make_rna_mas.sh error

[MrGao1997]

when I ran prediction, an error occurred. how can I fix it? Thanks!

/home/gt/RF2NA/RoseTTAFold2NA/input_prep/make_rna_msa.sh: 第 9 行： [: 缺少 `]' sed: 无法读取 rfam1.db.aa: 没有那个文件或目录 sed: 无法读取 rfam1.db.ab: 没有那个文件或目录 sed: 无法读取 rfam1.db.ac: 没有那个文件或目录 sed: 无法读取 rfam1.db.ad: 没有那个文件或目录 sed: 无法读取 rfam1.db.ae: 没有那个文件或目录 sed: 无法读取 rfam1.db.af: 没有那个文件或目录 cat: 'rfam1.db.': 没有那个文件或目录 rm: 无法删除'rfam1.db.': 没有那个文件或目录 sed: 无法读取 rfam2.db.aa: 没有那个文件或目录 sed: 无法读取 rfam2.db.ab: 没有那个文件或目录 sed: 无法读取 rfam2.db.ac: 没有那个文件或目录 cat: 'rfam2.db.': 没有那个文件或目录 rm: 无法删除'rfam2.db.': 没有那个文件或目录 blastn: symbol lookup error: /home/gt/anaconda3/envs/pymol24_py37/RF2NA/bin/../lib/ncbi-blast+/./libxcompress.so: undefined symbol: ZSTD_DCtx_loadDictionary head: 无法打开'blastn1.tab' 读取数据: 没有那个文件或目录 sed: 无法读取 blastn1.db.: 没有那个文件或目录 cat: 'blastn1.db.': 没有那个文件或目录 rm: 无法删除'blastn1.db.': 没有那个文件或目录 rm: 无法删除'blastn1.list.split.': 没有那个文件或目录 rm: 无法删除'blastn1.tab': 没有那个文件或目录 blastn: symbol lookup error: /home/gt/anaconda3/envs/pymol24_py37/RF2NA/bin/../lib/ncbi-blast+/./libxcompress.so: undefined symbol: ZSTD_DCtx_loadDictionary head: 无法打开'blastn2.tab' 读取数据: 没有那个文件或目录 sed: 无法读取 blastn2.db.: 没有那个文件或目录 cat: 'blastn2.db.': 没有那个文件或目录 rm: 无法删除'blastn2.db.': 没有那个文件或目录 rm: 无法删除'blastn2.list.split.': 没有那个文件或目录 rm: 无法删除'blastn2.tab': 没有那个文件或目录

Error: Failed to autodetect format for target sequence database db

Alignment input open failed. couldn't open nhmmer.a2m for reading

• 16:47:23.890 INFO: Input file = RNA.wquery.unfilt.afa

• 16:47:23.890 INFO: Output file = RNA.afa

• 16:47:23.891 ERROR: In /opt/conda/conda-bld/hhsuite_1690046720367/work/src/hhalignment.cpp:502: Read:

• 16:47:23.891 ERROR: No sequences found in file RNA.wquery.unfilt.afa

grep: RNA.afa: 没有那个文件或目录

Error: Failed to autodetect format for target sequence database db

Alignment input open failed. couldn't open nhmmer.a2m for reading

• 16:47:24.154 INFO: Input file = RNA.wquery.unfilt.afa

• 16:47:24.154 INFO: Output file = RNA.afa

• 16:47:24.155 ERROR: In /opt/conda/conda-bld/hhsuite_1690046720367/work/src/hhalignment.cpp:502: Read:

• 16:47:24.155 ERROR: No sequences found in file RNA.wquery.unfilt.afa

Error: Failed to autodetect format for target sequence database db

Alignment input open failed. couldn't open nhmmer.a2m for reading

• 16:47:24.333 INFO: Input file = RNA.wquery.unfilt.afa

• 16:47:24.333 INFO: Output file = RNA.afa

• 16:47:24.334 ERROR: In /opt/conda/conda-bld/hhsuite_1690046720367/work/src/hhalignment.cpp:502: Read:

