csv.Error: field larger than field limit (131072)

[lvbakker]

Hi,
I am trying to run OMGS to do scaffolding with a Bionano DLE-1 .cmap and a pacbio assembly as reference.
After running for a while, I get this message:

Reading file: /home/bionanosolve/input.fasta
---------------read .xmap file-------------------
Traceback (most recent call last):
File "/home/bionanosolve/external/OMGS/scripts/main.py", line 105, in
main()
File "/home/bionanosolve/external/OMGS/scripts/main.py", line 102, in main
stitch(paras_file, fasta_list_file, output_dir, REFALIGNER, GLPSOL, DIGEST, optmap_list_file)
File "/home/bionanosolve/external/OMGS/scripts/stitch.py", line 79, in stitch
core_operations(REFALIGNER, DIGEST, GLPSOL, sub_dir, refaligner_dir, input_fasta_file, optmap_list, optmap_type_list, refaligner_prefix, mtp_fasta_file, mtp_fasta_file_chname, unaligned_fasta_file, lowconf_fasta_file)
File "/home/bionanosolve/external/OMGS/scripts/core_operations.py", line 35, in core_operations
core(optmap_list, input_fasta_file, out_list, out2_list, sub_dir, GLPSOL)
File "/home/bionanosolve/external/OMGS/scripts/core.py", line 514, in core
alms, optmap,chimeric_pairs = pre_process(i, optmap_file, myfile, myfile2, output_dir, min_confidence)
File "/home/bionanosolve/external/OMGS/scripts/core.py", line 235, in pre_process
row = csvreader.next()
_csv.Error: field larger than field limit (131072)

This seems like an easy to fix issue. I will change the field_size_limit and try again, or maybe the other option presented in this topic (https://stackoverflow.com/questions/15063936/csv-error-field-larger-than-field-limit-131072) I will submit a pull request if this works.