[2024-01-24 13:40:32,787] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:32,789] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:32,789] [INFO] DQC Reference Directory: /var/lib/cwl/stg3e07ce9c-9807-4237-a745-ed016babb29c/dqc_reference
[2024-01-24 13:40:34,100] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:34,102] [INFO] Task started: Prodigal
[2024-01-24 13:40:34,102] [INFO] Running command: gunzip -c /var/lib/cwl/stg7fb941f4-826e-4c62-b851-b3e83b39b6e0/GCF_005497185.1_ASM549718v1_genomic.fna.gz | prodigal -d GCF_005497185.1_ASM549718v1_genomic.fna/cds.fna -a GCF_005497185.1_ASM549718v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:47,460] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:47,461] [INFO] Task started: HMMsearch
[2024-01-24 13:40:47,461] [INFO] Running command: hmmsearch --tblout GCF_005497185.1_ASM549718v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3e07ce9c-9807-4237-a745-ed016babb29c/dqc_reference/reference_markers.hmm GCF_005497185.1_ASM549718v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:47,780] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:47,781] [INFO] Found 6/6 markers.
[2024-01-24 13:40:47,823] [INFO] Query marker FASTA was written to GCF_005497185.1_ASM549718v1_genomic.fna/markers.fasta
[2024-01-24 13:40:47,824] [INFO] Task started: Blastn
[2024-01-24 13:40:47,824] [INFO] Running command: blastn -query GCF_005497185.1_ASM549718v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3e07ce9c-9807-4237-a745-ed016babb29c/dqc_reference/reference_markers.fasta -out GCF_005497185.1_ASM549718v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:48,679] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:48,682] [INFO] Selected 15 target genomes.
[2024-01-24 13:40:48,683] [INFO] Target genome list was writen to GCF_005497185.1_ASM549718v1_genomic.fna/target_genomes.txt
[2024-01-24 13:40:48,688] [INFO] Task started: fastANI
[2024-01-24 13:40:48,689] [INFO] Running command: fastANI --query /var/lib/cwl/stg7fb941f4-826e-4c62-b851-b3e83b39b6e0/GCF_005497185.1_ASM549718v1_genomic.fna.gz --refList GCF_005497185.1_ASM549718v1_genomic.fna/target_genomes.txt --output GCF_005497185.1_ASM549718v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:05,329] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:05,330] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3e07ce9c-9807-4237-a745-ed016babb29c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:05,330] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3e07ce9c-9807-4237-a745-ed016babb29c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:05,343] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:41:05,343] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:05,343] [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
Pectobacterium polonicum	strain=DPMP315	GCA_005497185.1	2485124	2485124	type	True	100.0	1576	1581	95	conclusive
Pectobacterium punjabense	strain=SS95	GCA_012427845.1	2108399	2108399	type	True	94.2198	1383	1581	95	below_threshold
Pectobacterium punjabense	strain=SS95	GCA_003028395.1	2108399	2108399	type	True	94.2056	1349	1581	95	below_threshold
Pectobacterium parmentieri	strain=RNS 08-42-1A	GCA_001742145.1	1905730	1905730	type	True	91.0646	1324	1581	95	below_threshold
Pectobacterium parmentieri	strain=RNS 08-42-1A	GCA_000757625.1	1905730	1905730	type	True	91.0406	1318	1581	95	below_threshold
Pectobacterium wasabiae	strain=CFBP 3304	GCA_000291725.1	55208	55208	type	True	91.0141	1321	1581	95	below_threshold
Pectobacterium wasabiae	strain=CFBP 3304	GCA_001742185.1	55208	55208	type	True	90.9994	1320	1581	95	below_threshold
Pectobacterium atrosepticum	strain=ICMP 1526	GCA_001038685.1	29471	29471	type	True	89.5934	1255	1581	95	below_threshold
Pectobacterium quasiaquaticum	strain=A477-S1-J17	GCA_014946775.2	2774015	2774015	type	True	89.5298	1239	1581	95	below_threshold
Pectobacterium colocasium	strain=LJ1	GCA_020181655.1	2878098	2878098	type	True	88.8688	1280	1581	95	below_threshold
Serratia entomophila	strain=A1	GCA_021462285.1	42906	42906	type	True	78.7325	410	1581	95	below_threshold
Serratia nevei	strain=S15	GCA_008364245.1	2703794	2703794	type	True	78.561	408	1581	95	below_threshold
Serratia bockelmannii	strain=S3	GCA_008011855.1	2703793	2703793	type	True	78.4249	405	1581	95	below_threshold
Providencia rustigianii	strain=NCTC11802	GCA_900455075.1	158850	158850	type	True	78.2446	122	1581	95	below_threshold
