[2024-01-24 11:35:23,305] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:35:23,309] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:35:23,309] [INFO] DQC Reference Directory: /var/lib/cwl/stgda2cf766-e252-4f9b-942a-48e656400d47/dqc_reference
[2024-01-24 11:35:26,243] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:35:26,244] [INFO] Task started: Prodigal
[2024-01-24 11:35:26,244] [INFO] Running command: gunzip -c /var/lib/cwl/stg8ebf2551-4554-4f52-a20c-25e06169bfa6/GCF_002847345.1_ASM284734v1_genomic.fna.gz | prodigal -d GCF_002847345.1_ASM284734v1_genomic.fna/cds.fna -a GCF_002847345.1_ASM284734v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:35:38,918] [INFO] Task succeeded: Prodigal
[2024-01-24 11:35:38,918] [INFO] Task started: HMMsearch
[2024-01-24 11:35:38,919] [INFO] Running command: hmmsearch --tblout GCF_002847345.1_ASM284734v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgda2cf766-e252-4f9b-942a-48e656400d47/dqc_reference/reference_markers.hmm GCF_002847345.1_ASM284734v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:35:39,286] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:35:39,288] [INFO] Found 6/6 markers.
[2024-01-24 11:35:39,337] [INFO] Query marker FASTA was written to GCF_002847345.1_ASM284734v1_genomic.fna/markers.fasta
[2024-01-24 11:35:39,337] [INFO] Task started: Blastn
[2024-01-24 11:35:39,337] [INFO] Running command: blastn -query GCF_002847345.1_ASM284734v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgda2cf766-e252-4f9b-942a-48e656400d47/dqc_reference/reference_markers.fasta -out GCF_002847345.1_ASM284734v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:40,185] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:40,188] [INFO] Selected 20 target genomes.
[2024-01-24 11:35:40,188] [INFO] Target genome list was writen to GCF_002847345.1_ASM284734v1_genomic.fna/target_genomes.txt
[2024-01-24 11:35:40,197] [INFO] Task started: fastANI
[2024-01-24 11:35:40,197] [INFO] Running command: fastANI --query /var/lib/cwl/stg8ebf2551-4554-4f52-a20c-25e06169bfa6/GCF_002847345.1_ASM284734v1_genomic.fna.gz --refList GCF_002847345.1_ASM284734v1_genomic.fna/target_genomes.txt --output GCF_002847345.1_ASM284734v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:36:02,394] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:02,394] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgda2cf766-e252-4f9b-942a-48e656400d47/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:36:02,395] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgda2cf766-e252-4f9b-942a-48e656400d47/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:36:02,409] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:36:02,410] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:36:02,410] [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 peruviense	strain=IFB5232	GCA_002847345.1	2066479	2066479	type	True	100.0	1564	1566	95	conclusive
Pectobacterium atrosepticum	strain=ICMP 1526	GCA_001038685.1	29471	29471	type	True	93.9483	1366	1566	95	below_threshold
Pectobacterium atrosepticum	strain=NCPPB 549	GCA_000749905.1	29471	29471	type	True	93.9157	1432	1566	95	below_threshold
Pectobacterium betavasculorum	strain=NCPPB 2795	GCA_000749845.1	55207	55207	type	True	92.189	1227	1566	95	below_threshold
Pectobacterium zantedeschiae	strain=9M	GCA_004137795.1	2034769	2034769	type	True	91.5887	1367	1566	95	below_threshold
Pectobacterium wasabiae	strain=CFBP 3304	GCA_001742185.1	55208	55208	type	True	90.0861	1258	1566	95	below_threshold
Pectobacterium wasabiae	strain=NCPPB 3701	GCA_000749865.1	55208	55208	type	True	90.0798	1262	1566	95	below_threshold
Pectobacterium wasabiae	strain=CFBP 3304	GCA_000291725.1	55208	55208	type	True	90.0439	1263	1566	95	below_threshold
Pectobacterium parmentieri	strain=RNS 08-42-1A	GCA_001742145.1	1905730	1905730	type	True	89.9066	1281	1566	95	below_threshold
Pectobacterium punjabense	strain=SS95	GCA_003028395.1	2108399	2108399	type	True	89.8344	1277	1566	95	below_threshold
Pectobacterium parvum	strain=s0421	GCA_900195285.2	2778550	2778550	type	True	89.8078	1235	1566	95	below_threshold
Pectobacterium polaris	strain=NIBIO1006	GCA_002307355.1	2042057	2042057	type	True	89.7897	1347	1566	95	below_threshold
Pectobacterium polonicum	strain=DPMP315	GCA_005497185.1	2485124	2485124	type	True	89.6495	1326	1566	95	below_threshold
Pectobacterium quasiaquaticum	strain=A477-S1-J17	GCA_014946775.2	2774015	2774015	type	True	89.4635	1215	1566	95	below_threshold
Pectobacterium colocasium	strain=LJ1	GCA_020181655.1	2878098	2878098	type	True	88.5069	1294	1566	95	below_threshold
Serratia entomophila	strain=A1	GCA_021462285.1	42906	42906	type	True	78.6712	390	1566	95	below_threshold
