[2024-01-24 11:26:36,942] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:36,945] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:36,945] [INFO] DQC Reference Directory: /var/lib/cwl/stg29c53c15-5dbd-40c4-886e-f7588772f99d/dqc_reference
[2024-01-24 11:26:38,182] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:38,183] [INFO] Task started: Prodigal
[2024-01-24 11:26:38,184] [INFO] Running command: gunzip -c /var/lib/cwl/stg5b692f87-f64f-4aba-96af-a9d7358c8c6a/GCF_000803315.1_ASM80331v1_genomic.fna.gz | prodigal -d GCF_000803315.1_ASM80331v1_genomic.fna/cds.fna -a GCF_000803315.1_ASM80331v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:52,534] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:52,535] [INFO] Task started: HMMsearch
[2024-01-24 11:26:52,535] [INFO] Running command: hmmsearch --tblout GCF_000803315.1_ASM80331v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg29c53c15-5dbd-40c4-886e-f7588772f99d/dqc_reference/reference_markers.hmm GCF_000803315.1_ASM80331v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:52,854] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:52,856] [INFO] Found 6/6 markers.
[2024-01-24 11:26:52,898] [INFO] Query marker FASTA was written to GCF_000803315.1_ASM80331v1_genomic.fna/markers.fasta
[2024-01-24 11:26:52,899] [INFO] Task started: Blastn
[2024-01-24 11:26:52,899] [INFO] Running command: blastn -query GCF_000803315.1_ASM80331v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg29c53c15-5dbd-40c4-886e-f7588772f99d/dqc_reference/reference_markers.fasta -out GCF_000803315.1_ASM80331v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:53,774] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:53,778] [INFO] Selected 16 target genomes.
[2024-01-24 11:26:53,779] [INFO] Target genome list was writen to GCF_000803315.1_ASM80331v1_genomic.fna/target_genomes.txt
[2024-01-24 11:26:53,792] [INFO] Task started: fastANI
[2024-01-24 11:26:53,792] [INFO] Running command: fastANI --query /var/lib/cwl/stg5b692f87-f64f-4aba-96af-a9d7358c8c6a/GCF_000803315.1_ASM80331v1_genomic.fna.gz --refList GCF_000803315.1_ASM80331v1_genomic.fna/target_genomes.txt --output GCF_000803315.1_ASM80331v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:27:12,546] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:12,547] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg29c53c15-5dbd-40c4-886e-f7588772f99d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:27:12,547] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg29c53c15-5dbd-40c4-886e-f7588772f99d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:27:12,560] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:27:12,560] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:27:12,561] [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 actinidiae	strain=KKH3	GCA_000803315.1	1507808	1507808	type	True	100.0	1639	1639	95	conclusive
Pectobacterium carotovorum subsp. carotovorum	strain=ICMP 5702	GCA_001039055.1	555	554	suspected-type	True	93.3905	1357	1639	95	below_threshold
Pectobacterium carotovorum subsp. carotovorum	strain=NCPPB 312	GCA_000749855.1	555	554	suspected-type	True	93.3782	1348	1639	95	below_threshold
Pectobacterium carotovorum	strain=DSM 30168	GCA_900129615.1	554	554	type	True	93.3366	1356	1639	95	below_threshold
Pectobacterium versatile	strain=CFBP6051	GCA_004296685.1	2488639	2488639	type	True	93.1283	1331	1639	95	below_threshold
Pectobacterium odoriferum	strain=NCPPB 3839	GCA_000754765.1	78398	78398	type	True	92.9884	1318	1639	95	below_threshold
Pectobacterium polaris	strain=NIBIO1006	GCA_002307355.1	2042057	2042057	type	True	91.958	1324	1639	95	below_threshold
Pectobacterium aquaticum	strain=A212-S19-A16	GCA_003382565.3	2204145	2204145	type	True	91.9149	1198	1639	95	below_threshold
Pectobacterium brasiliense	strain=LMG 21371	GCA_000754695.1	180957	180957	type	True	91.6874	1358	1639	95	below_threshold
Pectobacterium brasiliense	strain=IPO:3540 CFBP:6617 ATCC:BAA-417 IBSBF:1692	GCA_016950255.1	180957	180957	type	True	91.6794	1392	1639	95	below_threshold
Pectobacterium quasiaquaticum	strain=A477-S1-J17	GCA_014946775.2	2774015	2774015	type	True	91.3639	1220	1639	95	below_threshold
Pectobacterium colocasium	strain=LJ1	GCA_020181655.1	2878098	2878098	type	True	90.1227	1305	1639	95	below_threshold
Pectobacterium polonicum	strain=DPMP315	GCA_005497185.1	2485124	2485124	type	True	89.5994	1315	1639	95	below_threshold
