snippy-multi ERROR: Could not find .aligned.fa/.vcf in 100AEA1 #572
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Tried running just one genome against the reference with freebayes-parallel reference/ref.txt 16 -p 2 -P 0 -C 2 -F 0.05 --min-coverage 10 --min-repeat-entropy 1.0 -q 13 -m 60 --strict-vcf -f reference/ref.fa snps.bam > snps.raw.vcfvcfstreamsort: error while loading shared libraries: libtabixpp.so.0: cannot open shared object file: No such file or directory |
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Googled the error from the snps.log and found out I needed this: |
sorry, I have the same issue with you, may i know where you have found the answer? |
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You would need to work from the error in your snp.log. I only know what worked for me.
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From: songdanyang1118 ***@***.***>
Sent: Thursday, November 30, 2023 8:27:19 PM
To: tseemann/snippy ***@***.***>
Cc: Douglas Duane Rhoads ***@***.***>; Author ***@***.***>
Subject: Re: [tseemann/snippy] snippy-multi ERROR: Could not find .aligned.fa/.vcf in 100AEA1 (Issue #572)
Googled the error from the snps.log and found out I needed this: conda install -c bioconda tabixpp==1.1.0
sorry, I have the same issue with you, may i know where you have found the answer?
The attachment is my snps log , but after i try conda install -c bioconda tabixpp==1.00 , I still have the same error, I dont konw what to do.
snps.log<https://github.com/tseemann/snippy/files/13519875/snps.log>
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@drhoads I used your solution and it resolved the same error I got. Thanks for sharing. |
Running in WSL2Ubuntu. Have 227 assemblies in contigs in .fna.
commands:
snippy-multi files.txt --ref ../prokka227/SA1.gbk --cpus 16 > runme.sh
sh ./runme.sh
symptoms:
completes all the calls to snippy but then gets the error in the call to snippy-core:
snippy-core --ref '100AEA1/ref.fa' 100AEA1 108EA1 1212-11909 1415 1552 1675 170AEA1 1710s23 1711s24 1749 1750 1751 1752 1753 1754 1755 1756 1757 1758 197EA2 215EA1 2D5_DIV0622 ARS16 ARS48 ARS57 ARS60 ARS62 ARS64 ARS65 ARS71 ARS9 AS21 ATCC43198a ATCC43198b An144 An483 An69 B05581 BB-66 BRZ_PB__bin29 CB-32 CE1 CE2 CE3 CHD112EN CHD121EN CHD139EN CHD140EN CHD141EN CHD158EN CHD161EN CHD182EN CHD192EN CHD1EN CHD222EN CHD259EN CHD261EN CHD263EN CHD265EN CHD26EN CHD270EN CHD278EN CHD285EN CHD288EN CHD293EN CHD319EN CHD341EN CHD347EN CHD37EN CHD49EN CHD62EN CHD78EN CHD83EN CHD94EN CHD96EN CIRMBP-1195 CIRMBP-1196 CIRMBP-1197 CIRMBP-1205 CIRMBP-1206 CIRMBP-1207 CIRMBP-1208 CIRMBP-1209 CIRMBP-1210 CIRMBP-1211 CIRMBP-1212 CIRMBP-1213 CIRMBP-1214 CIRMBP-1215 CIRMBP-1216 CIRMBP-1217 CIRMBP-1218 CIRMBP-1219 CIRMBP-1220 CIRMBP-1221 CIRMBP-1222 