[2024-01-24 13:46:25,401] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:25,419] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:25,419] [INFO] DQC Reference Directory: /var/lib/cwl/stg008ddc56-feb0-488d-8abb-ba6a8405f3cc/dqc_reference
[2024-01-24 13:46:26,799] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:26,800] [INFO] Task started: Prodigal
[2024-01-24 13:46:26,800] [INFO] Running command: gunzip -c /var/lib/cwl/stg4e9c2602-18ca-4db6-89c6-01c3135121d4/GCF_022647325.1_ASM2264732v1_genomic.fna.gz | prodigal -d GCF_022647325.1_ASM2264732v1_genomic.fna/cds.fna -a GCF_022647325.1_ASM2264732v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:39,960] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:39,960] [INFO] Task started: HMMsearch
[2024-01-24 13:46:39,960] [INFO] Running command: hmmsearch --tblout GCF_022647325.1_ASM2264732v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg008ddc56-feb0-488d-8abb-ba6a8405f3cc/dqc_reference/reference_markers.hmm GCF_022647325.1_ASM2264732v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:40,392] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:40,393] [INFO] Found 6/6 markers.
[2024-01-24 13:46:40,434] [INFO] Query marker FASTA was written to GCF_022647325.1_ASM2264732v1_genomic.fna/markers.fasta
[2024-01-24 13:46:40,435] [INFO] Task started: Blastn
[2024-01-24 13:46:40,435] [INFO] Running command: blastn -query GCF_022647325.1_ASM2264732v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg008ddc56-feb0-488d-8abb-ba6a8405f3cc/dqc_reference/reference_markers.fasta -out GCF_022647325.1_ASM2264732v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:41,368] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:41,405] [INFO] Selected 11 target genomes.
[2024-01-24 13:46:41,406] [INFO] Target genome list was writen to GCF_022647325.1_ASM2264732v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:41,418] [INFO] Task started: fastANI
[2024-01-24 13:46:41,419] [INFO] Running command: fastANI --query /var/lib/cwl/stg4e9c2602-18ca-4db6-89c6-01c3135121d4/GCF_022647325.1_ASM2264732v1_genomic.fna.gz --refList GCF_022647325.1_ASM2264732v1_genomic.fna/target_genomes.txt --output GCF_022647325.1_ASM2264732v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:53,979] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:53,979] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg008ddc56-feb0-488d-8abb-ba6a8405f3cc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:53,980] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg008ddc56-feb0-488d-8abb-ba6a8405f3cc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:53,989] [INFO] Found 11 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:46:53,990] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:46:53,990] [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 deleyi	strain=LMG24200	GCA_022647325.1	470932	470932	type	True	100.0	1558	1558	95	conclusive
Pantoea deleyi	strain=LMG 24200	GCA_006494415.1	470932	470932	type	True	99.9703	1503	1558	95	conclusive
Pantoea deleyi	strain=LMG 24200	GCA_002095375.1	470932	470932	type	True	99.8389	1365	1558	95	conclusive
Pantoea agglomerans	strain=FDAARGOS 1447	GCA_019048385.1	549	549	suspected-type	True	88.5104	1285	1558	95	below_threshold
Pantoea agglomerans	strain=NBRC 102470	GCA_001598475.1	549	549	suspected-type	True	88.4599	1256	1558	95	below_threshold
Pantoea eucalypti	strain=LMG 24197	GCA_009646115.1	470933	470933	type	True	87.481	1281	1558	95	below_threshold
Pantoea conspicua	strain=LMG 24534	GCA_002095315.1	472705	472705	type	True	85.401	1088	1558	95	below_threshold
Pantoea stewartii subsp. indologenes	strain=LMG 2632	GCA_000757405.2	66270	66269	type	True	81.0354	862	1558	95	below_threshold
Erwinia aphidicola	strain=X001	GCA_024169515.1	68334	68334	type	True	79.9956	786	1558	95	below_threshold
Erwinia phyllosphaerae	strain=CMYE1	GCA_019132875.1	2853256	2853256	type	True	79.2069	648	1558	95	below_threshold
