[2024-01-24 12:06:11,956] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:11,959] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:11,959] [INFO] DQC Reference Directory: /var/lib/cwl/stg6703fa64-f184-4977-a8dd-6d29358c6bc4/dqc_reference
[2024-01-24 12:06:13,207] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:13,208] [INFO] Task started: Prodigal
[2024-01-24 12:06:13,208] [INFO] Running command: gunzip -c /var/lib/cwl/stgebee6780-1b8a-4e68-8d69-76402f9c49ed/GCF_016950255.1_ASM1695025v1_genomic.fna.gz | prodigal -d GCF_016950255.1_ASM1695025v1_genomic.fna/cds.fna -a GCF_016950255.1_ASM1695025v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:26,403] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:26,403] [INFO] Task started: HMMsearch
[2024-01-24 12:06:26,403] [INFO] Running command: hmmsearch --tblout GCF_016950255.1_ASM1695025v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6703fa64-f184-4977-a8dd-6d29358c6bc4/dqc_reference/reference_markers.hmm GCF_016950255.1_ASM1695025v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:26,775] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:26,776] [INFO] Found 6/6 markers.
[2024-01-24 12:06:26,823] [INFO] Query marker FASTA was written to GCF_016950255.1_ASM1695025v1_genomic.fna/markers.fasta
[2024-01-24 12:06:26,823] [INFO] Task started: Blastn
[2024-01-24 12:06:26,824] [INFO] Running command: blastn -query GCF_016950255.1_ASM1695025v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6703fa64-f184-4977-a8dd-6d29358c6bc4/dqc_reference/reference_markers.fasta -out GCF_016950255.1_ASM1695025v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:27,778] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:27,781] [INFO] Selected 11 target genomes.
[2024-01-24 12:06:27,782] [INFO] Target genome list was writen to GCF_016950255.1_ASM1695025v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:27,788] [INFO] Task started: fastANI
[2024-01-24 12:06:27,788] [INFO] Running command: fastANI --query /var/lib/cwl/stgebee6780-1b8a-4e68-8d69-76402f9c49ed/GCF_016950255.1_ASM1695025v1_genomic.fna.gz --refList GCF_016950255.1_ASM1695025v1_genomic.fna/target_genomes.txt --output GCF_016950255.1_ASM1695025v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:06:40,635] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:40,636] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6703fa64-f184-4977-a8dd-6d29358c6bc4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:06:40,637] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6703fa64-f184-4977-a8dd-6d29358c6bc4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:06:40,648] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:06:40,648] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:06:40,648] [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 brasiliense	strain=IPO:3540 CFBP:6617 ATCC:BAA-417 IBSBF:1692	GCA_016950255.1	180957	180957	type	True	100.0	1624	1624	95	conclusive
Pectobacterium brasiliense	strain=LMG 21371	GCA_000754695.1	180957	180957	type	True	99.9869	1575	1624	95	conclusive
Pectobacterium polaris	strain=NIBIO1006	GCA_002307355.1	2042057	2042057	type	True	94.067	1379	1624	95	below_threshold
Pectobacterium quasiaquaticum	strain=A477-S1-J17	GCA_014946775.2	2774015	2774015	type	True	93.9942	1253	1624	95	below_threshold
Pectobacterium carotovorum subsp. carotovorum	strain=ICMP 5702	GCA_001039055.1	555	554	suspected-type	True	93.3306	1358	1624	95	below_threshold
Pectobacterium carotovorum	strain=DSM 30168	GCA_900129615.1	554	554	type	True	93.3147	1361	1624	95	below_threshold
Pectobacterium carotovorum subsp. carotovorum	strain=NCPPB 312	GCA_000749855.1	555	554	suspected-type	True	93.2695	1364	1624	95	below_threshold
Pectobacterium colocasium	strain=LJ1	GCA_020181655.1	2878098	2878098	type	True	90.405	1319	1624	95	below_threshold
Enterobacter hormaechei	strain=FDAARGOS 1433	GCA_019048245.1	158836	158836	suspected-type	True	79.1196	367	1624	95	below_threshold
Rahnella rivi	strain=FC061912-K	GCA_019049655.1	2816249	2816249	type	True	78.5513	409	1624	95	below_threshold
