[2024-01-24 14:14:31,902] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:14:31,904] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:14:31,904] [INFO] DQC Reference Directory: /var/lib/cwl/stgbce402bc-7ca0-4c31-b08e-6b9bad368718/dqc_reference
[2024-01-24 14:14:33,155] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:14:33,156] [INFO] Task started: Prodigal
[2024-01-24 14:14:33,157] [INFO] Running command: gunzip -c /var/lib/cwl/stg2ef988ce-bbd2-422b-9eb0-6e6cb9573823/GCF_004137795.1_ASM413779v1_genomic.fna.gz | prodigal -d GCF_004137795.1_ASM413779v1_genomic.fna/cds.fna -a GCF_004137795.1_ASM413779v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:14:46,562] [INFO] Task succeeded: Prodigal
[2024-01-24 14:14:46,562] [INFO] Task started: HMMsearch
[2024-01-24 14:14:46,563] [INFO] Running command: hmmsearch --tblout GCF_004137795.1_ASM413779v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbce402bc-7ca0-4c31-b08e-6b9bad368718/dqc_reference/reference_markers.hmm GCF_004137795.1_ASM413779v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:14:46,928] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:14:46,930] [INFO] Found 6/6 markers.
[2024-01-24 14:14:46,973] [INFO] Query marker FASTA was written to GCF_004137795.1_ASM413779v1_genomic.fna/markers.fasta
[2024-01-24 14:14:46,973] [INFO] Task started: Blastn
[2024-01-24 14:14:46,973] [INFO] Running command: blastn -query GCF_004137795.1_ASM413779v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbce402bc-7ca0-4c31-b08e-6b9bad368718/dqc_reference/reference_markers.fasta -out GCF_004137795.1_ASM413779v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:47,879] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:47,883] [INFO] Selected 19 target genomes.
[2024-01-24 14:14:47,884] [INFO] Target genome list was writen to GCF_004137795.1_ASM413779v1_genomic.fna/target_genomes.txt
[2024-01-24 14:14:47,904] [INFO] Task started: fastANI
[2024-01-24 14:14:47,905] [INFO] Running command: fastANI --query /var/lib/cwl/stg2ef988ce-bbd2-422b-9eb0-6e6cb9573823/GCF_004137795.1_ASM413779v1_genomic.fna.gz --refList GCF_004137795.1_ASM413779v1_genomic.fna/target_genomes.txt --output GCF_004137795.1_ASM413779v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:15:09,059] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:09,059] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbce402bc-7ca0-4c31-b08e-6b9bad368718/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:15:09,060] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbce402bc-7ca0-4c31-b08e-6b9bad368718/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:15:09,080] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:15:09,080] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:15:09,080] [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 zantedeschiae	strain=9M	GCA_004137795.1	2034769	2034769	type	True	100.0	1679	1679	95	conclusive
Pectobacterium peruviense	strain=IFB5232	GCA_002847345.1	2066479	2066479	type	True	91.4757	1367	1679	95	below_threshold
Pectobacterium atrosepticum	strain=ICMP 1526	GCA_001038685.1	29471	29471	type	True	91.3019	1282	1679	95	below_threshold
Pectobacterium atrosepticum	strain=NCPPB 549	GCA_000749905.1	29471	29471	type	True	91.2814	1363	1679	95	below_threshold
Pectobacterium betavasculorum	strain=NCPPB 2795	GCA_000749845.1	55207	55207	type	True	91.2537	1256	1679	95	below_threshold
Pectobacterium carotovorum subsp. carotovorum	strain=NCPPB 312	GCA_000749855.1	555	554	suspected-type	True	89.3805	1368	1679	95	below_threshold
Pectobacterium carotovorum	strain=DSM 30168	GCA_900129615.1	554	554	type	True	89.3678	1367	1679	95	below_threshold
Pectobacterium carotovorum subsp. carotovorum	strain=ICMP 5702	GCA_001039055.1	555	554	suspected-type	True	89.3432	1368	1679	95	below_threshold
Pectobacterium wasabiae	strain=CFBP 3304	GCA_000291725.1	55208	55208	type	True	89.3061	1322	1679	95	below_threshold
Pectobacterium brasiliense	strain=LMG 21371	GCA_000754695.1	180957	180957	type	True	89.2606	1352	1679	95	below_threshold
Pectobacterium wasabiae	strain=CFBP 3304	GCA_001742185.1	55208	55208	type	True	89.2295	1340	1679	95	below_threshold
Pectobacterium brasiliense	strain=IPO:3540 CFBP:6617 ATCC:BAA-417 IBSBF:1692	GCA_016950255.1	180957	180957	type	True	89.1937	1368	1679	95	below_threshold
Pectobacterium odoriferum	strain=NCPPB 3839	GCA_000754765.1	78398	78398	type	True	89.0748	1321	1679	95	below_threshold
Pectobacterium quasiaquaticum	strain=A477-S1-J17	GCA_014946775.2	2774015	2774015	type	True	88.8817	1227	1679	95	below_threshold
Pectobacterium actinidiae	strain=KKH3	GCA_000803315.1	1507808	1507808	type	True	88.8226	1324	1679	95	below_threshold
Pectobacterium colocasium	strain=LJ1	GCA_020181655.1	2878098	2878098	type	True	88.4295	1366	1679	95	below_threshold
