[2024-01-25 19:48:50,670] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:48:50,674] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:48:50,674] [INFO] DQC Reference Directory: /var/lib/cwl/stg26752316-53d1-4e50-8543-31db78396e04/dqc_reference
[2024-01-25 19:48:51,845] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:48:51,846] [INFO] Task started: Prodigal
[2024-01-25 19:48:51,846] [INFO] Running command: gunzip -c /var/lib/cwl/stg1c5c48eb-c84a-4525-9cee-0c26a0a37035/GCF_002307475.1_ASM230747v1_genomic.fna.gz | prodigal -d GCF_002307475.1_ASM230747v1_genomic.fna/cds.fna -a GCF_002307475.1_ASM230747v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:49:03,984] [INFO] Task succeeded: Prodigal
[2024-01-25 19:49:03,984] [INFO] Task started: HMMsearch
[2024-01-25 19:49:03,984] [INFO] Running command: hmmsearch --tblout GCF_002307475.1_ASM230747v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg26752316-53d1-4e50-8543-31db78396e04/dqc_reference/reference_markers.hmm GCF_002307475.1_ASM230747v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:49:04,351] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:49:04,352] [INFO] Found 6/6 markers.
[2024-01-25 19:49:04,393] [INFO] Query marker FASTA was written to GCF_002307475.1_ASM230747v1_genomic.fna/markers.fasta
[2024-01-25 19:49:04,393] [INFO] Task started: Blastn
[2024-01-25 19:49:04,393] [INFO] Running command: blastn -query GCF_002307475.1_ASM230747v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg26752316-53d1-4e50-8543-31db78396e04/dqc_reference/reference_markers.fasta -out GCF_002307475.1_ASM230747v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:49:05,245] [INFO] Task succeeded: Blastn
[2024-01-25 19:49:05,248] [INFO] Selected 10 target genomes.
[2024-01-25 19:49:05,248] [INFO] Target genome list was writen to GCF_002307475.1_ASM230747v1_genomic.fna/target_genomes.txt
[2024-01-25 19:49:05,276] [INFO] Task started: fastANI
[2024-01-25 19:49:05,276] [INFO] Running command: fastANI --query /var/lib/cwl/stg1c5c48eb-c84a-4525-9cee-0c26a0a37035/GCF_002307475.1_ASM230747v1_genomic.fna.gz --refList GCF_002307475.1_ASM230747v1_genomic.fna/target_genomes.txt --output GCF_002307475.1_ASM230747v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:49:15,933] [INFO] Task succeeded: fastANI
[2024-01-25 19:49:15,933] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg26752316-53d1-4e50-8543-31db78396e04/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:49:15,934] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg26752316-53d1-4e50-8543-31db78396e04/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:49:15,941] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:49:15,941] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:49:15,941] [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 allii	strain=LMG 24248	GCA_002307475.1	574096	574096	type	True	100.0	1674	1714	95	conclusive
Pantoea allii	strain=LMG 24248	GCA_002095545.1	574096	574096	type	True	99.946	1613	1714	95	conclusive
Pantoea ananatis	strain=LMG 2665	GCA_000710035.2	553	553	type	True	88.9816	1378	1714	95	below_threshold
Pantoea ananatis	strain=LMG 2665	GCA_000661975.1	553	553	type	True	88.9418	1401	1714	95	below_threshold
Pantoea stewartii subsp. stewartii	strain=CCUG 26359	GCA_008801695.1	66271	66269	type	True	85.0516	1102	1714	95	below_threshold
Pantoea stewartii subsp. indologenes	strain=LMG 2632	GCA_000757405.2	66270	66269	type	True	84.8943	1252	1714	95	below_threshold
Pantoea deleyi	strain=LMG24200	GCA_022647325.1	470932	470932	type	True	81.0549	884	1714	95	below_threshold
Erwinia aphidicola	strain=X001	GCA_024169515.1	68334	68334	type	True	79.1345	560	1714	95	below_threshold
Erwinia phyllosphaerae	strain=CMYE1	GCA_019132875.1	2853256	2853256	type	True	78.8172	532	1714	95	below_threshold
Citrobacter rodentium	strain=DSM 16636	GCA_021278985.1	67825	67825	type	True	78.0735	381	1714	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:49:15,942] [INFO] DFAST Taxonomy check result was written to GCF_002307475.1_ASM230747v1_genomic.fna/tc_result.tsv
