[2024-01-25 17:34:07,128] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:34:07,133] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:34:07,133] [INFO] DQC Reference Directory: /var/lib/cwl/stg74b49050-9cd5-4786-a44a-d62cf3a8e154/dqc_reference
[2024-01-25 17:34:09,029] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:34:09,029] [INFO] Task started: Prodigal
[2024-01-25 17:34:09,030] [INFO] Running command: gunzip -c /var/lib/cwl/stgcfb148dd-dfb8-4d05-bfed-655dff106d10/GCF_002951615.1_ASM295161v1_genomic.fna.gz | prodigal -d GCF_002951615.1_ASM295161v1_genomic.fna/cds.fna -a GCF_002951615.1_ASM295161v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:34:22,436] [INFO] Task succeeded: Prodigal
[2024-01-25 17:34:22,437] [INFO] Task started: HMMsearch
[2024-01-25 17:34:22,437] [INFO] Running command: hmmsearch --tblout GCF_002951615.1_ASM295161v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg74b49050-9cd5-4786-a44a-d62cf3a8e154/dqc_reference/reference_markers.hmm GCF_002951615.1_ASM295161v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:34:22,767] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:34:22,768] [INFO] Found 6/6 markers.
[2024-01-25 17:34:22,809] [INFO] Query marker FASTA was written to GCF_002951615.1_ASM295161v1_genomic.fna/markers.fasta
[2024-01-25 17:34:22,809] [INFO] Task started: Blastn
[2024-01-25 17:34:22,809] [INFO] Running command: blastn -query GCF_002951615.1_ASM295161v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg74b49050-9cd5-4786-a44a-d62cf3a8e154/dqc_reference/reference_markers.fasta -out GCF_002951615.1_ASM295161v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:34:23,713] [INFO] Task succeeded: Blastn
[2024-01-25 17:34:23,716] [INFO] Selected 15 target genomes.
[2024-01-25 17:34:23,716] [INFO] Target genome list was writen to GCF_002951615.1_ASM295161v1_genomic.fna/target_genomes.txt
[2024-01-25 17:34:23,733] [INFO] Task started: fastANI
[2024-01-25 17:34:23,734] [INFO] Running command: fastANI --query /var/lib/cwl/stgcfb148dd-dfb8-4d05-bfed-655dff106d10/GCF_002951615.1_ASM295161v1_genomic.fna.gz --refList GCF_002951615.1_ASM295161v1_genomic.fna/target_genomes.txt --output GCF_002951615.1_ASM295161v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:34:44,647] [INFO] Task succeeded: fastANI
[2024-01-25 17:34:44,647] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg74b49050-9cd5-4786-a44a-d62cf3a8e154/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:34:44,647] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg74b49050-9cd5-4786-a44a-d62cf3a8e154/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:34:44,657] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 17:34:44,657] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 17:34:44,657] [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 laticis	strain=SAP-17	GCA_015644585.1	2787622	2787622	type	True	93.1423	1538	1841	95	below_threshold
Rahnella contaminans	strain=Lac-M11	GCA_011065485.1	2703882	2703882	type	True	92.0726	1457	1841	95	below_threshold
Rahnella victoriana	strain=DSM 27397	GCA_004330295.1	1510570	1510570	type	True	86.5971	1311	1841	95	below_threshold
Rahnella variigena	strain=CIP 105588	GCA_003610915.1	574964	574964	type	True	86.3389	1338	1841	95	below_threshold
Rahnella variigena	strain=CIP 105588	GCA_003602185.1	574964	574964	type	True	86.3362	1308	1841	95	below_threshold
Rahnella bonaserana	strain=H11b	GCA_019049675.1	2816248	2816248	type	True	86.2216	1330	1841	95	below_threshold
Rahnella aquatilis	strain=CIP 78.65	GCA_000241955.1	34038	34038	suspected-type	True	86.1677	1279	1841	95	below_threshold
Rahnella ecdela	strain=FRB 231	GCA_019049625.1	2816250	2816250	type	True	86.1341	1304	1841	95	below_threshold
Rahnella woolbedingensis	strain=DSM 27399	GCA_003602095.1	1510574	1510574	type	True	86.1268	1311	1841	95	below_threshold
Rahnella aquatilis	strain=ATCC 33071	GCA_000735505.1	34038	34038	suspected-type	True	86.1144	1215	1841	95	below_threshold
Rahnella bruchi	strain=DSM 27398	GCA_003614975.1	1510573	1510573	type	True	86.114	1308	1841	95	below_threshold
Rahnella rivi	strain=FC061912-K	GCA_019049655.1	2816249	2816249	type	True	85.7021	1300	1841	95	below_threshold
Rahnella inusitata	strain=DSM 30078	GCA_003263515.1	58169	58169	type	True	85.5461	1228	1841	95	below_threshold
Rahnella perminowiae	strain=SL6	GCA_019049755.1	2816244	2816244	type	True	85.3892	1135	1841	95	below_threshold
Serratia entomophila	strain=A1	GCA_021462285.1	42906	42906	type	True	79.446	627	1841	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:34:44,665] [INFO] DFAST Taxonomy check result was written to GCF_002951615.1_ASM295161v1_genomic.fna/tc_result.tsv