Serratia bockelmannii	strain=S3	GCA_008011855.1	2703793	2703793	type	True	78.4771	384	1566	95	below_threshold
Rahnella bonaserana	strain=H11b	GCA_019049675.1	2816248	2816248	type	True	78.422	367	1566	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:36:02,412] [INFO] DFAST Taxonomy check result was written to GCF_002847345.1_ASM284734v1_genomic.fna/tc_result.tsv
[2024-01-24 11:36:02,412] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:36:02,413] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:36:02,413] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgda2cf766-e252-4f9b-942a-48e656400d47/dqc_reference/checkm_data
[2024-01-24 11:36:02,414] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:36:02,465] [INFO] Task started: CheckM
[2024-01-24 11:36:02,466] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002847345.1_ASM284734v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002847345.1_ASM284734v1_genomic.fna/checkm_input GCF_002847345.1_ASM284734v1_genomic.fna/checkm_result
[2024-01-24 11:36:44,105] [INFO] Task succeeded: CheckM
[2024-01-24 11:36:44,106] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:36:44,136] [INFO] ===== Completeness check finished =====
[2024-01-24 11:36:44,137] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:36:44,137] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002847345.1_ASM284734v1_genomic.fna/markers.fasta)
[2024-01-24 11:36:44,137] [INFO] Task started: Blastn
[2024-01-24 11:36:44,138] [INFO] Running command: blastn -query GCF_002847345.1_ASM284734v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgda2cf766-e252-4f9b-942a-48e656400d47/dqc_reference/reference_markers_gtdb.fasta -out GCF_002847345.1_ASM284734v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:36:45,227] [INFO] Task succeeded: Blastn
[2024-01-24 11:36:45,232] [INFO] Selected 11 target genomes.
[2024-01-24 11:36:45,232] [INFO] Target genome list was writen to GCF_002847345.1_ASM284734v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:36:45,247] [INFO] Task started: fastANI
[2024-01-24 11:36:45,247] [INFO] Running command: fastANI --query /var/lib/cwl/stg8ebf2551-4554-4f52-a20c-25e06169bfa6/GCF_002847345.1_ASM284734v1_genomic.fna.gz --refList GCF_002847345.1_ASM284734v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002847345.1_ASM284734v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:36:58,940] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:58,955] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:36:58,955] [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_002847345.1	s__Pectobacterium peruviense	100.0	1564	1566	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	98.76	97.64	0.96	0.93	5	conclusive
GCF_019056595.1	s__Pectobacterium atrosepticum	93.9035	1426	1566	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	99.44	98.81	0.97	0.94	14	-
GCF_000749845.1	s__Pectobacterium betavasculorum	92.189	1227	1566	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	99.45	99.45	0.94	0.94	2	-
GCF_004137795.1	s__Pectobacterium zantedeschiae	91.5762	1368	1566	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	99.24	98.49	0.92	0.91	3	-
GCF_001742185.1	s__Pectobacterium wasabiae	90.083	1259	1566	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	99.99	99.99	0.99	0.98	4	-
GCF_001742145.1	s__Pectobacterium parmentieri	89.9065	1281	1566	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	99.20	98.87	0.95	0.90	33	-
GCF_002307355.1	s__Pectobacterium polaris	89.7897	1347	1566	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	96.45	95.13	0.88	0.82	21	-
GCF_012427845.1	s__Pectobacterium punjabense	89.7733	1319	1566	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	99.35	98.67	0.97	0.93	5	-
GCF_005497185.1	s__Pectobacterium polonicum	89.6516	1327	1566	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003382565.2	s__Pectobacterium aquaticum	89.5251	1181	1566	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	97.07	95.76	0.89	0.87	15	-
GCF_013449685.1	s__Pectobacterium brasiliense_A	89.4853	1235	1566	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	98.47	96.08	0.92	0.83	5	-
--------------------------------------------------------------------------------
[2024-01-24 11:36:58,957] [INFO] GTDB search result was written to GCF_002847345.1_ASM284734v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:36:58,958] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:36:58,961] [INFO] DFAST_QC result json was written to GCF_002847345.1_ASM284734v1_genomic.fna/dqc_result.json
[2024-01-24 11:36:58,962] [INFO] DFAST_QC completed!
[2024-01-24 11:36:58,962] [INFO] Total running time: 0h1m36s