[2023-06-27 05:00:00,022] [INFO] DFAST_QC pipeline started.
[2023-06-27 05:00:00,041] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 05:00:00,041] [INFO] DQC Reference Directory: /var/lib/cwl/stgf4127091-b3ba-471f-b643-64996d626811/dqc_reference
[2023-06-27 05:00:01,502] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 05:00:01,503] [INFO] Task started: Prodigal
[2023-06-27 05:00:01,503] [INFO] Running command: gunzip -c /var/lib/cwl/stg8d8df234-ae9b-4a7c-b666-87518fd94b4c/GCA_002338985.1_ASM233898v1_genomic.fna.gz | prodigal -d GCA_002338985.1_ASM233898v1_genomic.fna/cds.fna -a GCA_002338985.1_ASM233898v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 05:00:12,109] [INFO] Task succeeded: Prodigal
[2023-06-27 05:00:12,110] [INFO] Task started: HMMsearch
[2023-06-27 05:00:12,110] [INFO] Running command: hmmsearch --tblout GCA_002338985.1_ASM233898v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf4127091-b3ba-471f-b643-64996d626811/dqc_reference/reference_markers.hmm GCA_002338985.1_ASM233898v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 05:00:12,411] [INFO] Task succeeded: HMMsearch
[2023-06-27 05:00:12,412] [INFO] Found 6/6 markers.
[2023-06-27 05:00:12,453] [INFO] Query marker FASTA was written to GCA_002338985.1_ASM233898v1_genomic.fna/markers.fasta
[2023-06-27 05:00:12,453] [INFO] Task started: Blastn
[2023-06-27 05:00:12,453] [INFO] Running command: blastn -query GCA_002338985.1_ASM233898v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf4127091-b3ba-471f-b643-64996d626811/dqc_reference/reference_markers.fasta -out GCA_002338985.1_ASM233898v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 05:00:13,250] [INFO] Task succeeded: Blastn
[2023-06-27 05:00:13,255] [INFO] Selected 10 target genomes.
[2023-06-27 05:00:13,255] [INFO] Target genome list was writen to GCA_002338985.1_ASM233898v1_genomic.fna/target_genomes.txt
[2023-06-27 05:00:13,263] [INFO] Task started: fastANI
[2023-06-27 05:00:13,264] [INFO] Running command: fastANI --query /var/lib/cwl/stg8d8df234-ae9b-4a7c-b666-87518fd94b4c/GCA_002338985.1_ASM233898v1_genomic.fna.gz --refList GCA_002338985.1_ASM233898v1_genomic.fna/target_genomes.txt --output GCA_002338985.1_ASM233898v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 05:00:23,120] [INFO] Task succeeded: fastANI
[2023-06-27 05:00:23,121] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf4127091-b3ba-471f-b643-64996d626811/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 05:00:23,121] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf4127091-b3ba-471f-b643-64996d626811/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 05:00:23,135] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2023-06-27 05:00:23,135] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-27 05:00:23,135] [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
Hafnia paralvei	strain=ATCC 29927	GCA_023698525.1	546367	546367	type	True	99.0726	1289	1412	95	conclusive
Hafnia paralvei	strain=ATCC 29927	GCA_001655005.1	546367	546367	type	True	99.0332	1267	1412	95	conclusive
Obesumbacterium proteus	strain=DSM 2777	GCA_001586165.1	82983	82983	type	True	83.9413	1017	1412	95	below_threshold
Obesumbacterium proteus	strain=ATCC 12841	GCA_001655035.1	82983	82983	type	True	83.9356	998	1412	95	below_threshold
Hafnia alvei	strain=ATCC 13337	GCA_003668715.1	569	569	type	True	83.9197	1019	1412	95	below_threshold
Hafnia alvei	strain=ATCC 13337	GCA_000735375.1	569	569	type	True	83.8709	1013	1412	95	below_threshold
Yersinia aldovae	strain=IP06005	GCA_001091225.1	29483	29483	type	True	78.3764	235	1412	95	below_threshold
Serratia entomophila	strain=A1	GCA_021462285.1	42906	42906	type	True	78.1258	268	1412	95	below_threshold
Rahnella ecdela	strain=FRB 231	GCA_019049625.1	2816250	2816250	type	True	78.088	273	1412	95	below_threshold
Rahnella rivi	strain=FC061912-K	GCA_019049655.1	2816249	2816249	type	True	77.9384	269	1412	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 05:00:23,140] [INFO] DFAST Taxonomy check result was written to GCA_002338985.1_ASM233898v1_genomic.fna/tc_result.tsv
[2023-06-27 05:00:23,141] [INFO] ===== Taxonomy check completed =====
