[2024-01-25 20:12:05,637] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:12:05,638] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:12:05,638] [INFO] DQC Reference Directory: /var/lib/cwl/stg60ddc84d-c8e6-4fe4-b26c-f675991d0784/dqc_reference
[2024-01-25 20:12:06,844] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:12:06,845] [INFO] Task started: Prodigal
[2024-01-25 20:12:06,845] [INFO] Running command: gunzip -c /var/lib/cwl/stg86447515-ce01-4dbd-b96a-359f0bb1af02/GCF_009372235.1_ASM937223v1_genomic.fna.gz | prodigal -d GCF_009372235.1_ASM937223v1_genomic.fna/cds.fna -a GCF_009372235.1_ASM937223v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:12:19,671] [INFO] Task succeeded: Prodigal
[2024-01-25 20:12:19,672] [INFO] Task started: HMMsearch
[2024-01-25 20:12:19,672] [INFO] Running command: hmmsearch --tblout GCF_009372235.1_ASM937223v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg60ddc84d-c8e6-4fe4-b26c-f675991d0784/dqc_reference/reference_markers.hmm GCF_009372235.1_ASM937223v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:12:19,936] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:12:19,937] [INFO] Found 6/6 markers.
[2024-01-25 20:12:19,974] [INFO] Query marker FASTA was written to GCF_009372235.1_ASM937223v1_genomic.fna/markers.fasta
[2024-01-25 20:12:19,974] [INFO] Task started: Blastn
[2024-01-25 20:12:19,974] [INFO] Running command: blastn -query GCF_009372235.1_ASM937223v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg60ddc84d-c8e6-4fe4-b26c-f675991d0784/dqc_reference/reference_markers.fasta -out GCF_009372235.1_ASM937223v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:12:20,755] [INFO] Task succeeded: Blastn
[2024-01-25 20:12:20,758] [INFO] Selected 17 target genomes.
[2024-01-25 20:12:20,758] [INFO] Target genome list was writen to GCF_009372235.1_ASM937223v1_genomic.fna/target_genomes.txt
[2024-01-25 20:12:20,786] [INFO] Task started: fastANI
[2024-01-25 20:12:20,787] [INFO] Running command: fastANI --query /var/lib/cwl/stg86447515-ce01-4dbd-b96a-359f0bb1af02/GCF_009372235.1_ASM937223v1_genomic.fna.gz --refList GCF_009372235.1_ASM937223v1_genomic.fna/target_genomes.txt --output GCF_009372235.1_ASM937223v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:12:38,003] [INFO] Task succeeded: fastANI
[2024-01-25 20:12:38,004] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg60ddc84d-c8e6-4fe4-b26c-f675991d0784/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:12:38,004] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg60ddc84d-c8e6-4fe4-b26c-f675991d0784/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:12:38,013] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:12:38,014] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:12:38,014] [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 oryzae	strain=ZYY5	GCA_009372235.1	1240404	1240404	type	True	100.0	1516	1517	95	conclusive
Dickeya zeae	strain=NCPPB 2538	GCA_000406165.1	204042	204042	type	True	94.9144	1295	1517	95	below_threshold
Dickeya parazeae	strain=S31	GCA_017897605.1	2893572	2893572	type	True	94.4254	1292	1517	95	below_threshold
Dickeya chrysanthemi	strain=NCPPB 402	GCA_000406105.1	556	556	type	True	86.5274	1197	1517	95	below_threshold
Dickeya poaceiphila	strain=NCPPB 569	GCA_007858975.2	568768	568768	type	True	86.2872	1102	1517	95	below_threshold
Dickeya poaceiphila	strain=NCPPB 569	GCA_000406125.1	568768	568768	type	True	86.2048	1117	1517	95	below_threshold
Dickeya dianthicola	strain=NCPPB 453	GCA_000365305.1	204039	204039	type	True	85.5534	1192	1517	95	below_threshold
Dickeya fangzhongdai	strain=DSM 101947	GCA_002812485.1	1778540	1778540	type	True	85.4257	1194	1517	95	below_threshold
Dickeya dadantii subsp. dieffenbachiae	strain=NCPPB 2976	GCA_000406185.1	204040	204038	type	True	85.4073	1179	1517	95	below_threshold
Dickeya fangzhongdai	strain=CGMCC 1.15464	GCA_014642955.1	1778540	1778540	type	True	85.3701	1174	1517	95	below_threshold
Musicola keenii	strain=A3967	GCA_022761095.1	2884250	2884250	type	True	80.4046	741	1517	95	below_threshold
Serratia entomophila	strain=A1	GCA_021462285.1	42906	42906	type	True	78.6292	388	1517	95	below_threshold
Serratia nevei	strain=S15	GCA_008364245.1	2703794	2703794	type	True	78.4715	384	1517	95	below_threshold
Serratia bockelmannii	strain=S3	GCA_008011855.1	2703793	2703793	type	True	78.454	374	1517	95	below_threshold
