[2024-01-24 13:49:12,369] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:12,371] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:12,371] [INFO] DQC Reference Directory: /var/lib/cwl/stg0f9533c2-40fc-4932-bd46-ceb8783bdccb/dqc_reference
[2024-01-24 13:49:13,668] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:13,670] [INFO] Task started: Prodigal
[2024-01-24 13:49:13,671] [INFO] Running command: gunzip -c /var/lib/cwl/stg14440b28-72d5-4153-bfe3-94daf7256dc6/GCF_007858975.2_ASM785897v2_genomic.fna.gz | prodigal -d GCF_007858975.2_ASM785897v2_genomic.fna/cds.fna -a GCF_007858975.2_ASM785897v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:27,985] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:27,986] [INFO] Task started: HMMsearch
[2024-01-24 13:49:27,986] [INFO] Running command: hmmsearch --tblout GCF_007858975.2_ASM785897v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0f9533c2-40fc-4932-bd46-ceb8783bdccb/dqc_reference/reference_markers.hmm GCF_007858975.2_ASM785897v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:28,364] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:28,365] [INFO] Found 6/6 markers.
[2024-01-24 13:49:28,455] [INFO] Query marker FASTA was written to GCF_007858975.2_ASM785897v2_genomic.fna/markers.fasta
[2024-01-24 13:49:28,455] [INFO] Task started: Blastn
[2024-01-24 13:49:28,456] [INFO] Running command: blastn -query GCF_007858975.2_ASM785897v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg0f9533c2-40fc-4932-bd46-ceb8783bdccb/dqc_reference/reference_markers.fasta -out GCF_007858975.2_ASM785897v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:29,342] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:29,346] [INFO] Selected 19 target genomes.
[2024-01-24 13:49:29,346] [INFO] Target genome list was writen to GCF_007858975.2_ASM785897v2_genomic.fna/target_genomes.txt
[2024-01-24 13:49:29,354] [INFO] Task started: fastANI
[2024-01-24 13:49:29,354] [INFO] Running command: fastANI --query /var/lib/cwl/stg14440b28-72d5-4153-bfe3-94daf7256dc6/GCF_007858975.2_ASM785897v2_genomic.fna.gz --refList GCF_007858975.2_ASM785897v2_genomic.fna/target_genomes.txt --output GCF_007858975.2_ASM785897v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:49,204] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:49,205] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0f9533c2-40fc-4932-bd46-ceb8783bdccb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:49,206] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0f9533c2-40fc-4932-bd46-ceb8783bdccb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:49,230] [INFO] Found 19 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:49:49,231] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:49:49,231] [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
Dickeya poaceiphila	strain=NCPPB 569	GCA_007858975.2	568768	568768	type	True	100.0	1437	1439	95	conclusive
Dickeya poaceiphila	strain=NCPPB 569	GCA_000406125.1	568768	568768	type	True	99.9109	1403	1439	95	conclusive
Dickeya fangzhongdai	strain=DSM 101947	GCA_002812485.1	1778540	1778540	type	True	86.5368	1148	1439	95	below_threshold
Dickeya dadantii	strain=DSM 18020	GCA_003049785.1	204038	204038	type	True	86.4921	1138	1439	95	below_threshold
Dickeya fangzhongdai	strain=CGMCC 1.15464	GCA_014642955.1	1778540	1778540	type	True	86.469	1131	1439	95	below_threshold
Dickeya dadantii subsp. dieffenbachiae	strain=NCPPB 2976	GCA_000406185.1	204040	204038	type	True	86.3909	1126	1439	95	below_threshold
Dickeya oryzae	strain=ZYY5	GCA_009372235.1	1240404	1240404	type	True	86.385	1102	1439	95	below_threshold
Dickeya chrysanthemi	strain=NCPPB 402	GCA_000406105.1	556	556	type	True	86.3815	1099	1439	95	below_threshold
Dickeya solani	strain=IPO 2222	GCA_001644705.1	1089444	1089444	type	True	86.3804	1127	1439	95	below_threshold
Dickeya dadantii	strain=NCPPB 898	GCA_000406145.1	204038	204038	type	True	86.3622	1113	1439	95	below_threshold
Dickeya solani	strain=IPO 2222	GCA_000400795.1	1089444	1089444	type	True	86.1969	1122	1439	95	below_threshold
Dickeya parazeae	strain=S31	GCA_017897605.1	2893572	2893572	type	True	86.1675	1133	1439	95	below_threshold
Dickeya zeae	strain=NCPPB 2538	GCA_000406165.1	204042	204042	type	True	86.0469	1111	1439	95	below_threshold
Musicola keenii	strain=A3967	GCA_022761095.1	2884250	2884250	type	True	80.7653	710	1439	95	below_threshold
Pectobacterium colocasium	strain=LJ1	GCA_020181655.1	2878098	2878098	type	True	79.305	503	1439	95	below_threshold
