[2024-01-24 11:26:38,999] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:39,002] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:39,002] [INFO] DQC Reference Directory: /var/lib/cwl/stg6eff257d-330e-40bc-86ee-a95967a55eca/dqc_reference
[2024-01-24 11:26:40,346] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:40,347] [INFO] Task started: Prodigal
[2024-01-24 11:26:40,347] [INFO] Running command: gunzip -c /var/lib/cwl/stg02c37124-fac1-4795-a1cf-ae50fd22a4c0/GCF_004342665.1_ASM434266v1_genomic.fna.gz | prodigal -d GCF_004342665.1_ASM434266v1_genomic.fna/cds.fna -a GCF_004342665.1_ASM434266v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:50,609] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:50,610] [INFO] Task started: HMMsearch
[2024-01-24 11:26:50,610] [INFO] Running command: hmmsearch --tblout GCF_004342665.1_ASM434266v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6eff257d-330e-40bc-86ee-a95967a55eca/dqc_reference/reference_markers.hmm GCF_004342665.1_ASM434266v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:50,921] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:50,923] [INFO] Found 6/6 markers.
[2024-01-24 11:26:50,958] [INFO] Query marker FASTA was written to GCF_004342665.1_ASM434266v1_genomic.fna/markers.fasta
[2024-01-24 11:26:50,958] [INFO] Task started: Blastn
[2024-01-24 11:26:50,958] [INFO] Running command: blastn -query GCF_004342665.1_ASM434266v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6eff257d-330e-40bc-86ee-a95967a55eca/dqc_reference/reference_markers.fasta -out GCF_004342665.1_ASM434266v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:51,777] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:51,781] [INFO] Selected 21 target genomes.
[2024-01-24 11:26:51,781] [INFO] Target genome list was writen to GCF_004342665.1_ASM434266v1_genomic.fna/target_genomes.txt
[2024-01-24 11:26:51,790] [INFO] Task started: fastANI
[2024-01-24 11:26:51,790] [INFO] Running command: fastANI --query /var/lib/cwl/stg02c37124-fac1-4795-a1cf-ae50fd22a4c0/GCF_004342665.1_ASM434266v1_genomic.fna.gz --refList GCF_004342665.1_ASM434266v1_genomic.fna/target_genomes.txt --output GCF_004342665.1_ASM434266v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:27:11,118] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:11,119] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6eff257d-330e-40bc-86ee-a95967a55eca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:27:11,119] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6eff257d-330e-40bc-86ee-a95967a55eca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:27:11,147] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:27:11,147] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:27:11,147] [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 carotovorum	strain=DSM 30168	GCA_900129615.1	554	554	type	True	85.3494	1016	1277	95	below_threshold
Pectobacterium carotovorum subsp. carotovorum	strain=NCPPB 312	GCA_000749855.1	555	554	suspected-type	True	85.3475	1008	1277	95	below_threshold
Pectobacterium carotovorum subsp. carotovorum	strain=ICMP 5702	GCA_001039055.1	555	554	suspected-type	True	85.2917	1014	1277	95	below_threshold
Pectobacterium brasiliense	strain=IPO:3540 CFBP:6617 ATCC:BAA-417 IBSBF:1692	GCA_016950255.1	180957	180957	type	True	85.2267	1036	1277	95	below_threshold
Pectobacterium polaris	strain=NIBIO1006	GCA_002307355.1	2042057	2042057	type	True	85.2206	1021	1277	95	below_threshold
Pectobacterium brasiliense	strain=LMG 21371	GCA_000754695.1	180957	180957	type	True	85.1597	1051	1277	95	below_threshold
Pectobacterium parvum	strain=s0421	GCA_900195285.2	2778550	2778550	type	True	85.1254	969	1277	95	below_threshold
Pectobacterium odoriferum	strain=NCPPB 3839	GCA_000754765.1	78398	78398	type	True	85.0671	1000	1277	95	below_threshold
Pectobacterium colocasium	strain=LJ1	GCA_020181655.1	2878098	2878098	type	True	84.997	1013	1277	95	below_threshold
Pectobacterium actinidiae	strain=KKH3	GCA_000803315.1	1507808	1507808	type	True	84.9523	1023	1277	95	below_threshold
Pectobacterium quasiaquaticum	strain=A477-S1-J17	GCA_014946775.2	2774015	2774015	type	True	84.936	979	1277	95	below_threshold
Pectobacterium atrosepticum	strain=ICMP 1526	GCA_001038685.1	29471	29471	type	True	84.5756	973	1277	95	below_threshold
Pectobacterium atrosepticum	strain=NCPPB 549	GCA_000749905.1	29471	29471	type	True	84.5341	1041	1277	95	below_threshold
Pectobacterium polonicum	strain=DPMP315	GCA_005497185.1	2485124	2485124	type	True	84.4792	996	1277	95	below_threshold
Pectobacterium zantedeschiae	strain=9M	GCA_004137795.1	2034769	2034769	type	True	84.4716	1015	1277	95	below_threshold
Pectobacterium punjabense	strain=SS95	GCA_012427845.1	2108399	2108399	type	True	84.3133	997	1277	95	below_threshold
Pectobacterium punjabense	strain=SS95	GCA_003028395.1	2108399	2108399	type	True	84.2477	981	1277	95	below_threshold
Pectobacterium fontis	strain=M022	GCA_000803215.1	2558042	2558042	type	True	84.1865	930	1277	95	below_threshold