• 16:47:24.334 ERROR: No sequences found in file RNA.wquery.unfilt.afa

Error: Failed to autodetect format for target sequence database db

Alignment input open failed. couldn't open nhmmer.a2m for reading

• 16:47:24.467 INFO: Input file = RNA.wquery.unfilt.afa

• 16:47:24.467 INFO: Output file = RNA.afa

• 16:47:24.467 ERROR: In /opt/conda/conda-bld/hhsuite_1690046720367/work/src/hhalignment.cpp:502: Read:

• 16:47:24.467 ERROR: No sequences found in file RNA.wquery.unfilt.afa

Error: Failed to autodetect format for target sequence database db

Alignment input open failed. couldn't open nhmmer.a2m for reading

• 16:47:24.607 INFO: Input file = RNA.wquery.unfilt.afa

• 16:47:24.607 INFO: Output file = RNA.afa

• 16:47:24.608 ERROR: In /opt/conda/conda-bld/hhsuite_1690046720367/work/src/hhalignment.cpp:502: Read:

• 16:47:24.608 ERROR: No sequences found in file RNA.wquery.unfilt.afa

Error: Failed to autodetect format for target sequence database db

Alignment input open failed. couldn't open nhmmer.a2m for reading

• 16:47:24.752 INFO: Input file = RNA.wquery.unfilt.afa

• 16:47:24.752 INFO: Output file = RNA.afa

• 16:47:24.753 ERROR: In /opt/conda/conda-bld/hhsuite_1690046720367/work/src/hhalignment.cpp:502: Read:

• 16:47:24.753 ERROR: No sequences found in file RNA.wquery.unfilt.afa

rm: 无法删除'nhmmer.a2m': 没有那个文件或目录

[AngelaAmari]

Hi, can you check whether you also have a WARNING: Maximum number 65535 of sequences exceeded in file warning in your file make_msa.rna_binding_protein.stderr? Thanks!

[MrGao1997]

Hi, alex. I have checked the file you mentioned and there was an error you said. So how can I deal with it?

在 2023-12-12 02:25:06，"AngelaAmari" @.***> 写道：

Hi, can you check whether you also have a WARNING: Maximum number 65535 of sequences exceeded in file warning in your file make_msa.rna_binding_protein.stderr? Thanks!

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: @.***>

[AngelaAmari]

OK I have solved the 65535 problem by editing the bash script a bit, but I am still having the rfam1.db.* problem… not sure whether I have put the databases at a wrong place…

[MrGao1997]

So how to fix this problem?

---- Replied Message ---- | From | @.> | | Date | 12/13/2023 06:45 | | To | @.> | | Cc | @.>@.> | | Subject | Re: [uw-ipd/RoseTTAFold2NA] make_rna_mas.sh error (Issue #68) |

OK I have solved the 65535 problem by editing the bash script a bit, but I am still having the rfam1.db.* problem… not sure whether I have put the databases at a wrong place…

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: @.***>

[AngelaAmari]

So how to fix this problem? … ---- Replied Message ---- | From | @.> | | Date | 12/13/2023 06:45 | | To | @.> | | Cc | @.>@.> | | Subject | Re: [uw-ipd/RoseTTAFold2NA] make_rna_mas.sh error (Issue #68) | OK I have solved the 65535 problem by editing the bash script a bit, but I am still having the rfam1.db.* problem… not sure whether I have put the databases at a wrong place… — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: @.***>

Hi Gao, For me, it seems like the rnacentral.fasta file is missing so the database was not correctly built. Maybe check whether your gunzip -c rnacentral_species_specific_ids.fasta.gz | makeblastdb -in - -dbtype nucl -parse_seqids -out rnacentral.fasta -title "RNACentral" cmd was correctly executed and go from there.