[2024-01-24 13:57:13,571] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:13,573] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:13,573] [INFO] DQC Reference Directory: /var/lib/cwl/stg63e7680f-58c8-4470-a52c-30de95ace98a/dqc_reference
[2024-01-24 13:57:14,843] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:14,844] [INFO] Task started: Prodigal
[2024-01-24 13:57:14,845] [INFO] Running command: gunzip -c /var/lib/cwl/stgde24729c-4ce1-447d-9da3-8fd21a1b8292/GCF_000757405.2_LMG2632assem4_genomic.fna.gz | prodigal -d GCF_000757405.2_LMG2632assem4_genomic.fna/cds.fna -a GCF_000757405.2_LMG2632assem4_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:27,502] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:27,502] [INFO] Task started: HMMsearch
[2024-01-24 13:57:27,502] [INFO] Running command: hmmsearch --tblout GCF_000757405.2_LMG2632assem4_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg63e7680f-58c8-4470-a52c-30de95ace98a/dqc_reference/reference_markers.hmm GCF_000757405.2_LMG2632assem4_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:27,796] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:27,797] [INFO] Found 6/6 markers.
[2024-01-24 13:57:27,837] [INFO] Query marker FASTA was written to GCF_000757405.2_LMG2632assem4_genomic.fna/markers.fasta
[2024-01-24 13:57:27,838] [INFO] Task started: Blastn
[2024-01-24 13:57:27,838] [INFO] Running command: blastn -query GCF_000757405.2_LMG2632assem4_genomic.fna/markers.fasta -db /var/lib/cwl/stg63e7680f-58c8-4470-a52c-30de95ace98a/dqc_reference/reference_markers.fasta -out GCF_000757405.2_LMG2632assem4_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:28,731] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:28,734] [INFO] Selected 10 target genomes.
[2024-01-24 13:57:28,734] [INFO] Target genome list was writen to GCF_000757405.2_LMG2632assem4_genomic.fna/target_genomes.txt
[2024-01-24 13:57:28,738] [INFO] Task started: fastANI
[2024-01-24 13:57:28,738] [INFO] Running command: fastANI --query /var/lib/cwl/stgde24729c-4ce1-447d-9da3-8fd21a1b8292/GCF_000757405.2_LMG2632assem4_genomic.fna.gz --refList GCF_000757405.2_LMG2632assem4_genomic.fna/target_genomes.txt --output GCF_000757405.2_LMG2632assem4_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:57:38,912] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:38,912] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg63e7680f-58c8-4470-a52c-30de95ace98a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:57:38,913] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg63e7680f-58c8-4470-a52c-30de95ace98a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:57:38,922] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:57:38,922] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:57:38,922] [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 stewartii subsp. indologenes	strain=LMG 2632	GCA_000757405.2	66270	66269	type	True	100.0	1540	1542	95	conclusive
Pantoea stewartii subsp. stewartii	strain=CCUG 26359	GCA_008801695.1	66271	66269	type	True	98.7303	1227	1542	95	conclusive
Pantoea allii	strain=LMG 24248	GCA_002307475.1	574096	574096	type	True	84.8663	1248	1542	95	below_threshold
Pantoea ananatis	strain=LMG 2665	GCA_000710035.2	553	553	type	True	84.8657	1232	1542	95	below_threshold
Pantoea ananatis	strain=LMG 2665	GCA_000661975.1	553	553	type	True	84.8378	1244	1542	95	below_threshold
Pantoea allii	strain=LMG 24248	GCA_002095545.1	574096	574096	type	True	84.8368	1214	1542	95	below_threshold
Pantoea deleyi	strain=LMG24200	GCA_022647325.1	470932	470932	type	True	81.1831	843	1542	95	below_threshold
Erwinia aphidicola	strain=X001	GCA_024169515.1	68334	68334	type	True	78.9294	556	1542	95	below_threshold
Enterobacter sichuanensis	strain=WCHECL1597	GCA_025002605.1	2071710	2071710	type	True	78.5189	358	1542	95	below_threshold
Enterobacter hormaechei	strain=FDAARGOS 1433	GCA_019048245.1	158836	158836	suspected-type	True	78.3629	372	1542	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:57:38,924] [INFO] DFAST Taxonomy check result was written to GCF_000757405.2_LMG2632assem4_genomic.fna/tc_result.tsv