Enterobacter roggenkampii	strain=DSM 16690	GCA_024390995.1	1812935	1812935	type	True	78.4238	384	1624	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:06:40,650] [INFO] DFAST Taxonomy check result was written to GCF_016950255.1_ASM1695025v1_genomic.fna/tc_result.tsv
[2024-01-24 12:06:40,651] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:06:40,651] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:06:40,652] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6703fa64-f184-4977-a8dd-6d29358c6bc4/dqc_reference/checkm_data
[2024-01-24 12:06:40,654] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:06:40,702] [INFO] Task started: CheckM
[2024-01-24 12:06:40,703] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016950255.1_ASM1695025v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016950255.1_ASM1695025v1_genomic.fna/checkm_input GCF_016950255.1_ASM1695025v1_genomic.fna/checkm_result
[2024-01-24 12:07:24,952] [INFO] Task succeeded: CheckM
[2024-01-24 12:07:24,953] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:07:24,972] [INFO] ===== Completeness check finished =====
[2024-01-24 12:07:24,973] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:07:24,973] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016950255.1_ASM1695025v1_genomic.fna/markers.fasta)
[2024-01-24 12:07:24,974] [INFO] Task started: Blastn
[2024-01-24 12:07:24,974] [INFO] Running command: blastn -query GCF_016950255.1_ASM1695025v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6703fa64-f184-4977-a8dd-6d29358c6bc4/dqc_reference/reference_markers_gtdb.fasta -out GCF_016950255.1_ASM1695025v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:26,094] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:26,098] [INFO] Selected 9 target genomes.
[2024-01-24 12:07:26,099] [INFO] Target genome list was writen to GCF_016950255.1_ASM1695025v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:07:26,105] [INFO] Task started: fastANI
[2024-01-24 12:07:26,106] [INFO] Running command: fastANI --query /var/lib/cwl/stgebee6780-1b8a-4e68-8d69-76402f9c49ed/GCF_016950255.1_ASM1695025v1_genomic.fna.gz --refList GCF_016950255.1_ASM1695025v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016950255.1_ASM1695025v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:07:36,599] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:36,613] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:07:36,613] [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_000754695.1	s__Pectobacterium brasiliense	99.9869	1575	1624	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	96.37	95.20	0.89	0.82	92	conclusive
GCF_013449685.1	s__Pectobacterium brasiliense_A	94.8665	1239	1624	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	98.47	96.08	0.92	0.83	5	-
GCF_002307355.1	s__Pectobacterium polaris	94.0687	1378	1624	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	96.45	95.13	0.88	0.82	21	-
GCF_900129615.1	s__Pectobacterium carotovorum	93.3147	1361	1624	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	96.11	95.19	0.90	0.85	81	-
GCF_003382565.2	s__Pectobacterium aquaticum	93.0205	1172	1624	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	91.6325	1399	1624	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	99.49	98.49	0.97	0.92	4	-
GCF_015689195.1	s__Pectobacterium aroidearum	91.0271	1374	1624	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	90.8575	1257	1624	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000010085.1	s__Sodalis glossinidius	78.0724	208	1624	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Sodalis	95.0	99.91	99.91	0.97	0.97	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:07:36,616] [INFO] GTDB search result was written to GCF_016950255.1_ASM1695025v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:07:36,617] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:07:36,620] [INFO] DFAST_QC result json was written to GCF_016950255.1_ASM1695025v1_genomic.fna/dqc_result.json
[2024-01-24 12:07:36,620] [INFO] DFAST_QC completed!
[2024-01-24 12:07:36,621] [INFO] Total running time: 0h1m25s