Providencia rustigianii	strain=DSM 4541	GCA_000156395.1	158850	158850	type	True	78.0836	120	1581	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:05,345] [INFO] DFAST Taxonomy check result was written to GCF_005497185.1_ASM549718v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:05,345] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:05,345] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:05,346] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3e07ce9c-9807-4237-a745-ed016babb29c/dqc_reference/checkm_data
[2024-01-24 13:41:05,347] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:05,396] [INFO] Task started: CheckM
[2024-01-24 13:41:05,396] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005497185.1_ASM549718v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005497185.1_ASM549718v1_genomic.fna/checkm_input GCF_005497185.1_ASM549718v1_genomic.fna/checkm_result
[2024-01-24 13:41:48,840] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:48,841] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:48,864] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:48,864] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:48,865] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005497185.1_ASM549718v1_genomic.fna/markers.fasta)
[2024-01-24 13:41:48,865] [INFO] Task started: Blastn
[2024-01-24 13:41:48,865] [INFO] Running command: blastn -query GCF_005497185.1_ASM549718v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3e07ce9c-9807-4237-a745-ed016babb29c/dqc_reference/reference_markers_gtdb.fasta -out GCF_005497185.1_ASM549718v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:50,121] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:50,126] [INFO] Selected 10 target genomes.
[2024-01-24 13:41:50,126] [INFO] Target genome list was writen to GCF_005497185.1_ASM549718v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:50,137] [INFO] Task started: fastANI
[2024-01-24 13:41:50,138] [INFO] Running command: fastANI --query /var/lib/cwl/stg7fb941f4-826e-4c62-b851-b3e83b39b6e0/GCF_005497185.1_ASM549718v1_genomic.fna.gz --refList GCF_005497185.1_ASM549718v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005497185.1_ASM549718v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:02,264] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:02,281] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:02,282] [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_005497185.1	s__Pectobacterium polonicum	100.0	1576	1581	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_012427845.1	s__Pectobacterium punjabense	94.2198	1383	1581	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	99.35	98.67	0.97	0.93	5	-
GCF_001742145.1	s__Pectobacterium parmentieri	91.0614	1325	1581	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	99.20	98.87	0.95	0.90	33	-
GCF_001742185.1	s__Pectobacterium wasabiae	90.982	1322	1581	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	99.99	99.99	0.99	0.98	4	-
GCF_003382565.2	s__Pectobacterium aquaticum	89.7714	1188	1581	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	97.07	95.76	0.89	0.87	15	-
GCF_002847345.1	s__Pectobacterium peruviense	89.6855	1330	1581	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	98.76	97.64	0.96	0.93	5	-
GCF_019056595.1	s__Pectobacterium atrosepticum	89.6035	1321	1581	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	99.44	98.81	0.97	0.94	14	-
GCF_013449685.1	s__Pectobacterium brasiliense_A	89.537	1229	1581	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	98.47	96.08	0.92	0.83	5	-
GCF_004137795.1	s__Pectobacterium zantedeschiae	89.272	1346	1581	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	99.24	98.49	0.92	0.91	3	-
GCF_000156395.1	s__Providencia rustigianii	78.0934	119	1581	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Providencia	95.0	99.28	98.46	0.94	0.90	9	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:02,284] [INFO] GTDB search result was written to GCF_005497185.1_ASM549718v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:02,284] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:02,287] [INFO] DFAST_QC result json was written to GCF_005497185.1_ASM549718v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:02,288] [INFO] DFAST_QC completed!
[2024-01-24 13:42:02,288] [INFO] Total running time: 0h1m30s