Serratia nevei	strain=S15	GCA_008364245.1	2703794	2703794	type	True	78.7183	414	1277	95	below_threshold
Serratia bockelmannii	strain=S3	GCA_008011855.1	2703793	2703793	type	True	78.558	403	1277	95	below_threshold
Enterobacter roggenkampii	strain=DSM 16690	GCA_024390995.1	1812935	1812935	type	True	77.9698	338	1277	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:27:11,149] [INFO] DFAST Taxonomy check result was written to GCF_004342665.1_ASM434266v1_genomic.fna/tc_result.tsv
[2024-01-24 11:27:11,150] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:27:11,150] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:27:11,150] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6eff257d-330e-40bc-86ee-a95967a55eca/dqc_reference/checkm_data
[2024-01-24 11:27:11,151] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:27:11,190] [INFO] Task started: CheckM
[2024-01-24 11:27:11,190] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004342665.1_ASM434266v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004342665.1_ASM434266v1_genomic.fna/checkm_input GCF_004342665.1_ASM434266v1_genomic.fna/checkm_result
[2024-01-24 11:27:46,135] [INFO] Task succeeded: CheckM
[2024-01-24 11:27:46,136] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:27:46,158] [INFO] ===== Completeness check finished =====
[2024-01-24 11:27:46,158] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:27:46,159] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004342665.1_ASM434266v1_genomic.fna/markers.fasta)
[2024-01-24 11:27:46,159] [INFO] Task started: Blastn
[2024-01-24 11:27:46,159] [INFO] Running command: blastn -query GCF_004342665.1_ASM434266v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6eff257d-330e-40bc-86ee-a95967a55eca/dqc_reference/reference_markers_gtdb.fasta -out GCF_004342665.1_ASM434266v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:47,355] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:47,359] [INFO] Selected 15 target genomes.
[2024-01-24 11:27:47,360] [INFO] Target genome list was writen to GCF_004342665.1_ASM434266v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:27:47,374] [INFO] Task started: fastANI
[2024-01-24 11:27:47,374] [INFO] Running command: fastANI --query /var/lib/cwl/stg02c37124-fac1-4795-a1cf-ae50fd22a4c0/GCF_004342665.1_ASM434266v1_genomic.fna.gz --refList GCF_004342665.1_ASM434266v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004342665.1_ASM434266v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:28:01,480] [INFO] Task succeeded: fastANI
[2024-01-24 11:28:01,497] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:28:01,497] [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_004342665.1	s__Samsonia erythrinae	100.0	1270	1277	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Samsonia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900129615.1	s__Pectobacterium carotovorum	85.3494	1016	1277	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	96.11	95.19	0.90	0.85	81	-
GCF_015689195.1	s__Pectobacterium aroidearum	85.2303	1033	1277	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	98.07	97.92	0.91	0.90	12	-
GCF_002307355.1	s__Pectobacterium polaris	85.2269	1020	1277	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	96.45	95.13	0.88	0.82	21	-
GCF_000754695.1	s__Pectobacterium brasiliense	85.1745	1049	1277	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	96.37	95.20	0.89	0.82	92	-
GCF_003382565.2	s__Pectobacterium aquaticum	84.9882	970	1277	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	97.07	95.76	0.89	0.87	15	-
GCF_000803315.1	s__Pectobacterium actinidiae	84.9457	1025	1277	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	99.49	98.49	0.97	0.92	4	-
GCF_013449375.1	s__Pectobacterium sp013449375	84.7315	977	1277	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019056595.1	s__Pectobacterium atrosepticum	84.627	1023	1277	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	99.44	98.81	0.97	0.94	14	-
GCF_005497185.1	s__Pectobacterium polonicum	84.4704	996	1277	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004137795.1	s__Pectobacterium zantedeschiae	84.4566	1017	1277	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	99.24	98.49	0.92	0.91	3	-
GCF_012427845.1	s__Pectobacterium punjabense	84.3159	996	1277	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	99.35	98.67	0.97	0.93	5	-
GCF_000803215.1	s__Pectobacterium fontis	84.1969	929	1277	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 11:28:01,499] [INFO] GTDB search result was written to GCF_004342665.1_ASM434266v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:28:01,499] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:28:01,504] [INFO] DFAST_QC result json was written to GCF_004342665.1_ASM434266v1_genomic.fna/dqc_result.json
[2024-01-24 11:28:01,504] [INFO] DFAST_QC completed!
[2024-01-24 11:28:01,504] [INFO] Total running time: 0h1m23s