CIRMBP-1223 CIRMBP-1224 CIRMBP-1225 CIRMBP-1226 CIRMBP-1227 CIRMBP-1228 CIRMBP-1229 CIRMBP-1230 CIRMBP-1231 CIRMBP-1232 CIRMBP-1233 CIRMBP-1234 CIRMBP-1235 CIRMBP-1236 CIRMBP-1237 CIRMBP-1238 CIRMBP-1239 CIRMBP-1240 CIRMBP-1241 CIRMBP-1242 CIRMBP-1243 CIRMBP-1244 CIRMBP-1245 CIRMBP-1246 CIRMBP-1247 CIRMBP-1248 CIRMBP-1249 CIRMBP-1250 CIRMBP-1251 CIRMBP-1252 CIRMBP-1253 CIRMBP-1254 CIRMBP-1255 CIRMBP-1256 CIRMBP-1257 CIRMBP-1258 CIRMBP-1259 CIRMBP-1260 CIRMBP-1261 CIRMBP-1262 CIRMBP-1263 CIRMBP-1264 CIRMBP-1265 CIRMBP-1266 CIRMBP-1267 CIRMBP-1268 CIRMBP-1269 CIRMBP-1270 CIRMBP-1271 CIRMBP-1272 CIRMBP-1273 CIRMBP-1274 CIRMBP-1275 CIRMBP-1276 CIRMBP-1277 CIRMBP-1278 CIRMBP-1279 CIRMBP-1280 CIRMBP-1281 CIRMBP-1282 CIRMBP-1283 CIRMBP-1284 CIRMBP-1285 CIRMBP-1286 CIRMBP-1287 CIRMBP-1288 CIRMBP-1289 CIRMBP-1290 CIRMBP-1291 CIRMBP-1292 CIRMBP-1293 CIRMBP-1294 CIRMBP-1295 CIRMBP-1296 CIRMBP-1297 CIRMBP-1298 CIRMBP-1299 CIRMBP-1300 CIRMBP-1301 CIRMBP-1302 CIRMBP-1303 CIRMBP-1304 CL-1 D-104 DSM20682a DSM20682b E1062 ERR3414584 ESM13AIC1 ESM13C1 ESM877AIC1 G-29 LB5753 LB5754 LB5756 LB5759 LB5800 LB5836 LB5840 LB5843 LB5856 LB5857 LB5860 LB5864 LB5872 LB5876 LB5880 LB5916 LB5922 LB5923 LB5924 LB5925 LB5926 LB5927 LBV_466 NCTC12421 NCTC12422 PS1 PS10 PS11 PS2 PS3 PS5 PS6 PS7 PS8 SA1 SA2 SA3 WCA-380 mag_170
Last of outptu:
This is snippy-core 4.6.0
Obtained from http://github.com/tseemann/snippy
Enabling bundled tools for linux
Found any2fasta - /home/drhoads/miniconda3/envs/r-ldweaver/bin/any2fasta
Found samtools - /home/drhoads/miniconda3/envs/r-ldweaver/bin/samtools
Found minimap2 - /home/drhoads/miniconda3/envs/r-ldweaver/bin/minimap2
Found bedtools - /home/drhoads/miniconda3/envs/r-ldweaver/bin/bedtools
Found snp-sites - /home/drhoads/miniconda3/envs/r-ldweaver/bin/snp-sites
Saving reference FASTA: core.ref.fa
This is any2fasta 0.4.2
Opening '100AEA1/ref.fa'
Detected FASTA format
Read 37690 lines from '100AEA1/ref.fa'
Wrote 1 sequences from FASTA file.
Processed 1 files.
Done.
Loaded 1 sequences totalling 2261297 bp.
Will mask 0 regions totalling 0 bp ~ 0.00%
ERROR: Could not find .aligned.fa/.vcf in 100AEA1
The snippy output created a folder for 100AEA1 that contains:
.:
total 97272
92148 fake_reads.fq
0 files.txt
0 ref.fa
0 ref.fa.fai
0 reference
5116 snps.bam
4 snps.bam.bai
4 snps.log
0 snps.raw.vcf
./reference:
total 7376
0 genomes
0 ref
2248 ref.fa
4 ref.fa.amb
0 ref.fa.ann
2212 ref.fa.bwt
0 ref.fa.fai
556 ref.fa.pac
1108 ref.fa.sa
1232 ref.gff
4 ref.txt
12 snpeff.config
./reference/genomes:
total 2248
2248 ref.fa
./reference/ref:
total 1296
500 genes.gff.gz
796 snpEffectPredictor.bin
Seems there are a couple of times this issue has come up in these archives but has been closed without a clear resolution.
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