remote command line BLAST job ends in CPU error and gives MBEDTLS version mismatch
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11 weeks ago


I am trying to perform a remote blastn search through blast+ from the command line (on Linux Ubuntu). This results in an XML file with the following error message:

internal_error: (Severe Error) Blast search error: Details: search failed. # Informational Message: [blastsrv4.REAL]: Error: CPU usage limit was exceeded, resulting in SIGXCPU (24). No hits found

I have tried several (not too long) sequences. I used the following command:

blastn -db nt -query sequence.fasta -evalue 0.05 -word_size 6 -max_target_seqs 10 -out blast_output.xml -outfmt 5 -remote.

I know that a CPU error can happen when your search has a lot of sequences or a very long sequence, but sequence.fasta contains the sequence with accession code FS507595 which has 489bp. I also tried it with a different sequence, but had the same result. (I ran it with existing sequences, because I want to be sure that there should be hits) I also tried running the command from a different IP, which did not help.

Also, before blast starts running, I get the following message:

Critical: [blastn] External MBEDTLS version mismatch: 2.16.2 headers vs. 2.16.3 runtime.

I tried reinstalling blast+ and its dependencies, which did not help.

Does anyone have an idea on how to solve this? Your help would be much appreciated!

blastn mbedtls blast linux blast+ • 460 views
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There may be an issue at NCBI's end. I would suggest waiting until tomorrow and checking back. You are using the latest blast+ available?

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I noticed that I was not installing the latest version of blast+ when using apt, so I installed it manually. This helped with the MBEDTLS error, but I still get the CPU error. (I tried running it two days ago, so I am afraid waiting much longer won't help.)


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