[2024-01-24 14:39:14,642] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:39:14,644] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:39:14,644] [INFO] DQC Reference Directory: /var/lib/cwl/stg20ee4cc9-8206-4e3a-a75e-6e4d54c26ee6/dqc_reference
[2024-01-24 14:39:16,083] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:39:16,084] [INFO] Task started: Prodigal
[2024-01-24 14:39:16,084] [INFO] Running command: gunzip -c /var/lib/cwl/stgfdbb2469-0817-4bef-a8f6-d9c38ebf9c1e/GCF_019880205.1_ASM1988020v1_genomic.fna.gz | prodigal -d GCF_019880205.1_ASM1988020v1_genomic.fna/cds.fna -a GCF_019880205.1_ASM1988020v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:39:29,519] [INFO] Task succeeded: Prodigal
[2024-01-24 14:39:29,519] [INFO] Task started: HMMsearch
[2024-01-24 14:39:29,519] [INFO] Running command: hmmsearch --tblout GCF_019880205.1_ASM1988020v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg20ee4cc9-8206-4e3a-a75e-6e4d54c26ee6/dqc_reference/reference_markers.hmm GCF_019880205.1_ASM1988020v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:39:29,833] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:39:29,834] [INFO] Found 6/6 markers.
[2024-01-24 14:39:29,875] [INFO] Query marker FASTA was written to GCF_019880205.1_ASM1988020v1_genomic.fna/markers.fasta
[2024-01-24 14:39:29,875] [INFO] Task started: Blastn
[2024-01-24 14:39:29,875] [INFO] Running command: blastn -query GCF_019880205.1_ASM1988020v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg20ee4cc9-8206-4e3a-a75e-6e4d54c26ee6/dqc_reference/reference_markers.fasta -out GCF_019880205.1_ASM1988020v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:39:30,848] [INFO] Task succeeded: Blastn
[2024-01-24 14:39:30,852] [INFO] Selected 10 target genomes.
[2024-01-24 14:39:30,852] [INFO] Target genome list was writen to GCF_019880205.1_ASM1988020v1_genomic.fna/target_genomes.txt
[2024-01-24 14:39:30,857] [INFO] Task started: fastANI
[2024-01-24 14:39:30,857] [INFO] Running command: fastANI --query /var/lib/cwl/stgfdbb2469-0817-4bef-a8f6-d9c38ebf9c1e/GCF_019880205.1_ASM1988020v1_genomic.fna.gz --refList GCF_019880205.1_ASM1988020v1_genomic.fna/target_genomes.txt --output GCF_019880205.1_ASM1988020v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:39:42,323] [INFO] Task succeeded: fastANI
[2024-01-24 14:39:42,324] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg20ee4cc9-8206-4e3a-a75e-6e4d54c26ee6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:39:42,325] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg20ee4cc9-8206-4e3a-a75e-6e4d54c26ee6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:39:42,342] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:39:42,342] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:39:42,343] [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	91.6053	1382	1577	95	below_threshold
Pantoea agglomerans	strain=NBRC 102470	GCA_001598475.1	549	549	suspected-type	True	91.5201	1369	1577	95	below_threshold
Pantoea eucalypti	strain=LMG 24197	GCA_009646115.1	470933	470933	type	True	90.114	1335	1577	95	below_threshold
Pantoea eucalypti	strain=LMG 24197	GCA_006494355.1	470933	470933	type	True	90.057	1310	1577	95	below_threshold
Pantoea deleyi	strain=LMG 24200	GCA_002095375.1	470932	470932	type	True	88.0443	1144	1577	95	below_threshold
Pantoea deleyi	strain=LMG24200	GCA_022647325.1	470932	470932	type	True	87.9962	1308	1577	95	below_threshold
Pantoea stewartii subsp. indologenes	strain=LMG 2632	GCA_000757405.2	66270	66269	type	True	80.9931	843	1577	95	below_threshold
Erwinia aphidicola	strain=X001	GCA_024169515.1	68334	68334	type	True	79.734	747	1577	95	below_threshold
Erwinia phyllosphaerae	strain=CMYE1	GCA_019132875.1	2853256	2853256	type	True	79.0374	607	1577	95	below_threshold
Serratia nevei	strain=S15	GCA_008364245.1	2703794	2703794	type	True	78.5017	479	1577	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:39:42,344] [INFO] DFAST Taxonomy check result was written to GCF_019880205.1_ASM1988020v1_genomic.fna/tc_result.tsv
[2024-01-24 14:39:42,345] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:39:42,345] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:39:42,346] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg20ee4cc9-8206-4e3a-a75e-6e4d54c26ee6/dqc_reference/checkm_data
[2024-01-24 14:39:42,348] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:39:42,397] [INFO] Task started: CheckM
[2024-01-24 14:39:42,398] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019880205.1_ASM1988020v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019880205.1_ASM1988020v1_genomic.fna/checkm_input GCF_019880205.1_ASM1988020v1_genomic.fna/checkm_result
[2024-01-24 14:40:26,263] [INFO] Task succeeded: CheckM
[2024-01-24 14:40:26,265] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:40:26,293] [INFO] ===== Completeness check finished =====
[2024-01-24 14:40:26,294] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:40:26,294] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019880205.1_ASM1988020v1_genomic.fna/markers.fasta)
[2024-01-24 14:40:26,295] [INFO] Task started: Blastn
[2024-01-24 14:40:26,295] [INFO] Running command: blastn -query GCF_019880205.1_ASM1988020v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg20ee4cc9-8206-4e3a-a75e-6e4d54c26ee6/dqc_reference/reference_markers_gtdb.fasta -out GCF_019880205.1_ASM1988020v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:40:27,898] [INFO] Task succeeded: Blastn
[2024-01-24 14:40:27,902] [INFO] Selected 7 target genomes.
[2024-01-24 14:40:27,902] [INFO] Target genome list was writen to GCF_019880205.1_ASM1988020v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:40:27,910] [INFO] Task started: fastANI
[2024-01-24 14:40:27,910] [INFO] Running command: fastANI --query /var/lib/cwl/stgfdbb2469-0817-4bef-a8f6-d9c38ebf9c1e/GCF_019880205.1_ASM1988020v1_genomic.fna.gz --refList GCF_019880205.1_ASM1988020v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019880205.1_ASM1988020v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:40:37,065] [INFO] Task succeeded: fastANI
[2024-01-24 14:40:37,073] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:40:37,073] [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_009905795.1	s__Pantoea sp003512445	99.31	1403	1577	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	99.25	99.25	0.92	0.92	2	conclusive
GCF_008632075.1	s__Pantoea sp008632075	94.7997	1390	1577	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	94.6883	1406	1577	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	97.00	95.86	0.91	0.88	14	-
GCF_001598475.1	s__Pantoea agglomerans	91.5201	1369	1577	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	98.21	96.93	0.94	0.88	124	-
GCF_900115075.1	s__Pantoea sp900115075	91.2596	1370	1577	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	96.06	96.06	0.92	0.92	2	-
GCF_013415305.1	s__Pantoea sp002419935	90.575	1331	1577	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	90.114	1335	1577	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 14:40:37,074] [INFO] GTDB search result was written to GCF_019880205.1_ASM1988020v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:40:37,075] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:40:37,078] [INFO] DFAST_QC result json was written to GCF_019880205.1_ASM1988020v1_genomic.fna/dqc_result.json
[2024-01-24 14:40:37,078] [INFO] DFAST_QC completed!
[2024-01-24 14:40:37,078] [INFO] Total running time: 0h1m22s