[2024-01-24 13:57:38,925] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:57:38,925] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:57:38,925] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg63e7680f-58c8-4470-a52c-30de95ace98a/dqc_reference/checkm_data
[2024-01-24 13:57:38,926] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:57:38,972] [INFO] Task started: CheckM
[2024-01-24 13:57:38,972] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000757405.2_LMG2632assem4_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000757405.2_LMG2632assem4_genomic.fna/checkm_input GCF_000757405.2_LMG2632assem4_genomic.fna/checkm_result
[2024-01-24 13:58:23,101] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:23,103] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:23,133] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:23,133] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:23,133] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000757405.2_LMG2632assem4_genomic.fna/markers.fasta)
[2024-01-24 13:58:23,134] [INFO] Task started: Blastn
[2024-01-24 13:58:23,134] [INFO] Running command: blastn -query GCF_000757405.2_LMG2632assem4_genomic.fna/markers.fasta -db /var/lib/cwl/stg63e7680f-58c8-4470-a52c-30de95ace98a/dqc_reference/reference_markers_gtdb.fasta -out GCF_000757405.2_LMG2632assem4_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:24,632] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:24,635] [INFO] Selected 13 target genomes.
[2024-01-24 13:58:24,635] [INFO] Target genome list was writen to GCF_000757405.2_LMG2632assem4_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:24,654] [INFO] Task started: fastANI
[2024-01-24 13:58:24,654] [INFO] Running command: fastANI --query /var/lib/cwl/stgde24729c-4ce1-447d-9da3-8fd21a1b8292/GCF_000757405.2_LMG2632assem4_genomic.fna.gz --refList GCF_000757405.2_LMG2632assem4_genomic.fna/target_genomes_gtdb.txt --output GCF_000757405.2_LMG2632assem4_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:58:38,017] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:38,029] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:58:38,029] [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_008801695.1	s__Pantoea stewartii	98.714	1228	1542	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	98.82	98.55	0.82	0.77	34	conclusive
GCF_002307475.1	s__Pantoea allii	84.871	1247	1542	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	98.91	98.49	0.92	0.90	6	-
GCF_000710035.2	s__Pantoea ananatis	84.8657	1232	1542	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	98.81	96.45	0.92	0.81	152	-
GCA_002434205.1	s__Pantoea sp002434205	81.4305	824	1542	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002095315.1	s__Pantoea conspicua	81.3957	792	1542	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002095305.1	s__Pantoea brenneri	81.2126	807	1542	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	99.27	99.10	0.90	0.85	24	-
GCF_006494415.1	s__Pantoea deleyi	81.1712	835	1542	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	99.95	99.95	0.98	0.98	2	-
GCF_004792415.1	s__Pantoea vagans	81.1583	859	1542	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	81.0104	798	1542	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	98.92	98.92	0.97	0.97	2	-
GCA_018842655.1	s__Pantoea sp018842655	80.7666	747	1542	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018842675.1	s__Pantoea sp018842675	80.5836	745	1542	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002920175.1	s__Pantoea sp002920175	80.1684	754	1542	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	99.09	99.09	0.94	0.94	2	-
GCF_002858935.1	s__Pantoea endophytica	79.9236	739	1542	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	97.84	95.24	0.93	0.88	7	-
--------------------------------------------------------------------------------
[2024-01-24 13:58:38,032] [INFO] GTDB search result was written to GCF_000757405.2_LMG2632assem4_genomic.fna/result_gtdb.tsv
[2024-01-24 13:58:38,033] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:58:38,037] [INFO] DFAST_QC result json was written to GCF_000757405.2_LMG2632assem4_genomic.fna/dqc_result.json
[2024-01-24 13:58:38,037] [INFO] DFAST_QC completed!
[2024-01-24 13:58:38,037] [INFO] Total running time: 0h1m24s