Rahnella ecdela	strain=FRB 231	GCA_019049625.1	2816250	2816250	type	True	78.5001	386	1639	95	below_threshold
Enterobacter roggenkampii	strain=DSM 16690	GCA_024390995.1	1812935	1812935	type	True	78.4612	357	1639	95	below_threshold
Serratia bockelmannii	strain=S3	GCA_008011855.1	2703793	2703793	type	True	78.4448	443	1639	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:27:12,563] [INFO] DFAST Taxonomy check result was written to GCF_000803315.1_ASM80331v1_genomic.fna/tc_result.tsv
[2024-01-24 11:27:12,563] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:27:12,563] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:27:12,564] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg29c53c15-5dbd-40c4-886e-f7588772f99d/dqc_reference/checkm_data
[2024-01-24 11:27:12,565] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:27:12,612] [INFO] Task started: CheckM
[2024-01-24 11:27:12,613] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000803315.1_ASM80331v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000803315.1_ASM80331v1_genomic.fna/checkm_input GCF_000803315.1_ASM80331v1_genomic.fna/checkm_result
[2024-01-24 11:27:58,424] [INFO] Task succeeded: CheckM
[2024-01-24 11:27:58,426] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:27:58,448] [INFO] ===== Completeness check finished =====
[2024-01-24 11:27:58,449] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:27:58,449] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000803315.1_ASM80331v1_genomic.fna/markers.fasta)
[2024-01-24 11:27:58,450] [INFO] Task started: Blastn
[2024-01-24 11:27:58,450] [INFO] Running command: blastn -query GCF_000803315.1_ASM80331v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg29c53c15-5dbd-40c4-886e-f7588772f99d/dqc_reference/reference_markers_gtdb.fasta -out GCF_000803315.1_ASM80331v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:59,798] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:59,803] [INFO] Selected 9 target genomes.
[2024-01-24 11:27:59,803] [INFO] Target genome list was writen to GCF_000803315.1_ASM80331v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:27:59,805] [INFO] Task started: fastANI
[2024-01-24 11:27:59,805] [INFO] Running command: fastANI --query /var/lib/cwl/stg5b692f87-f64f-4aba-96af-a9d7358c8c6a/GCF_000803315.1_ASM80331v1_genomic.fna.gz --refList GCF_000803315.1_ASM80331v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000803315.1_ASM80331v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:28:11,361] [INFO] Task succeeded: fastANI
[2024-01-24 11:28:11,374] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:28:11,374] [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_000803315.1	s__Pectobacterium actinidiae	100.0	1639	1639	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	99.49	98.49	0.97	0.92	4	conclusive
GCF_900129615.1	s__Pectobacterium carotovorum	93.3357	1356	1639	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	96.11	95.19	0.90	0.85	81	-
GCF_002307355.1	s__Pectobacterium polaris	91.9711	1323	1639	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	96.45	95.13	0.88	0.82	21	-
GCF_003382565.2	s__Pectobacterium aquaticum	91.9006	1166	1639	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	97.07	95.76	0.89	0.87	15	-
GCF_000754695.1	s__Pectobacterium brasiliense	91.6874	1358	1639	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	96.37	95.20	0.89	0.82	92	-
GCF_013449685.1	s__Pectobacterium brasiliense_A	91.1752	1223	1639	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	98.47	96.08	0.92	0.83	5	-
GCF_015689195.1	s__Pectobacterium aroidearum	89.8662	1364	1639	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	98.07	97.92	0.91	0.90	12	-
GCF_013449375.1	s__Pectobacterium sp013449375	89.638	1239	1639	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005497185.1	s__Pectobacterium polonicum	89.5811	1317	1639	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:28:11,376] [INFO] GTDB search result was written to GCF_000803315.1_ASM80331v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:28:11,376] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:28:11,380] [INFO] DFAST_QC result json was written to GCF_000803315.1_ASM80331v1_genomic.fna/dqc_result.json
[2024-01-24 11:28:11,380] [INFO] DFAST_QC completed!
[2024-01-24 11:28:11,380] [INFO] Total running time: 0h1m34s