[2024-01-25 19:49:15,943] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:49:15,943] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:49:15,943] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg26752316-53d1-4e50-8543-31db78396e04/dqc_reference/checkm_data
[2024-01-25 19:49:15,944] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:49:15,995] [INFO] Task started: CheckM
[2024-01-25 19:49:15,995] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002307475.1_ASM230747v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002307475.1_ASM230747v1_genomic.fna/checkm_input GCF_002307475.1_ASM230747v1_genomic.fna/checkm_result
[2024-01-25 19:49:54,420] [INFO] Task succeeded: CheckM
[2024-01-25 19:49:54,421] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:49:54,438] [INFO] ===== Completeness check finished =====
[2024-01-25 19:49:54,438] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:49:54,438] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002307475.1_ASM230747v1_genomic.fna/markers.fasta)
[2024-01-25 19:49:54,439] [INFO] Task started: Blastn
[2024-01-25 19:49:54,439] [INFO] Running command: blastn -query GCF_002307475.1_ASM230747v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg26752316-53d1-4e50-8543-31db78396e04/dqc_reference/reference_markers_gtdb.fasta -out GCF_002307475.1_ASM230747v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:49:55,855] [INFO] Task succeeded: Blastn
[2024-01-25 19:49:55,858] [INFO] Selected 12 target genomes.
[2024-01-25 19:49:55,858] [INFO] Target genome list was writen to GCF_002307475.1_ASM230747v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:49:55,879] [INFO] Task started: fastANI
[2024-01-25 19:49:55,880] [INFO] Running command: fastANI --query /var/lib/cwl/stg1c5c48eb-c84a-4525-9cee-0c26a0a37035/GCF_002307475.1_ASM230747v1_genomic.fna.gz --refList GCF_002307475.1_ASM230747v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002307475.1_ASM230747v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:50:09,412] [INFO] Task succeeded: fastANI
[2024-01-25 19:50:09,421] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:50:09,421] [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_002307475.1	s__Pantoea allii	100.0	1680	1714	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	98.91	98.49	0.92	0.90	6	conclusive
GCF_000710035.2	s__Pantoea ananatis	88.9816	1378	1714	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	98.81	96.45	0.92	0.81	152	-
GCF_008801695.1	s__Pantoea stewartii	85.0608	1101	1714	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	98.82	98.55	0.82	0.77	34	-
GCA_002434205.1	s__Pantoea sp002434205	81.5158	853	1714	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	81.4301	831	1714	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004792415.1	s__Pantoea vagans	81.1633	873	1714	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	81.1308	884	1714	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	96.06	96.06	0.92	0.92	2	-
GCA_002095305.1	s__Pantoea brenneri	81.093	891	1714	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	99.27	99.10	0.90	0.85	24	-
GCF_006494375.1	s__Pantoea anthophila	81.0456	884	1714	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	98.39	98.21	0.92	0.90	16	-
GCF_008632075.1	s__Pantoea sp008632075	80.9288	871	1714	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	99.47	99.36	0.95	0.94	34	-
GCA_018842655.1	s__Pantoea sp018842655	80.852	788	1714	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	80.7348	799	1714	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:50:09,423] [INFO] GTDB search result was written to GCF_002307475.1_ASM230747v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:50:09,423] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:50:09,426] [INFO] DFAST_QC result json was written to GCF_002307475.1_ASM230747v1_genomic.fna/dqc_result.json
[2024-01-25 19:50:09,427] [INFO] DFAST_QC completed!
[2024-01-25 19:50:09,427] [INFO] Total running time: 0h1m19s