[2023-06-19 04:28:48,444] [INFO] DFAST_QC pipeline started.
[2023-06-19 04:28:48,447] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 04:28:48,447] [INFO] DQC Reference Directory: /var/lib/cwl/stg85ed753e-f8f5-4127-af06-f7553dbd2657/dqc_reference
[2023-06-19 04:28:52,001] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 04:28:52,004] [INFO] Task started: Prodigal
[2023-06-19 04:28:52,005] [INFO] Running command: gunzip -c /var/lib/cwl/stgd0810d0f-76ab-4551-a2c9-8350476a5e57/GCA_013152425.1_ASM1315242v1_genomic.fna.gz | prodigal -d GCA_013152425.1_ASM1315242v1_genomic.fna/cds.fna -a GCA_013152425.1_ASM1315242v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 04:29:10,521] [INFO] Task succeeded: Prodigal
[2023-06-19 04:29:10,521] [INFO] Task started: HMMsearch
[2023-06-19 04:29:10,521] [INFO] Running command: hmmsearch --tblout GCA_013152425.1_ASM1315242v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg85ed753e-f8f5-4127-af06-f7553dbd2657/dqc_reference/reference_markers.hmm GCA_013152425.1_ASM1315242v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 04:29:10,875] [INFO] Task succeeded: HMMsearch
[2023-06-19 04:29:10,877] [INFO] Found 6/6 markers.
[2023-06-19 04:29:10,927] [INFO] Query marker FASTA was written to GCA_013152425.1_ASM1315242v1_genomic.fna/markers.fasta
[2023-06-19 04:29:10,928] [INFO] Task started: Blastn
[2023-06-19 04:29:10,928] [INFO] Running command: blastn -query GCA_013152425.1_ASM1315242v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg85ed753e-f8f5-4127-af06-f7553dbd2657/dqc_reference/reference_markers.fasta -out GCA_013152425.1_ASM1315242v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 04:29:11,817] [INFO] Task succeeded: Blastn
[2023-06-19 04:29:11,841] [INFO] Selected 22 target genomes.
[2023-06-19 04:29:11,841] [INFO] Target genome list was writen to GCA_013152425.1_ASM1315242v1_genomic.fna/target_genomes.txt
[2023-06-19 04:29:11,847] [INFO] Task started: fastANI
[2023-06-19 04:29:11,848] [INFO] Running command: fastANI --query /var/lib/cwl/stgd0810d0f-76ab-4551-a2c9-8350476a5e57/GCA_013152425.1_ASM1315242v1_genomic.fna.gz --refList GCA_013152425.1_ASM1315242v1_genomic.fna/target_genomes.txt --output GCA_013152425.1_ASM1315242v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 04:29:34,096] [INFO] Task succeeded: fastANI
[2023-06-19 04:29:34,096] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg85ed753e-f8f5-4127-af06-f7553dbd2657/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 04:29:34,097] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg85ed753e-f8f5-4127-af06-f7553dbd2657/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 04:29:34,120] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 04:29:34,120] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 04:29:34,120] [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
Ralstonia insidiosa	strain=CCUG 46789	GCA_008801405.1	190721	190721	type	True	94.0818	1440	1750	95	below_threshold
Ralstonia pickettii	strain=NBRC 102503	GCA_001544155.1	329	329	type	True	86.7612	1178	1750	95	below_threshold
Ralstonia mannitolilytica	strain=LMG 6866	GCA_905397375.1	105219	105219	type	True	86.7224	1187	1750	95	below_threshold
Ralstonia pickettii	strain=FDAARGOS_1535	GCA_020341455.1	329	329	type	True	86.7169	1223	1750	95	below_threshold
Ralstonia pickettii	strain=K-288	GCA_016466415.2	329	329	type	True	86.7038	1211	1750	95	below_threshold
Ralstonia pickettii	strain=NCTC11149	GCA_900455835.1	329	329	type	True	86.688	1207	1750	95	below_threshold
