STREME Complex regular subexpression recursion limit (32766) exceeded

[Kyra Fetter]

Hello,

I am trying to run STREME (meme-5.5.0) on a set of 10929 sequences. I do not provide control sequences so the negative sequences are shuffled primary sequences. Here is the command I use: 

streme --oc motif/streme/fore_short.bkgd_random --minw 5 --p motif/input_fasta_s.fa

STREME generates an empty HTML file. I get the error "Complex regular subexpression recursion limit (32766) exceeded at /.../packages/meme_suite/meme/lib/meme-5.5.0/perl/CheckingSAX.pm line 151, <$fh> line 60.". This message is followed by "Failed to write HTML output due to errors processing the XML: motif@site_distr has invalid value", where this invalid value appears to be a count matrix. Here are some snapshots of the end of the log. Please note that there are non-zero values in the matrix that are not shown in the images.

STREME does successfully generate 159 best sequences which are output to streme.txt. These are followed by the message "Stopped because 3 consecutive motifs exceeded the p-value threshold (0.05)." Here is a snapshot:

If helpful, when I run make check, I pass all tests:

I am using perl v5.26.3.

I'd appreciate some guidance on how I may resolve this issue. Thank you for the help!

[cegrant]

This was a bug in the STREME conversion of XML into HML for very long sequences. It was fixed in the 5.5.2 release. We'd recommend that you upgraded to the latest version. The current release is 5.5.5.

[Kyra Fetter]

Thank you, I will upgrade to the latest version