Serratia bockelmannii	strain=S3	GCA_008011855.1	2703793	2703793	type	True	78.5489	387	1679	95	below_threshold
Serratia entomophila	strain=A1	GCA_021462285.1	42906	42906	type	True	78.3939	392	1679	95	below_threshold
Serratia nevei	strain=S15	GCA_008364245.1	2703794	2703794	type	True	78.3398	399	1679	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:15:09,082] [INFO] DFAST Taxonomy check result was written to GCF_004137795.1_ASM413779v1_genomic.fna/tc_result.tsv
[2024-01-24 14:15:09,082] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:15:09,083] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:15:09,083] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbce402bc-7ca0-4c31-b08e-6b9bad368718/dqc_reference/checkm_data
[2024-01-24 14:15:09,084] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:15:09,136] [INFO] Task started: CheckM
[2024-01-24 14:15:09,136] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004137795.1_ASM413779v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004137795.1_ASM413779v1_genomic.fna/checkm_input GCF_004137795.1_ASM413779v1_genomic.fna/checkm_result
[2024-01-24 14:15:54,673] [INFO] Task succeeded: CheckM
[2024-01-24 14:15:54,675] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:15:54,698] [INFO] ===== Completeness check finished =====
[2024-01-24 14:15:54,698] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:15:54,699] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004137795.1_ASM413779v1_genomic.fna/markers.fasta)
[2024-01-24 14:15:54,699] [INFO] Task started: Blastn
[2024-01-24 14:15:54,700] [INFO] Running command: blastn -query GCF_004137795.1_ASM413779v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbce402bc-7ca0-4c31-b08e-6b9bad368718/dqc_reference/reference_markers_gtdb.fasta -out GCF_004137795.1_ASM413779v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:56,195] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:56,199] [INFO] Selected 13 target genomes.
[2024-01-24 14:15:56,199] [INFO] Target genome list was writen to GCF_004137795.1_ASM413779v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:15:56,209] [INFO] Task started: fastANI
[2024-01-24 14:15:56,209] [INFO] Running command: fastANI --query /var/lib/cwl/stg2ef988ce-bbd2-422b-9eb0-6e6cb9573823/GCF_004137795.1_ASM413779v1_genomic.fna.gz --refList GCF_004137795.1_ASM413779v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004137795.1_ASM413779v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:16:13,124] [INFO] Task succeeded: fastANI
[2024-01-24 14:16:13,136] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:16:13,136] [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_004137795.1	s__Pectobacterium zantedeschiae	100.0	1679	1679	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	99.24	98.49	0.92	0.91	3	conclusive
GCF_002847345.1	s__Pectobacterium peruviense	91.4757	1367	1679	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	91.2848	1360	1679	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	91.2537	1256	1679	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	99.45	99.45	0.94	0.94	2	-
GCF_015689195.1	s__Pectobacterium aroidearum	89.5532	1439	1679	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	98.07	97.92	0.91	0.90	12	-
GCF_900129615.1	s__Pectobacterium carotovorum	89.3709	1366	1679	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	96.11	95.19	0.90	0.85	81	-
GCF_000754695.1	s__Pectobacterium brasiliense	89.2653	1351	1679	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	96.37	95.20	0.89	0.82	92	-
GCF_005497185.1	s__Pectobacterium polonicum	89.2598	1341	1679	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001742185.1	s__Pectobacterium wasabiae	89.227	1339	1679	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	89.0824	1327	1679	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	99.20	98.87	0.95	0.90	33	-
GCF_013449685.1	s__Pectobacterium brasiliense_A	89.0284	1225	1679	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	98.47	96.08	0.92	0.83	5	-
GCF_003382565.2	s__Pectobacterium aquaticum	88.9966	1154	1679	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	88.8236	1324	1679	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	99.49	98.49	0.97	0.92	4	-
--------------------------------------------------------------------------------
[2024-01-24 14:16:13,138] [INFO] GTDB search result was written to GCF_004137795.1_ASM413779v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:16:13,139] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:16:13,143] [INFO] DFAST_QC result json was written to GCF_004137795.1_ASM413779v1_genomic.fna/dqc_result.json
[2024-01-24 14:16:13,143] [INFO] DFAST_QC completed!
[2024-01-24 14:16:13,143] [INFO] Total running time: 0h1m41s