Error during second step

[jenniferlu717]

Hi, I got the following error during the second step. I'm using the downloaded miniSeq+H database

Outputting mappings with adjusted alignment qualities. mashmap: src/meta/taxonomy.h:64: std::string meta::taxonomy::getFirstNonXNode(std::string): Assertion nodeID.find("x") == std::string::npos' failed. Aborted (core dumped)

Command Lines: mashmap mapDirectly --all -r miniSeq+H/DB.fa -q sample1.fastq -o sample1_metamaps_classification mashmap classify --mappings sample1_metamaps_classification --DB miniSeq+H

[AlexanderDilthey]

Hi Jennifer, Thank you for spotting this. I've added a debug message that should reveal what's going on. Could you pull from GitHub and recompile? Alternatively you could also send me the FASTQ.

[jenniferlu717]

It still gives me the same error as before? I'm not sure why. I reinstalled the code.

[AlexanderDilthey]

The error is not fixed, but it should print additional debug information.

Can you try a complete rebuild with 'make clean' and then 'make metamaps' (the makefile error is fixed now), and then use the metamaps command instead of mashmap? It should then print the variables 'runningNodeID' and 'nodeID'.

[jenniferlu717]

It doesn't print the values unfortunately.

EM round 30 EM round 30, read << 60000 / 69799 Log likelihood: -1.52751e+06 Improvement: 0.985079 Relative : 0.999999 Outputting mappings with adjusted alignment qualities. metamaps: src/meta/taxonomy.h:71: std::string meta::taxonomy::getFirstNonXNode(std::string): Assertion nodeID.find("x") == std::string::npos' failed. Aborted (core dumped)

[AlexanderDilthey]

Hi Jen, the bug should be fixed now (the original one, and not the bug in the debug function ;-))

[jenniferlu717]

It works now! Thanks :)