[2023-06-27 05:00:23,141] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 05:00:23,141] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf4127091-b3ba-471f-b643-64996d626811/dqc_reference/checkm_data
[2023-06-27 05:00:23,143] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 05:00:23,194] [INFO] Task started: CheckM
[2023-06-27 05:00:23,194] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002338985.1_ASM233898v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002338985.1_ASM233898v1_genomic.fna/checkm_input GCA_002338985.1_ASM233898v1_genomic.fna/checkm_result
[2023-06-27 05:00:59,266] [INFO] Task succeeded: CheckM
[2023-06-27 05:00:59,267] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 72.92%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-27 05:00:59,290] [INFO] ===== Completeness check finished =====
[2023-06-27 05:00:59,291] [INFO] ===== Start GTDB Search =====
[2023-06-27 05:00:59,291] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002338985.1_ASM233898v1_genomic.fna/markers.fasta)
[2023-06-27 05:00:59,291] [INFO] Task started: Blastn
[2023-06-27 05:00:59,292] [INFO] Running command: blastn -query GCA_002338985.1_ASM233898v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf4127091-b3ba-471f-b643-64996d626811/dqc_reference/reference_markers_gtdb.fasta -out GCA_002338985.1_ASM233898v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 05:01:00,297] [INFO] Task succeeded: Blastn
[2023-06-27 05:01:00,320] [INFO] Selected 12 target genomes.
[2023-06-27 05:01:00,320] [INFO] Target genome list was writen to GCA_002338985.1_ASM233898v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 05:01:00,344] [INFO] Task started: fastANI
[2023-06-27 05:01:00,345] [INFO] Running command: fastANI --query /var/lib/cwl/stg8d8df234-ae9b-4a7c-b666-87518fd94b4c/GCA_002338985.1_ASM233898v1_genomic.fna.gz --refList GCA_002338985.1_ASM233898v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002338985.1_ASM233898v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 05:01:10,985] [INFO] Task succeeded: fastANI
[2023-06-27 05:01:11,003] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-27 05:01:11,003] [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_001655005.1	s__Hafnia paralvei	99.0332	1267	1412	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Hafnia	95.0	98.49	95.65	0.88	0.84	34	conclusive
GCF_001586165.1	s__Hafnia proteus	83.9484	1016	1412	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Hafnia	95.0	98.09	96.49	0.93	0.89	5	-
GCF_000735375.1	s__Hafnia alvei	83.8801	1012	1412	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Hafnia	95.0	97.59	95.60	0.91	0.87	31	-
GCF_900095695.1	s__Hafnia alvei_B	83.8692	1022	1412	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Hafnia	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001112925.1	s__Yersinia nurmii	78.2439	255	1412	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003363015.1	s__Enterobacillus tribolii	78.1359	347	1412	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017832355.1	s__Serratia sp017832355	78.0983	297	1412	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002951615.1	s__Rahnella sp002951615	77.797	270	1412	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rahnella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900635475.1	s__Kluyvera intermedia	77.7752	255	1412	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kluyvera	95.0	99.24	98.87	0.94	0.90	4	-
GCF_018035235.1	s__Citrobacter freundii_A	77.7572	220	1412	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter	95.0	99.33	99.24	0.91	0.90	6	-
GCF_900079995.3	s__Citrobacter europaeus	77.749	228	1412	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter	95.0	99.13	99.04	0.92	0.90	21	-
--------------------------------------------------------------------------------
[2023-06-27 05:01:11,006] [INFO] GTDB search result was written to GCA_002338985.1_ASM233898v1_genomic.fna/result_gtdb.tsv
[2023-06-27 05:01:11,007] [INFO] ===== GTDB Search completed =====
[2023-06-27 05:01:11,011] [INFO] DFAST_QC result json was written to GCA_002338985.1_ASM233898v1_genomic.fna/dqc_result.json
[2023-06-27 05:01:11,011] [INFO] DFAST_QC completed!
[2023-06-27 05:01:11,011] [INFO] Total running time: 0h1m11s