Ralstonia pickettii	strain=ATCC 27511	GCA_000743455.1	329	329	type	True	86.6466	1210	1750	95	below_threshold
Ralstonia pseudosolanacearum	strain=LMG 9673	GCA_919586305.1	1310165	1310165	type	True	85.2425	962	1750	95	below_threshold
Ralstonia pseudosolanacearum	strain=LMG 9673	GCA_024925465.1	1310165	1310165	type	True	85.0403	1014	1750	95	below_threshold
Ralstonia solanacearum	strain=NCPPB 325	GCA_015910705.1	305	305	type	True	84.9112	1009	1750	95	below_threshold
Ralstonia solanacearum	strain=K60	GCA_002251695.1	305	305	type	True	84.9015	1014	1750	95	below_threshold
Cupriavidus oxalaticus	strain=NBRC 13593	GCA_001592245.1	96344	96344	type	True	80.8485	621	1750	95	below_threshold
Cupriavidus oxalaticus	strain=Ox1	GCA_016894385.1	96344	96344	type	True	80.767	641	1750	95	below_threshold
Cupriavidus respiraculi	strain=LMG 21510	GCA_914271545.1	195930	195930	type	True	80.0632	591	1750	95	below_threshold
Burkholderia perseverans	strain=INN12	GCA_022870505.1	2615214	2615214	type	True	78.6706	477	1750	95	below_threshold
Massilia norwichensis	strain=LMG 28164	GCA_024753245.1	1442366	1442366	type	True	78.1372	332	1750	95	below_threshold
Paraburkholderia podalyriae	strain=WC7.3b	GCA_014397785.1	1938811	1938811	type	True	78.0784	413	1750	95	below_threshold
Pseudomonas viridiflava	strain=ICMP2848	GCA_001401215.1	33069	33069	type	True	76.0242	102	1750	95	below_threshold
Pseudomonas viridiflava	strain=ICMP 2848	GCA_001642795.1	33069	33069	type	True	75.9937	104	1750	95	below_threshold
Pseudomonas viridiflava	strain=DSM 6694	GCA_001305955.1	33069	33069	type	True	75.9869	103	1750	95	below_threshold
Pseudomonas syringae group genomosp. 3	strain=ICMP3956	GCA_001400635.1	251701	251701	pathovar	True	75.9845	98	1750	95	below_threshold
Pseudomonas syringae group genomosp. 3	strain=ICMP3882	GCA_001400955.1	251701	251701	pathovar	True	75.9578	105	1750	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 04:29:34,122] [INFO] DFAST Taxonomy check result was written to GCA_013152425.1_ASM1315242v1_genomic.fna/tc_result.tsv
[2023-06-19 04:29:34,123] [INFO] ===== Taxonomy check completed =====
[2023-06-19 04:29:34,123] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 04:29:34,123] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg85ed753e-f8f5-4127-af06-f7553dbd2657/dqc_reference/checkm_data
[2023-06-19 04:29:34,125] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 04:29:34,177] [INFO] Task started: CheckM
[2023-06-19 04:29:34,178] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_013152425.1_ASM1315242v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_013152425.1_ASM1315242v1_genomic.fna/checkm_input GCA_013152425.1_ASM1315242v1_genomic.fna/checkm_result
[2023-06-19 04:30:32,102] [INFO] Task succeeded: CheckM
[2023-06-19 04:30:32,107] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 04:30:32,129] [INFO] ===== Completeness check finished =====
[2023-06-19 04:30:32,130] [INFO] ===== Start GTDB Search =====
[2023-06-19 04:30:32,130] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_013152425.1_ASM1315242v1_genomic.fna/markers.fasta)
[2023-06-19 04:30:32,131] [INFO] Task started: Blastn
[2023-06-19 04:30:32,131] [INFO] Running command: blastn -query GCA_013152425.1_ASM1315242v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg85ed753e-f8f5-4127-af06-f7553dbd2657/dqc_reference/reference_markers_gtdb.fasta -out GCA_013152425.1_ASM1315242v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 04:30:33,641] [INFO] Task succeeded: Blastn
[2023-06-19 04:30:33,647] [INFO] Selected 18 target genomes.