[2024-01-25 17:34:44,665] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:34:44,665] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:34:44,666] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg74b49050-9cd5-4786-a44a-d62cf3a8e154/dqc_reference/checkm_data
[2024-01-25 17:34:44,667] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:34:44,719] [INFO] Task started: CheckM
[2024-01-25 17:34:44,719] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002951615.1_ASM295161v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002951615.1_ASM295161v1_genomic.fna/checkm_input GCF_002951615.1_ASM295161v1_genomic.fna/checkm_result
[2024-01-25 17:35:25,476] [INFO] Task succeeded: CheckM
[2024-01-25 17:35:25,478] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:35:25,498] [INFO] ===== Completeness check finished =====
[2024-01-25 17:35:25,498] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:35:25,498] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002951615.1_ASM295161v1_genomic.fna/markers.fasta)
[2024-01-25 17:35:25,498] [INFO] Task started: Blastn
[2024-01-25 17:35:25,499] [INFO] Running command: blastn -query GCF_002951615.1_ASM295161v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg74b49050-9cd5-4786-a44a-d62cf3a8e154/dqc_reference/reference_markers_gtdb.fasta -out GCF_002951615.1_ASM295161v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:35:26,818] [INFO] Task succeeded: Blastn
[2024-01-25 17:35:26,821] [INFO] Selected 14 target genomes.
[2024-01-25 17:35:26,822] [INFO] Target genome list was writen to GCF_002951615.1_ASM295161v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:35:26,838] [INFO] Task started: fastANI
[2024-01-25 17:35:26,838] [INFO] Running command: fastANI --query /var/lib/cwl/stgcfb148dd-dfb8-4d05-bfed-655dff106d10/GCF_002951615.1_ASM295161v1_genomic.fna.gz --refList GCF_002951615.1_ASM295161v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002951615.1_ASM295161v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:35:44,645] [INFO] Task succeeded: fastANI
[2024-01-25 17:35:44,654] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:35:44,655] [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_002951615.1	s__Rahnella sp002951615	100.0	1840	1841	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rahnella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_015644585.1	s__Rahnella laticis	93.1423	1538	1841	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rahnella	95.0	96.65	95.20	0.90	0.83	8	-
GCF_002834385.1	s__Rahnella sp002834385	90.1402	1444	1841	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rahnella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004330295.1	s__Rahnella victoriana	86.5991	1311	1841	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rahnella	95.0	98.74	98.62	0.94	0.93	5	-
GCF_003610915.1	s__Rahnella variigena	86.3451	1336	1841	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rahnella	95.0	97.86	97.35	0.92	0.89	8	-
GCF_000241955.1	s__Rahnella aquatilis	86.1584	1280	1841	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rahnella	95.0	99.30	98.90	0.94	0.91	4	-
GCF_003614975.1	s__Rahnella bruchi	86.1114	1308	1841	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	86.1093	1314	1841	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	85.565	1309	1841	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rahnella	95.0	98.18	98.11	0.91	0.87	5	-
GCF_003263515.1	s__Rahnella inusitata	85.5424	1228	1841	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rahnella	95.0	99.32	98.94	0.97	0.94	4	-
GCA_013457415.1	s__Rahnella sp013457415	85.1292	1301	1841	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rahnella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001047675.1	s__Yersinia aleksiciae	79.5646	362	1841	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.22	98.37	0.87	0.82	10	-
GCF_001155565.1	s__Yersinia frederiksenii_A	79.1788	317	1841	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.53	99.44	0.95	0.92	10	-
GCA_000027065.2	s__Cronobacter turicensis	78.6591	471	1841	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Cronobacter	95.0	97.17	96.06	0.93	0.89	18	-
--------------------------------------------------------------------------------
[2024-01-25 17:35:44,656] [INFO] GTDB search result was written to GCF_002951615.1_ASM295161v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:35:44,657] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:35:44,660] [INFO] DFAST_QC result json was written to GCF_002951615.1_ASM295161v1_genomic.fna/dqc_result.json
[2024-01-25 17:35:44,660] [INFO] DFAST_QC completed!
[2024-01-25 17:35:44,660] [INFO] Total running time: 0h1m38s