	95	below_threshold
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	78.6027	517	1563	95	below_threshold
Cronobacter sakazakii	strain=ATCC 29544	GCA_001971035.1	28141	28141	type	True	78.5749	481	1563	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:37:24,059] [INFO] DFAST Taxonomy check result was written to GCF_019048385.1_ASM1904838v1_genomic.fna/tc_result.tsv
[2024-01-24 12:37:24,059] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:37:24,060] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:37:24,060] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3bcb9fdf-91c2-474f-bb90-ddb5fcf1e2f6/dqc_reference/checkm_data
[2024-01-24 12:37:24,061] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:37:24,111] [INFO] Task started: CheckM
[2024-01-24 12:37:24,112] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019048385.1_ASM1904838v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019048385.1_ASM1904838v1_genomic.fna/checkm_input GCF_019048385.1_ASM1904838v1_genomic.fna/checkm_result
[2024-01-24 12:38:05,332] [INFO] Task succeeded: CheckM
[2024-01-24 12:38:05,333] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:38:05,358] [INFO] ===== Completeness check finished =====
[2024-01-24 12:38:05,359] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:38:05,359] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019048385.1_ASM1904838v1_genomic.fna/markers.fasta)
[2024-01-24 12:38:05,360] [INFO] Task started: Blastn
[2024-01-24 12:38:05,360] [INFO] Running command: blastn -query GCF_019048385.1_ASM1904838v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3bcb9fdf-91c2-474f-bb90-ddb5fcf1e2f6/dqc_reference/reference_markers_gtdb.fasta -out GCF_019048385.1_ASM1904838v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:38:06,919] [INFO] Task succeeded: Blastn
[2024-01-24 12:38:06,923] [INFO] Selected 7 target genomes.
[2024-01-24 12:38:06,924] [INFO] Target genome list was writen to GCF_019048385.1_ASM1904838v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:38:06,953] [INFO] Task started: fastANI
[2024-01-24 12:38:06,953] [INFO] Running command: fastANI --query /var/lib/cwl/stg924061f0-ebb9-4421-9ca4-2051c2425d15/GCF_019048385.1_ASM1904838v1_genomic.fna.gz --refList GCF_019048385.1_ASM1904838v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019048385.1_ASM1904838v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:38:16,331] [INFO] Task succeeded: fastANI
[2024-01-24 12:38:16,342] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:38:16,342] [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_001598475.1	s__Pantoea agglomerans	99.9803	1537	1563	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	98.21	96.93	0.94	0.88	124	conclusive
GCF_900115075.1	s__Pantoea sp900115075	92.2212	1400	1563	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	96.06	96.06	0.92	0.92	2	-
GCF_009905795.1	s__Pantoea sp003512445	91.5746	1323	1563	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	99.25	99.25	0.92	0.92	2	-
GCF_004792415.1	s__Pantoea vagans	91.2539	1387	1563	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	97.00	95.86	0.91	0.88	14	-
GCF_013415305.1	s__Pantoea sp002419935	91.1548	1345	1563	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	98.92	98.92	0.97	0.97	2	-
GCF_009646115.1	s__Pantoea eucalypti	90.6729	1344	1563	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	99.21	98.96	0.95	0.93	16	-
GCF_008632075.1	s__Pantoea sp008632075	90.6495	1329	1563	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	99.47	99.36	0.95	0.94	34	-
--------------------------------------------------------------------------------
[2024-01-24 12:38:16,344] [INFO] GTDB search result was written to GCF_019048385.1_ASM1904838v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:38:16,345] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:38:16,348] [INFO] DFAST_QC result json was written to GCF_019048385.1_ASM1904838v1_genomic.fna/dqc_result.json
[2024-01-24 12:38:16,348] [INFO] DFAST_QC completed!
[2024-01-24 12:38:16,348] [INFO] Total running time: 0h1m22s