[2024-01-24 13:40:29,982] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:29,985] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:29,985] [INFO] DQC Reference Directory: /var/lib/cwl/stgb410d7b9-c45f-4b0c-b7cc-af9f8be9755a/dqc_reference
[2024-01-24 13:40:31,319] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:31,320] [INFO] Task started: Prodigal
[2024-01-24 13:40:31,320] [INFO] Running command: gunzip -c /var/lib/cwl/stg131d9992-cac3-4107-a03d-36151d48a28b/GCF_009800925.1_ASM980092v1_genomic.fna.gz | prodigal -d GCF_009800925.1_ASM980092v1_genomic.fna/cds.fna -a GCF_009800925.1_ASM980092v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:39,277] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:39,277] [INFO] Task started: HMMsearch
[2024-01-24 13:40:39,278] [INFO] Running command: hmmsearch --tblout GCF_009800925.1_ASM980092v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb410d7b9-c45f-4b0c-b7cc-af9f8be9755a/dqc_reference/reference_markers.hmm GCF_009800925.1_ASM980092v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:39,569] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:39,571] [INFO] Found 6/6 markers.
[2024-01-24 13:40:39,606] [INFO] Query marker FASTA was written to GCF_009800925.1_ASM980092v1_genomic.fna/markers.fasta
[2024-01-24 13:40:39,606] [INFO] Task started: Blastn
[2024-01-24 13:40:39,607] [INFO] Running command: blastn -query GCF_009800925.1_ASM980092v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb410d7b9-c45f-4b0c-b7cc-af9f8be9755a/dqc_reference/reference_markers.fasta -out GCF_009800925.1_ASM980092v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:40,437] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:40,440] [INFO] Selected 12 target genomes.
[2024-01-24 13:40:40,440] [INFO] Target genome list was writen to GCF_009800925.1_ASM980092v1_genomic.fna/target_genomes.txt
[2024-01-24 13:40:40,452] [INFO] Task started: fastANI
[2024-01-24 13:40:40,452] [INFO] Running command: fastANI --query /var/lib/cwl/stg131d9992-cac3-4107-a03d-36151d48a28b/GCF_009800925.1_ASM980092v1_genomic.fna.gz --refList GCF_009800925.1_ASM980092v1_genomic.fna/target_genomes.txt --output GCF_009800925.1_ASM980092v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:40:50,378] [INFO] Task succeeded: fastANI
[2024-01-24 13:40:50,378] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb410d7b9-c45f-4b0c-b7cc-af9f8be9755a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:40:50,379] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb410d7b9-c45f-4b0c-b7cc-af9f8be9755a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:40:50,390] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:40:50,390] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:40:50,390] [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
Budvicia diplopodorum	strain=D9	GCA_009800925.1	1119056	1119056	type	True	100.0	1183	1185	95	conclusive
Budvicia aquatica	strain=NCTC12282	GCA_900706715.1	82979	82979	type	True	81.9535	783	1185	95	below_threshold
Budvicia aquatica	strain=DSM 5075	GCA_000427805.1	82979	82979	type	True	81.9359	764	1185	95	below_threshold
Jinshanibacter zhutongyuii	strain=CF-458	GCA_004295645.1	2498113	2498113	type	True	79.3498	470	1185	95	below_threshold
Pragia fontium	strain=DSM 5563	GCA_004959795.1	82985	82985	type	True	79.3029	459	1185	95	below_threshold
Jinshanibacter allomyrinae	strain=BWR-B9	GCA_016649425.1	2791986	2791986	type	True	79.2488	483	1185	95	below_threshold
Pragia fontium	strain=DSM 5563	GCA_900112475.1	82985	82985	type	True	79.2422	465	1185	95	below_threshold
Rahnella rivi	strain=FC061912-K	GCA_019049655.1	2816249	2816249	type	True	77.7724	156	1185	95	below_threshold
Serratia entomophila	strain=A1	GCA_021462285.1	42906	42906	type	True	77.7366	158	1185	95	below_threshold
Serratia nevei	strain=S15	GCA_008364245.1	2703794	2703794	type	True	77.6497	152	1185	95	below_threshold
Serratia bockelmannii	strain=S3	GCA_008011855.1	2703793	2703793	type	True	77.3303	154	1185	95	below_threshold
Erwinia phyllosphaerae	strain=CMYE1	GCA_019132875.1	2853256	2853256	type	True	77.2523	147	1185	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:40:50,392] [INFO] DFAST Taxonomy check result was written to GCF_009800925.1_ASM980092v1_genomic.fna/tc_result.tsv
[2024-01-24 13:40:50,392] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:40:50,393] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:40:50,393] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb410d7b9-c45f-4b0c-b7cc-af9f8be9755a/dqc_reference/checkm_data
[2024-01-24 13:40:50,394] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:40:50,430] [INFO] Task started: CheckM
[2024-01-24 13:40:50,431] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009800925.1_ASM980092v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009800925.1_ASM980092v1_genomic.fna/checkm_input GCF_009800925.1_ASM980092v1_genomic.fna/checkm_result
[2024-01-24 13:41:21,150] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:21,152] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:21,178] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:21,179] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:21,179] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009800925.1_ASM980092v1_genomic.fna/markers.fasta)
[2024-01-24 13:41:21,180] [INFO] Task started: Blastn
[2024-01-24 13:41:21,180] [INFO] Running command: blastn -query GCF_009800925.1_ASM980092v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb410d7b9-c45f-4b0c-b7cc-af9f8be9755a/dqc_reference/reference_markers_gtdb.fasta -out GCF_009800925.1_ASM980092v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:22,435] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:22,438] [INFO] Selected 7 target genomes.
[2024-01-24 13:41:22,438] [INFO] Target genome list was writen to GCF_009800925.1_ASM980092v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:22,444] [INFO] Task started: fastANI
[2024-01-24 13:41:22,444] [INFO] Running command: fastANI --query /var/lib/cwl/stg131d9992-cac3-4107-a03d-36151d48a28b/GCF_009800925.1_ASM980092v1_genomic.fna.gz --refList GCF_009800925.1_ASM980092v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009800925.1_ASM980092v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:41:28,574] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:28,582] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:41:28,582] [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_009800925.1	s__Budvicia diplopodorum	100.0	1182	1185	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Budvicia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000427805.1	s__Budvicia aquatica	81.9429	762	1185	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Budvicia	95.0	99.94	99.91	1.00	1.00	3	-
GCF_003096015.2	s__Limnobaculum parvum	79.7687	431	1185	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Limnobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013394855.1	s__Limnobaculum xujianqingii	79.3838	468	1185	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Limnobaculum	95.0	98.42	97.65	0.92	0.89	4	-
GCF_004295645.1	s__Limnobaculum zhutongyuii	79.3498	470	1185	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Limnobaculum	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900112475.1	s__Pragia fontium	79.2482	464	1185	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pragia	95.0	99.20	98.63	0.97	0.95	5	-
GCA_016649425.1	s__Limnobaculum allomyrinae	79.243	485	1185	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Limnobaculum	95.0	99.99	99.99	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:41:28,583] [INFO] GTDB search result was written to GCF_009800925.1_ASM980092v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:41:28,584] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:41:28,587] [INFO] DFAST_QC result json was written to GCF_009800925.1_ASM980092v1_genomic.fna/dqc_result.json
[2024-01-24 13:41:28,587] [INFO] DFAST_QC completed!
[2024-01-24 13:41:28,587] [INFO] Total running time: 0h0m59s