[2023-06-19 04:30:33,647] [INFO] Target genome list was writen to GCA_013152425.1_ASM1315242v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 04:30:33,662] [INFO] Task started: fastANI
[2023-06-19 04:30:33,662] [INFO] Running command: fastANI --query /var/lib/cwl/stgd0810d0f-76ab-4551-a2c9-8350476a5e57/GCA_013152425.1_ASM1315242v1_genomic.fna.gz --refList GCA_013152425.1_ASM1315242v1_genomic.fna/target_genomes_gtdb.txt --output GCA_013152425.1_ASM1315242v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 04:30:54,597] [INFO] Task succeeded: fastANI
[2023-06-19 04:30:54,617] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 04:30:54,617] [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_001078575.1	s__Ralstonia sp001078575	99.8665	1631	1750	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ralstonia	95.0	99.81	99.41	0.97	0.93	9	conclusive
GCF_008801405.1	s__Ralstonia insidiosa	94.07	1441	1750	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ralstonia	95.0	97.92	96.99	0.90	0.85	9	-
GCF_016429285.1	s__Ralstonia sp016429285	91.4585	1265	1750	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ralstonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000801955.1	s__Ralstonia sp000801955	90.2152	1364	1750	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ralstonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002298975.1	s__Ralstonia sp002298975	87.4825	1168	1750	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ralstonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000020205.1	s__Ralstonia pickettii_B	87.399	1198	1750	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ralstonia	95.0	98.08	96.31	0.87	0.83	22	-
GCF_000620465.1	s__Ralstonia sp000620465	87.1628	1241	1750	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ralstonia	95.0	96.59	96.59	0.94	0.94	2	-
GCF_003851545.1	s__Ralstonia sp003851545	86.996	1135	1750	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ralstonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007997035.1	s__Ralstonia sp007997035	86.9429	1175	1750	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ralstonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000955795.1	s__Ralstonia sp000955795	86.929	1251	1750	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ralstonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_905397375.1	s__Ralstonia mannitolilytica	86.7246	1187	1750	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ralstonia	95.0	98.68	96.05	0.93	0.87	14	-
GCF_900115545.1	s__Ralstonia sp900115545	86.6727	1238	1750	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ralstonia	95.0	98.84	98.84	0.97	0.97	2	-
GCF_003999715.1	s__Ralstonia pseudosolanacearum	85.0887	1017	1750	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ralstonia	95.0	98.86	95.79	0.91	0.82	165	-
GCF_002251695.1	s__Ralstonia solanacearum	84.8829	1015	1750	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ralstonia	95.0	96.27	95.49	0.87	0.78	131	-
GCF_001642795.1	s__Pseudomonas_E viridiflava	75.9937	104	1750	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.35	96.41	0.93	0.89	1379	-
GCF_002723575.1	s__Pseudomonas_E viridiflava_B	75.7629	92	1750	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.78	98.76	0.95	0.94	5	-
GCF_001297015.1	s__Pseudomonas_E sp001297015	75.6989	110	1750	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.81	98.77	0.95	0.94	9	-
GCF_902497875.1	s__Pseudomonas_E fluorescens_BR	75.5768	109	1750	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 04:30:54,619] [INFO] GTDB search result was written to GCA_013152425.1_ASM1315242v1_genomic.fna/result_gtdb.tsv
[2023-06-19 04:30:54,620] [INFO] ===== GTDB Search completed =====
[2023-06-19 04:30:54,624] [INFO] DFAST_QC result json was written to GCA_013152425.1_ASM1315242v1_genomic.fna/dqc_result.json
[2023-06-19 04:30:54,625] [INFO] DFAST_QC completed!
[2023-06-19 04:30:54,625] [INFO] Total running time: 0h2m6s