[2024-01-24 13:56:56,865] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:56:56,866] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:56:56,867] [INFO] DQC Reference Directory: /var/lib/cwl/stg33bde27f-f3e1-480d-b366-88c63cc85de1/dqc_reference
[2024-01-24 13:56:58,165] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:56:58,165] [INFO] Task started: Prodigal
[2024-01-24 13:56:58,166] [INFO] Running command: gunzip -c /var/lib/cwl/stg20b09a89-1cf5-4bce-af77-9259c12b5ea8/GCF_004296685.1_ASM429668v1_genomic.fna.gz | prodigal -d GCF_004296685.1_ASM429668v1_genomic.fna/cds.fna -a GCF_004296685.1_ASM429668v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:11,411] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:11,412] [INFO] Task started: HMMsearch
[2024-01-24 13:57:11,412] [INFO] Running command: hmmsearch --tblout GCF_004296685.1_ASM429668v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg33bde27f-f3e1-480d-b366-88c63cc85de1/dqc_reference/reference_markers.hmm GCF_004296685.1_ASM429668v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:11,769] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:11,770] [INFO] Found 6/6 markers.
[2024-01-24 13:57:11,814] [INFO] Query marker FASTA was written to GCF_004296685.1_ASM429668v1_genomic.fna/markers.fasta
[2024-01-24 13:57:11,815] [INFO] Task started: Blastn
[2024-01-24 13:57:11,815] [INFO] Running command: blastn -query GCF_004296685.1_ASM429668v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg33bde27f-f3e1-480d-b366-88c63cc85de1/dqc_reference/reference_markers.fasta -out GCF_004296685.1_ASM429668v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:12,786] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:12,789] [INFO] Selected 13 target genomes.
[2024-01-24 13:57:12,790] [INFO] Target genome list was writen to GCF_004296685.1_ASM429668v1_genomic.fna/target_genomes.txt
[2024-01-24 13:57:12,795] [INFO] Task started: fastANI
[2024-01-24 13:57:12,795] [INFO] Running command: fastANI --query /var/lib/cwl/stg20b09a89-1cf5-4bce-af77-9259c12b5ea8/GCF_004296685.1_ASM429668v1_genomic.fna.gz --refList GCF_004296685.1_ASM429668v1_genomic.fna/target_genomes.txt --output GCF_004296685.1_ASM429668v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:57:28,527] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:28,528] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg33bde27f-f3e1-480d-b366-88c63cc85de1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:57:28,529] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg33bde27f-f3e1-480d-b366-88c63cc85de1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:57:28,547] [INFO] Found 13 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 13:57:28,547] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:57:28,547] [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 versatile	strain=CFBP6051	GCA_004296685.1	2488639	2488639	type	True	100.0	1590	1600	95	inconclusive
Pectobacterium carotovorum subsp. carotovorum	strain=ICMP 5702	GCA_001039055.1	555	554	suspected-type	True	95.7389	1431	1600	95	inconclusive
Pectobacterium carotovorum subsp. carotovorum	strain=NCPPB 312	GCA_000749855.1	555	554	suspected-type	True	95.7247	1426	1600	95	inconclusive
Pectobacterium carotovorum	strain=DSM 30168	GCA_900129615.1	554	554	type	True	95.7198	1421	1600	95	inconclusive
Pectobacterium odoriferum	strain=NCPPB 3839	GCA_000754765.1	78398	78398	type	True	95.0151	1351	1600	95	inconclusive
Pectobacterium aquaticum	strain=A212-S19-A16	GCA_003382565.3	2204145	2204145	type	True	94.4698	1209	1600	95	below_threshold
Pectobacterium parvum	strain=s0421	GCA_900195285.2	2778550	2778550	type	True	93.8459	1257	1600	95	below_threshold
Pectobacterium polaris	strain=NIBIO1006	GCA_002307355.1	2042057	2042057	type	True	93.8386	1415	1600	95	below_threshold
Pectobacterium quasiaquaticum	strain=A477-S1-J17	GCA_014946775.2	2774015	2774015	type	True	92.9852	1255	1600	95	below_threshold
Pectobacterium colocasium	strain=LJ1	GCA_020181655.1	2878098	2878098	type	True	90.4311	1324	1600	95	below_threshold
