error2：Regarding the Search Function

[ATPasepoly]

Hello.
When I perform a search operation, MMSeq2 dies after write error2, “Failed to execute tmp/8060895184449876350/blastp.sh with error 2.”
Anyone knows why this happens?
Thanks.

[milot-mirdita]

I've seen people report this issue before if they placed MMseqs2's tmp directory into a directory that was mounted with noexec. E.g. some Linux distributions mount /tmp as noexec, and if you place MMseqs2's tmp dir within /tmp you would see this error.

If this is the case, specifying a different directory might work.

[ATPasepoly]

Thank you for your reply! I made some changes based on your suggestions, but I'm still encountering error2.
I'm running the project on a Windows system. I tried changing the tmp directory, but I'm still encountering error2.
Do you happen to know what might be causing this? Many thanks!

[milot-mirdita]

Is this WSL or the Cygwin windows binary?

The former will likely be much more reliable, we do very little testing beyond the automated continuous integration for the Cygwin binary

[milot-mirdita]

Also please post the full log

[ATPasepoly]

Thank you! Below are the logs and operational status.
We use the Cygwin windows binary

Logs:
Failed to execute /cygdrive/d/workmmseqs/tmp/8806684838454580593/createindex.sh with error 2.

operational status:
createindex targetDB D:\workmmseqs\tmp -v 3

MMseqs Version: 8cc5ce3
Seed substitution matrix aa:VTML80.out,nucl:nucleotide.out
k-mer length 0
Alphabet size aa:21,nucl:5
Compositional bias 1
Compositional bias scale 1
Max sequence length 65535
Max results per query 300
Mask residues 1
Mask residues probability 0.9
Mask lower case residues 0
Mask lower letter repeating N times 0
Spaced k-mers 1
Spaced k-mer pattern
Sensitivity 7.5
k-score seq:0,prof:0
Check compatible 0
Search type 0
Split database 0
Split memory limit 0
Index subset 0
Verbosity 3
Threads 20
Min codons in orf 30
Max codons in length 32734
Max orf gaps 2147483647
Contig start mode 2
Contig end mode 2
Orf start mode 1
Forward frames 1,2,3
Reverse frames 1,2,3
Translation table 1
Translate orf 0
Use all table starts false
Offset of numeric ids 0
Create lookup 0
Compressed 0
Overlap between sequences 0
Sequence split mode 1
Header split mode 0
Translation mode 0
Strand selection 1
Remove temporary files false

Thanks again.

[milot-mirdita]

Does createindex targetDB tmp -v 3 work? (same directory)?

[ATPasepoly]

Thank you for your suggestions! Below are the results after I modified the code as you advised:
It seems I've encountered error2 again. Do you know why this error2 occurred this time?
Thank you so much!

MMseqs Version: 8cc5ce3
Database type 0
Shuffle input database true
Createdb mode 0
Write lookup file 1
Offset of numeric ids 0
Threads 20
Compressed 0
Mask residues 0
Mask residues probability 0.9
Mask lower case residues 0
Mask lower letter repeating N times 0
Use GPU 0
Verbosity 3

Converting sequences
[574186] 3s 330ms
Time for merging to targetDB_h: 0h 0m 0s 193ms
Time for merging to targetDB: 0h 0m 0s 254ms
Database type: Aminoacid
Time for processing: 0h 0m 5s 842ms

createindex targetDB tmp -v 3

MMseqs Version: 8cc5ce3
Seed substitution matrix aa:VTML80.out,nucl:nucleotide.out
k-mer length 0
Alphabet size aa:21,nucl:5
Compositional bias 1
Compositional bias scale 1
Max sequence length 65535
Max results per query 300
Mask residues 1
Mask residues probability 0.9
Mask lower case residues 0
Mask lower letter repeating N times 0
Spaced k-mers 1
Spaced k-mer pattern
Sensitivity 7.5
k-score seq:0,prof:0
Check compatible 0
Search type 0
Split database 0
Split memory limit 0
Index subset 0
Verbosity 3
Threads 20
Min codons in orf 30
Max codons in length 32734
Max orf gaps 2147483647
Contig start mode 2
Contig end mode 2
Orf start mode 1
Forward frames 1,2,3
Reverse frames 1,2,3
Translation table 1
Translate orf 0
Use all table starts false
Offset of numeric ids 0
Create lookup 0
Compressed 0
Overlap between sequences 0
Sequence split mode 1
Header split mode 0
Translation mode 0
Strand selection 1
Remove temporary files false

createindex targetDB tmp -v 3

MMseqs Version: 8cc5ce3
Seed substitution matrix aa:VTML80.out,nucl:nucleotide.out
k-mer length 0
Alphabet size aa:21,nucl:5
Compositional bias 1
Compositional bias scale 1
Max sequence length 65535
Max results per query 300
Mask residues 1
Mask residues probability 0.9
Mask lower case residues 0
Mask lower letter repeating N times 0
Spaced k-mers 1
Spaced k-mer pattern
Sensitivity 7.5
k-score seq:0,prof:0
Check compatible 0
Search type 0
Split database 0
Split memory limit 0
Index subset 0
Verbosity 3
Threads 20
Min codons in orf 30
Max codons in length 32734
Max orf gaps 2147483647
Contig start mode 2
Contig end mode 2
Orf start mode 1
Forward frames 1,2,3
Reverse frames 1,2,3
Translation table 1
Translate orf 0
Use all table starts false
Offset of numeric ids 0
Create lookup 0
Compressed 0
Overlap between sequences 0
Sequence split mode 1
Header split mode 0
Translation mode 0
Strand selection 1
Remove temporary files false

Failed to execute tmp/1074567755743095492/createindex.sh with error 2.