[2024-01-24 11:59:22,961] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:59:22,962] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:59:22,962] [INFO] DQC Reference Directory: /var/lib/cwl/stgefff59a0-ebad-4190-a8b8-e1835e15c812/dqc_reference
[2024-01-24 11:59:25,640] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:59:25,641] [INFO] Task started: Prodigal
[2024-01-24 11:59:25,641] [INFO] Running command: gunzip -c /var/lib/cwl/stgd4e63cb6-08a8-4bd0-aa1a-aa6595f0b8e0/GCF_003263515.1_ASM326351v1_genomic.fna.gz | prodigal -d GCF_003263515.1_ASM326351v1_genomic.fna/cds.fna -a GCF_003263515.1_ASM326351v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:59:38,623] [INFO] Task succeeded: Prodigal
[2024-01-24 11:59:38,624] [INFO] Task started: HMMsearch
[2024-01-24 11:59:38,624] [INFO] Running command: hmmsearch --tblout GCF_003263515.1_ASM326351v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgefff59a0-ebad-4190-a8b8-e1835e15c812/dqc_reference/reference_markers.hmm GCF_003263515.1_ASM326351v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:59:38,905] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:59:38,907] [INFO] Found 6/6 markers.
[2024-01-24 11:59:38,952] [INFO] Query marker FASTA was written to GCF_003263515.1_ASM326351v1_genomic.fna/markers.fasta
[2024-01-24 11:59:38,953] [INFO] Task started: Blastn
[2024-01-24 11:59:38,953] [INFO] Running command: blastn -query GCF_003263515.1_ASM326351v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgefff59a0-ebad-4190-a8b8-e1835e15c812/dqc_reference/reference_markers.fasta -out GCF_003263515.1_ASM326351v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:39,873] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:39,878] [INFO] Selected 13 target genomes.
[2024-01-24 11:59:39,878] [INFO] Target genome list was writen to GCF_003263515.1_ASM326351v1_genomic.fna/target_genomes.txt
[2024-01-24 11:59:39,904] [INFO] Task started: fastANI
[2024-01-24 11:59:39,904] [INFO] Running command: fastANI --query /var/lib/cwl/stgd4e63cb6-08a8-4bd0-aa1a-aa6595f0b8e0/GCF_003263515.1_ASM326351v1_genomic.fna.gz --refList GCF_003263515.1_ASM326351v1_genomic.fna/target_genomes.txt --output GCF_003263515.1_ASM326351v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:59:55,549] [INFO] Task succeeded: fastANI
[2024-01-24 11:59:55,549] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgefff59a0-ebad-4190-a8b8-e1835e15c812/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:59:55,550] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgefff59a0-ebad-4190-a8b8-e1835e15c812/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:59:55,565] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:59:55,565] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:59:55,565] [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
Rahnella inusitata	strain=DSM 30078	GCA_003263515.1	58169	58169	type	True	100.0	1599	1602	95	conclusive
Rahnella inusitata	strain=DSM 30078	GCA_003602055.1	58169	58169	type	True	99.9971	1593	1602	95	conclusive
Rahnella rivi	strain=FC061912-K	GCA_019049655.1	2816249	2816249	type	True	87.9785	1363	1602	95	below_threshold
Rahnella victoriana	strain=DSM 27397	GCA_004330295.1	1510570	1510570	type	True	85.7832	1243	1602	95	below_threshold
Rahnella laticis	strain=SAP-17	GCA_015644585.1	2787622	2787622	type	True	85.5698	1293	1602	95	below_threshold
Rahnella woolbedingensis	strain=DSM 27399	GCA_003602095.1	1510574	1510574	type	True	85.4828	1252	1602	95	below_threshold
Rahnella contaminans	strain=Lac-M11	GCA_011065485.1	2703882	2703882	type	True	85.415	1280	1602	95	below_threshold
Rahnella ecdela	strain=FRB 231	GCA_019049625.1	2816250	2816250	type	True	85.3858	1271	1602	95	below_threshold
Rahnella bonaserana	strain=H11b	GCA_019049675.1	2816248	2816248	type	True	85.3451	1262	1602	95	below_threshold
Rahnella aquatilis	strain=ATCC 33071	GCA_000735505.1	34038	34038	suspected-type	True	85.2655	1167	1602	95	below_threshold
Rahnella aquatilis	strain=CIP 78.65	GCA_000241955.1	34038	34038	suspected-type	True	85.1896	1226	1602	95	below_threshold
Rahnella perminowiae	strain=SL6	GCA_019049755.1	2816244	2816244	type	True	84.6594	1057	1602	95	below_threshold
Serratia entomophila	strain=A1	GCA_021462285.1	42906	42906	type	True	79.0045	629	1602	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:59:55,567] [INFO] DFAST Taxonomy check result was written to GCF_003263515.1_ASM326351v1_genomic.fna/tc_result.tsv