Serratia bockelmannii	strain=S3	GCA_008011855.1	2703793	2703793	type	True	78.7371	411	1600	95	below_threshold
Rahnella ecdela	strain=FRB 231	GCA_019049625.1	2816250	2816250	type	True	78.4544	395	1600	95	below_threshold
Rahnella rivi	strain=FC061912-K	GCA_019049655.1	2816249	2816249	type	True	78.3637	405	1600	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:57:28,549] [INFO] DFAST Taxonomy check result was written to GCF_004296685.1_ASM429668v1_genomic.fna/tc_result.tsv
[2024-01-24 13:57:28,550] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:57:28,550] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:57:28,550] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg33bde27f-f3e1-480d-b366-88c63cc85de1/dqc_reference/checkm_data
[2024-01-24 13:57:28,552] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:57:28,602] [INFO] Task started: CheckM
[2024-01-24 13:57:28,602] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004296685.1_ASM429668v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004296685.1_ASM429668v1_genomic.fna/checkm_input GCF_004296685.1_ASM429668v1_genomic.fna/checkm_result
[2024-01-24 13:58:11,525] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:11,526] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:11,545] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:11,545] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:11,546] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004296685.1_ASM429668v1_genomic.fna/markers.fasta)
[2024-01-24 13:58:11,546] [INFO] Task started: Blastn
[2024-01-24 13:58:11,546] [INFO] Running command: blastn -query GCF_004296685.1_ASM429668v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg33bde27f-f3e1-480d-b366-88c63cc85de1/dqc_reference/reference_markers_gtdb.fasta -out GCF_004296685.1_ASM429668v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:13,014] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:13,018] [INFO] Selected 7 target genomes.
[2024-01-24 13:58:13,019] [INFO] Target genome list was writen to GCF_004296685.1_ASM429668v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:13,024] [INFO] Task started: fastANI
[2024-01-24 13:58:13,025] [INFO] Running command: fastANI --query /var/lib/cwl/stg20b09a89-1cf5-4bce-af77-9259c12b5ea8/GCF_004296685.1_ASM429668v1_genomic.fna.gz --refList GCF_004296685.1_ASM429668v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004296685.1_ASM429668v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:58:22,112] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:22,120] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:58:22,120] [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_900129615.1	s__Pectobacterium carotovorum	95.7198	1421	1600	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	96.11	95.19	0.90	0.85	81	conclusive
GCF_003382565.2	s__Pectobacterium aquaticum	94.5174	1187	1600	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	97.07	95.76	0.89	0.87	15	-
GCF_002307355.1	s__Pectobacterium polaris	93.8386	1415	1600	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	96.45	95.13	0.88	0.82	21	-
GCF_000803315.1	s__Pectobacterium actinidiae	93.0676	1353	1600	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	99.49	98.49	0.97	0.92	4	-
GCF_000754695.1	s__Pectobacterium brasiliense	92.9344	1365	1600	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	92.6564	1253	1600	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	98.47	96.08	0.92	0.83	5	-
GCF_000749845.1	s__Pectobacterium betavasculorum	89.4782	1223	1600	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	99.45	99.45	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:58:22,122] [INFO] GTDB search result was written to GCF_004296685.1_ASM429668v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:58:22,122] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:58:22,128] [INFO] DFAST_QC result json was written to GCF_004296685.1_ASM429668v1_genomic.fna/dqc_result.json
[2024-01-24 13:58:22,128] [INFO] DFAST_QC completed!
[2024-01-24 13:58:22,128] [INFO] Total running time: 0h1m25s