Serratia entomophila	strain=A1	GCA_021462285.1	42906	42906	type	True	78.9008	440	1439	95	below_threshold
Serratia nevei	strain=S15	GCA_008364245.1	2703794	2703794	type	True	78.7397	416	1439	95	below_threshold
Serratia bockelmannii	strain=S3	GCA_008011855.1	2703793	2703793	type	True	78.5191	404	1439	95	below_threshold
Mixta calida	strain=LMG 25383	GCA_002095355.1	665913	665913	type	True	78.049	332	1439	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:49,233] [INFO] DFAST Taxonomy check result was written to GCF_007858975.2_ASM785897v2_genomic.fna/tc_result.tsv
[2024-01-24 13:49:49,234] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:49,235] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:49,235] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0f9533c2-40fc-4932-bd46-ceb8783bdccb/dqc_reference/checkm_data
[2024-01-24 13:49:49,237] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:49,285] [INFO] Task started: CheckM
[2024-01-24 13:49:49,285] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007858975.2_ASM785897v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007858975.2_ASM785897v2_genomic.fna/checkm_input GCF_007858975.2_ASM785897v2_genomic.fna/checkm_result
[2024-01-24 13:50:32,792] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:32,794] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:32,811] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:32,812] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:32,812] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007858975.2_ASM785897v2_genomic.fna/markers.fasta)
[2024-01-24 13:50:32,812] [INFO] Task started: Blastn
[2024-01-24 13:50:32,812] [INFO] Running command: blastn -query GCF_007858975.2_ASM785897v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg0f9533c2-40fc-4932-bd46-ceb8783bdccb/dqc_reference/reference_markers_gtdb.fasta -out GCF_007858975.2_ASM785897v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:33,860] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:33,863] [INFO] Selected 10 target genomes.
[2024-01-24 13:50:33,863] [INFO] Target genome list was writen to GCF_007858975.2_ASM785897v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:33,875] [INFO] Task started: fastANI
[2024-01-24 13:50:33,875] [INFO] Running command: fastANI --query /var/lib/cwl/stg14440b28-72d5-4153-bfe3-94daf7256dc6/GCF_007858975.2_ASM785897v2_genomic.fna.gz --refList GCF_007858975.2_ASM785897v2_genomic.fna/target_genomes_gtdb.txt --output GCF_007858975.2_ASM785897v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:44,833] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:44,840] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:50:44,841] [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_007858975.2	s__Dickeya poaceiphila	100.0	1435	1439	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Dickeya	95.0	99.40	98.88	0.98	0.96	3	conclusive
GCF_002812485.1	s__Dickeya fangzhongdai	86.5597	1149	1439	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Dickeya	95.0	98.62	96.33	0.95	0.90	15	-
GCF_000365305.1	s__Dickeya dianthicola	86.4848	1089	1439	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Dickeya	95.0	99.46	97.48	0.95	0.91	50	-
GCF_009372235.1	s__Dickeya oryzae	86.402	1102	1439	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Dickeya	95.0	97.59	96.04	0.90	0.83	10	-
GCF_001644705.1	s__Dickeya solani	86.388	1127	1439	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Dickeya	95.0	99.95	98.75	1.00	0.95	38	-
GCF_000406105.1	s__Dickeya chrysanthemi	86.3749	1100	1439	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Dickeya	95.0	96.33	96.25	0.88	0.87	6	-
GCF_000406145.1	s__Dickeya dadantii	86.3584	1115	1439	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Dickeya	95.0	98.21	96.30	0.92	0.86	14	-
GCF_000406165.1	s__Dickeya zeae	86.0637	1109	1439	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Dickeya	95.0	97.51	96.16	0.94	0.92	9	-
--------------------------------------------------------------------------------
[2024-01-24 13:50:44,842] [INFO] GTDB search result was written to GCF_007858975.2_ASM785897v2_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:44,843] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:44,846] [INFO] DFAST_QC result json was written to GCF_007858975.2_ASM785897v2_genomic.fna/dqc_result.json
[2024-01-24 13:50:44,847] [INFO] DFAST_QC completed!
[2024-01-24 13:50:44,847] [INFO] Total running time: 0h1m32s