Pantoea deleyi	strain=LMG24200	GCA_022647325.1	470932	470932	type	True	77.7857	304	1517	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:12:38,015] [INFO] DFAST Taxonomy check result was written to GCF_009372235.1_ASM937223v1_genomic.fna/tc_result.tsv
[2024-01-25 20:12:38,015] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:12:38,015] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:12:38,016] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg60ddc84d-c8e6-4fe4-b26c-f675991d0784/dqc_reference/checkm_data
[2024-01-25 20:12:38,016] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:12:38,062] [INFO] Task started: CheckM
[2024-01-25 20:12:38,062] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009372235.1_ASM937223v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009372235.1_ASM937223v1_genomic.fna/checkm_input GCF_009372235.1_ASM937223v1_genomic.fna/checkm_result
[2024-01-25 20:13:19,342] [INFO] Task succeeded: CheckM
[2024-01-25 20:13:19,343] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:13:19,380] [INFO] ===== Completeness check finished =====
[2024-01-25 20:13:19,381] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:13:19,381] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009372235.1_ASM937223v1_genomic.fna/markers.fasta)
[2024-01-25 20:13:19,381] [INFO] Task started: Blastn
[2024-01-25 20:13:19,381] [INFO] Running command: blastn -query GCF_009372235.1_ASM937223v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg60ddc84d-c8e6-4fe4-b26c-f675991d0784/dqc_reference/reference_markers_gtdb.fasta -out GCF_009372235.1_ASM937223v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:13:20,445] [INFO] Task succeeded: Blastn
[2024-01-25 20:13:20,448] [INFO] Selected 12 target genomes.
[2024-01-25 20:13:20,448] [INFO] Target genome list was writen to GCF_009372235.1_ASM937223v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:13:20,459] [INFO] Task started: fastANI
[2024-01-25 20:13:20,459] [INFO] Running command: fastANI --query /var/lib/cwl/stg86447515-ce01-4dbd-b96a-359f0bb1af02/GCF_009372235.1_ASM937223v1_genomic.fna.gz --refList GCF_009372235.1_ASM937223v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009372235.1_ASM937223v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:13:33,293] [INFO] Task succeeded: fastANI
[2024-01-25 20:13:33,301] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:13:33,301] [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_009372235.1	s__Dickeya oryzae	100.0	1517	1517	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Dickeya	95.0	97.59	96.04	0.90	0.83	10	conclusive
GCF_000406165.1	s__Dickeya zeae	94.9144	1295	1517	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Dickeya	95.0	97.51	96.16	0.94	0.92	9	-
GCF_000406105.1	s__Dickeya chrysanthemi	86.5193	1198	1517	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Dickeya	95.0	96.33	96.25	0.88	0.87	6	-
GCF_007858975.2	s__Dickeya poaceiphila	86.2914	1104	1517	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Dickeya	95.0	99.40	98.88	0.98	0.96	3	-
GCF_000365305.1	s__Dickeya dianthicola	85.5498	1193	1517	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Dickeya	95.0	99.46	97.48	0.95	0.91	50	-
GCF_002812485.1	s__Dickeya fangzhongdai	85.4213	1195	1517	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Dickeya	95.0	98.62	96.33	0.95	0.90	15	-
GCF_001644705.1	s__Dickeya solani	85.3395	1211	1517	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Dickeya	95.0	99.95	98.75	1.00	0.95	38	-
GCF_000406145.1	s__Dickeya dadantii	85.2427	1151	1517	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Dickeya	95.0	98.21	96.30	0.92	0.86	14	-
GCF_000784735.1	s__Dickeya undicola	84.8747	1107	1517	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Dickeya	95.0	99.06	99.05	0.94	0.93	3	-
GCF_003934295.1	s__Dickeya lacustris	82.1501	869	1517	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Dickeya	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900095885.1	s__Dickeya aquatica	82.1451	909	1517	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Dickeya	95.0	99.90	99.87	0.99	0.98	3	-
--------------------------------------------------------------------------------
[2024-01-25 20:13:33,303] [INFO] GTDB search result was written to GCF_009372235.1_ASM937223v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:13:33,303] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:13:33,306] [INFO] DFAST_QC result json was written to GCF_009372235.1_ASM937223v1_genomic.fna/dqc_result.json
[2024-01-25 20:13:33,306] [INFO] DFAST_QC completed!
[2024-01-25 20:13:33,306] [INFO] Total running time: 0h1m28s