[2024-01-24 11:43:37,649] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:43:37,651] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:43:37,652] [INFO] DQC Reference Directory: /var/lib/cwl/stgca97c180-088c-4d25-b1b4-8814c5f34cd3/dqc_reference
[2024-01-24 11:43:38,890] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:43:38,891] [INFO] Task started: Prodigal
[2024-01-24 11:43:38,891] [INFO] Running command: gunzip -c /var/lib/cwl/stg55839d89-0ae9-414b-ae81-92903c11a7f7/GCF_001039055.1_ASM103905v1_genomic.fna.gz | prodigal -d GCF_001039055.1_ASM103905v1_genomic.fna/cds.fna -a GCF_001039055.1_ASM103905v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:43:52,262] [INFO] Task succeeded: Prodigal
[2024-01-24 11:43:52,262] [INFO] Task started: HMMsearch
[2024-01-24 11:43:52,262] [INFO] Running command: hmmsearch --tblout GCF_001039055.1_ASM103905v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgca97c180-088c-4d25-b1b4-8814c5f34cd3/dqc_reference/reference_markers.hmm GCF_001039055.1_ASM103905v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:43:52,646] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:43:52,647] [INFO] Found 6/6 markers.
[2024-01-24 11:43:52,692] [INFO] Query marker FASTA was written to GCF_001039055.1_ASM103905v1_genomic.fna/markers.fasta
[2024-01-24 11:43:52,692] [INFO] Task started: Blastn
[2024-01-24 11:43:52,692] [INFO] Running command: blastn -query GCF_001039055.1_ASM103905v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgca97c180-088c-4d25-b1b4-8814c5f34cd3/dqc_reference/reference_markers.fasta -out GCF_001039055.1_ASM103905v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:43:53,652] [INFO] Task succeeded: Blastn
[2024-01-24 11:43:53,657] [INFO] Selected 13 target genomes.
[2024-01-24 11:43:53,657] [INFO] Target genome list was writen to GCF_001039055.1_ASM103905v1_genomic.fna/target_genomes.txt
[2024-01-24 11:43:53,663] [INFO] Task started: fastANI
[2024-01-24 11:43:53,663] [INFO] Running command: fastANI --query /var/lib/cwl/stg55839d89-0ae9-414b-ae81-92903c11a7f7/GCF_001039055.1_ASM103905v1_genomic.fna.gz --refList GCF_001039055.1_ASM103905v1_genomic.fna/target_genomes.txt --output GCF_001039055.1_ASM103905v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:44:08,760] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:08,761] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgca97c180-088c-4d25-b1b4-8814c5f34cd3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:44:08,761] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgca97c180-088c-4d25-b1b4-8814c5f34cd3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:44:08,781] [INFO] Found 13 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 11:44:08,781] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 11:44:08,781] [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 subsp. carotovorum	strain=ICMP 5702	GCA_001039055.1	555	554	suspected-type	True	100.0	1578	1578	95	inconclusive
Pectobacterium carotovorum	strain=DSM 30168	GCA_900129615.1	554	554	type	True	99.9951	1567	1578	95	inconclusive
Pectobacterium carotovorum subsp. carotovorum	strain=NCPPB 312	GCA_000749855.1	555	554	suspected-type	True	99.9838	1563	1578	95	inconclusive
Pectobacterium versatile	strain=CFBP6051	GCA_004296685.1	2488639	2488639	type	True	95.7154	1415	1578	95	inconclusive
Pectobacterium odoriferum	strain=NCPPB 3839	GCA_000754765.1	78398	78398	type	True	95.2536	1346	1578	95	inconclusive
Pectobacterium aquaticum	strain=A212-S19-A16	GCA_003382565.3	2204145	2204145	type	True	94.105	1220	1578	95	below_threshold
Pectobacterium brasiliense	strain=LMG 21371	GCA_000754695.1	180957	180957	type	True	93.3076	1371	1578	95	below_threshold
Pectobacterium brasiliense	strain=IPO:3540 CFBP:6617 ATCC:BAA-417 IBSBF:1692	GCA_016950255.1	180957	180957	type	True	93.3032	1379	1578	95	below_threshold
Pectobacterium quasiaquaticum	strain=A477-S1-J17	GCA_014946775.2	2774015	2774015	type	True	93.0179	1237	1578	95	below_threshold