Serratia nevei	strain=S15	GCA_008364245.1	2703794	2703794	type	True	78.9077	597	1558	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:53,992] [INFO] DFAST Taxonomy check result was written to GCF_022647325.1_ASM2264732v1_genomic.fna/tc_result.tsv
[2024-01-24 13:46:53,992] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:53,992] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:53,993] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg008ddc56-feb0-488d-8abb-ba6a8405f3cc/dqc_reference/checkm_data
[2024-01-24 13:46:53,994] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:54,043] [INFO] Task started: CheckM
[2024-01-24 13:46:54,044] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022647325.1_ASM2264732v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022647325.1_ASM2264732v1_genomic.fna/checkm_input GCF_022647325.1_ASM2264732v1_genomic.fna/checkm_result
[2024-01-24 13:47:37,224] [INFO] Task succeeded: CheckM
[2024-01-24 13:47:37,226] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:47:37,245] [INFO] ===== Completeness check finished =====
[2024-01-24 13:47:37,246] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:47:37,246] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022647325.1_ASM2264732v1_genomic.fna/markers.fasta)
[2024-01-24 13:47:37,246] [INFO] Task started: Blastn
[2024-01-24 13:47:37,247] [INFO] Running command: blastn -query GCF_022647325.1_ASM2264732v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg008ddc56-feb0-488d-8abb-ba6a8405f3cc/dqc_reference/reference_markers_gtdb.fasta -out GCF_022647325.1_ASM2264732v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:38,447] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:38,450] [INFO] Selected 9 target genomes.
[2024-01-24 13:47:38,450] [INFO] Target genome list was writen to GCF_022647325.1_ASM2264732v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:47:38,461] [INFO] Task started: fastANI
[2024-01-24 13:47:38,462] [INFO] Running command: fastANI --query /var/lib/cwl/stg4e9c2602-18ca-4db6-89c6-01c3135121d4/GCF_022647325.1_ASM2264732v1_genomic.fna.gz --refList GCF_022647325.1_ASM2264732v1_genomic.fna/target_genomes_gtdb.txt --output GCF_022647325.1_ASM2264732v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:47:49,249] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:49,263] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:47:49,263] [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_006494415.1	s__Pantoea deleyi	99.9695	1503	1558	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	99.95	99.95	0.98	0.98	2	conclusive
GCF_003236715.1	s__Pantoea sp003236715	94.699	1285	1558	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001598475.1	s__Pantoea agglomerans	88.4599	1256	1558	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	98.21	96.93	0.94	0.88	124	-
GCF_004792415.1	s__Pantoea vagans	88.3426	1288	1558	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	97.00	95.86	0.91	0.88	14	-
GCF_900115075.1	s__Pantoea sp900115075	88.0872	1294	1558	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	88.0644	1227	1558	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	99.25	99.25	0.92	0.92	2	-
GCF_008632075.1	s__Pantoea sp008632075	87.8972	1256	1558	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	99.47	99.36	0.95	0.94	34	-
GCF_006494375.1	s__Pantoea anthophila	87.4863	1266	1558	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	98.39	98.21	0.92	0.90	16	-
GCF_009646115.1	s__Pantoea eucalypti	87.4812	1281	1558	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	99.21	98.96	0.95	0.93	16	-
--------------------------------------------------------------------------------
[2024-01-24 13:47:49,265] [INFO] GTDB search result was written to GCF_022647325.1_ASM2264732v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:47:49,265] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:47:49,270] [INFO] DFAST_QC result json was written to GCF_022647325.1_ASM2264732v1_genomic.fna/dqc_result.json
[2024-01-24 13:47:49,270] [INFO] DFAST_QC completed!
[2024-01-24 13:47:49,270] [INFO] Total running time: 0h1m24s