[2024-01-24 11:59:55,567] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:59:55,568] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:59:55,568] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgefff59a0-ebad-4190-a8b8-e1835e15c812/dqc_reference/checkm_data
[2024-01-24 11:59:55,569] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:59:55,630] [INFO] Task started: CheckM
[2024-01-24 11:59:55,630] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003263515.1_ASM326351v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003263515.1_ASM326351v1_genomic.fna/checkm_input GCF_003263515.1_ASM326351v1_genomic.fna/checkm_result
[2024-01-24 12:00:36,999] [INFO] Task succeeded: CheckM
[2024-01-24 12:00:37,001] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:00:37,025] [INFO] ===== Completeness check finished =====
[2024-01-24 12:00:37,026] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:00:37,027] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003263515.1_ASM326351v1_genomic.fna/markers.fasta)
[2024-01-24 12:00:37,027] [INFO] Task started: Blastn
[2024-01-24 12:00:37,027] [INFO] Running command: blastn -query GCF_003263515.1_ASM326351v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgefff59a0-ebad-4190-a8b8-e1835e15c812/dqc_reference/reference_markers_gtdb.fasta -out GCF_003263515.1_ASM326351v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:00:38,450] [INFO] Task succeeded: Blastn
[2024-01-24 12:00:38,453] [INFO] Selected 10 target genomes.
[2024-01-24 12:00:38,453] [INFO] Target genome list was writen to GCF_003263515.1_ASM326351v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:00:38,476] [INFO] Task started: fastANI
[2024-01-24 12:00:38,477] [INFO] Running command: fastANI --query /var/lib/cwl/stgd4e63cb6-08a8-4bd0-aa1a-aa6595f0b8e0/GCF_003263515.1_ASM326351v1_genomic.fna.gz --refList GCF_003263515.1_ASM326351v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003263515.1_ASM326351v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:00:52,136] [INFO] Task succeeded: fastANI
[2024-01-24 12:00:52,159] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:00:52,159] [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_003263515.1	s__Rahnella inusitata	100.0	1599	1602	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rahnella	95.0	99.32	98.94	0.97	0.94	4	conclusive
GCA_013457415.1	s__Rahnella sp013457415	92.6516	1426	1602	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rahnella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001422575.1	s__Rahnella sp001422575	87.9313	1381	1602	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rahnella	95.0	98.18	98.11	0.91	0.87	5	-
GCF_004330295.1	s__Rahnella victoriana	85.7835	1243	1602	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rahnella	95.0	98.74	98.62	0.94	0.93	5	-
GCF_015644585.1	s__Rahnella laticis	85.5893	1290	1602	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rahnella	95.0	96.65	95.20	0.90	0.83	8	-
GCF_002951615.1	s__Rahnella sp002951615	85.5821	1248	1602	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rahnella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003602095.1	s__Rahnella woolbedingensis	85.4828	1252	1602	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rahnella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019049625.1	s__Rahnella sp019049625	85.3823	1272	1602	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rahnella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019049675.1	s__Rahnella sp019049675	85.356	1261	1602	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rahnella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000241955.1	s__Rahnella aquatilis	85.1813	1226	1602	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rahnella	95.0	99.30	98.90	0.94	0.91	4	-
--------------------------------------------------------------------------------
[2024-01-24 12:00:52,160] [INFO] GTDB search result was written to GCF_003263515.1_ASM326351v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:00:52,162] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:00:52,165] [INFO] DFAST_QC result json was written to GCF_003263515.1_ASM326351v1_genomic.fna/dqc_result.json
[2024-01-24 12:00:52,166] [INFO] DFAST_QC completed!
[2024-01-24 12:00:52,166] [INFO] Total running time: 0h1m29s