terminate called after throwing an instance of 'std::runtime_error' what(): BUG: dead end in get_color_set_id

[dbu008]

Hi Themisto developers,
After running themisto build I wanted to use pseudoaligment.
I am getting an error:
terminate called after throwing an instance of 'std::runtime_error'
what(): BUG: dead end in get_color_set_id

The command is:
themisto pseudoalign --query-file /cluster/work/users/.../Repair_4/1/abc_1.repair.fastq.gz --out-file /cluster/work/users/.../mSWEEP/1/abc_R1_Kleb_pseudo_alignment.aln --rc --index-prefix /cluster/work/users/.../mSWEEP/themisto_index/themisto --temp-dir /cluster/work/users/.../mSWEEP/tmp_sweep --n-threads 8 --sort-output-lines --gzip-output

Could you tell me where is the problem coming from?

I am using themisto_linux_v3.2.0.

Best,
Dorota

[jnalanko]

I would like to try to reproduce the crash to debug it. Is the data used in the indexing available?

In the meantime, as a quick workaround, constructing the index with the flag -d 1 might solve your problem. This makes the index larger, but does not affect the pseudoalignment answers.

[dbu008]

Thank you jnalanko for a fast answer.
The data are published, however the assemblies are taken from two different papers and connected with other defults. However, I can send you the file with a pleasure. Could you tell me how I can send? It is relatively a big file.

I will create the index with -d 1 and see how it goes.

Thx:)

[jnalanko]

Could you upload it to Dropbox or Google drive and share the link?

[dbu008]

I will share with the Google drive link.
Sorry it takes so long.

[https://drive.google.com/file/d/1o9DkYThgIk3Vynj9ryQXPG3MwpTByayD/view?usp=share_link]

Please let me know if it works and I can delete the file from google?

[jnalanko]

Downloaded! Thank you. You can delete the file now. One more request: could please you give the command you used to build the index?

[dbu008]

Thank you for all the help:)
I am still running with the -d 1 as you mentioned.
The command I used previously is:
themisto build --k 31 --input-file /cluster/all_sequences_extra.fasta.gz --sequence-colors --index-prefix /cluster/themisto --temp-dir /cluster/tmp_themisto --mem-gigas 2 --n-threads 4

Best,
Dorota

[dbu008]

Hi again,
I finished the themisto index with the -d 1 and I am still getting the same error in pseudoalignment part.

terminate called after throwing an instance of 'std::runtime_error'
what(): BUG: dead end in get_color_set_id
caught signal: 6
Cleaning up temporary files
Aborting

[jnalanko]

That is strange. We're still working on this. Hang tight.

[jnalanko]

I think I found the problem! The following sequence in your input contains an empty line at the end, which messes up our FASTA parser:

AP007209.1_Bacillus_cereus_C7401_genomic_DA_complete_genome

So, to fix this, please remove ALL empty lines from the input fasta file.

For future, I made it so that the parser now detects this situation, and crashes with an error message: 782009d

This error message will be included in the next Themisto release, which will be out shortly.

[jnalanko]

We could also make it so that empty lines would just be ignored, but for example the FASTA spec at NCBI says that no empty lines are allowed in the format, so maybe it's better to crash with an error message because empty lines could indicate some problem with the data.

https://blast.ncbi.nlm.nih.gov/doc/blast-topics/

[dbu008]

Thank You!!!!
Thank You!!!

I will remove all blank lines, I did not know I have it in the input file at all!
I will run the index soon.

Thank you, have a great day
Dorota

[jnalanko]

Let me know if it works. In that case, I will close the issue.

[jnalanko]

Hi Dorota, it's been two weeks. Is your issue fixed?