Pectobacterium colocasium	strain=LJ1	GCA_020181655.1	2878098	2878098	type	True	90.6214	1319	1578	95	below_threshold
Serratia bockelmannii	strain=S3	GCA_008011855.1	2703793	2703793	type	True	78.6194	449	1578	95	below_threshold
Rahnella ecdela	strain=FRB 231	GCA_019049625.1	2816250	2816250	type	True	78.5417	415	1578	95	below_threshold
Rahnella rivi	strain=FC061912-K	GCA_019049655.1	2816249	2816249	type	True	78.4559	425	1578	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:44:08,783] [INFO] DFAST Taxonomy check result was written to GCF_001039055.1_ASM103905v1_genomic.fna/tc_result.tsv
[2024-01-24 11:44:08,784] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:44:08,784] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:44:08,784] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgca97c180-088c-4d25-b1b4-8814c5f34cd3/dqc_reference/checkm_data
[2024-01-24 11:44:08,785] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:44:08,836] [INFO] Task started: CheckM
[2024-01-24 11:44:08,836] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001039055.1_ASM103905v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001039055.1_ASM103905v1_genomic.fna/checkm_input GCF_001039055.1_ASM103905v1_genomic.fna/checkm_result
[2024-01-24 11:44:52,133] [INFO] Task succeeded: CheckM
[2024-01-24 11:44:52,135] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:44:52,158] [INFO] ===== Completeness check finished =====
[2024-01-24 11:44:52,158] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:44:52,158] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001039055.1_ASM103905v1_genomic.fna/markers.fasta)
[2024-01-24 11:44:52,159] [INFO] Task started: Blastn
[2024-01-24 11:44:52,159] [INFO] Running command: blastn -query GCF_001039055.1_ASM103905v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgca97c180-088c-4d25-b1b4-8814c5f34cd3/dqc_reference/reference_markers_gtdb.fasta -out GCF_001039055.1_ASM103905v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:53,486] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:53,490] [INFO] Selected 8 target genomes.
[2024-01-24 11:44:53,491] [INFO] Target genome list was writen to GCF_001039055.1_ASM103905v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:44:53,498] [INFO] Task started: fastANI
[2024-01-24 11:44:53,498] [INFO] Running command: fastANI --query /var/lib/cwl/stg55839d89-0ae9-414b-ae81-92903c11a7f7/GCF_001039055.1_ASM103905v1_genomic.fna.gz --refList GCF_001039055.1_ASM103905v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001039055.1_ASM103905v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:45:03,733] [INFO] Task succeeded: fastANI
[2024-01-24 11:45:03,745] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:45:03,745] [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	99.9951	1567	1578	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	94.1107	1195	1578	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	93.6193	1396	1578	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	93.34	1366	1578	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	93.2976	1372	1578	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	92.9075	1262	1578	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	98.47	96.08	0.92	0.83	5	-
GCF_013449375.1	s__Pectobacterium sp013449375	90.4865	1268	1578	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015689195.1	s__Pectobacterium aroidearum	90.4855	1368	1578	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	98.07	97.92	0.91	0.90	12	-
--------------------------------------------------------------------------------
[2024-01-24 11:45:03,747] [INFO] GTDB search result was written to GCF_001039055.1_ASM103905v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:45:03,747] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:45:03,750] [INFO] DFAST_QC result json was written to GCF_001039055.1_ASM103905v1_genomic.fna/dqc_result.json
[2024-01-24 11:45:03,751] [INFO] DFAST_QC completed!
[2024-01-24 11:45:03,751] [INFO] Total running time: 0h1m26s