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isovic / racon

Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads. http://genome.cshlp.org/content/early/2017/01/18/gr.214270.116 Note: This was the original repository which will no longer be officially maintained. Please use the new official repository here:
https://github.com/lbcb-sci/racon
MIT License
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[bioparser::FastaParser] error: invalid file format! #145

Closed astulaaa closed 4 years ago

astulaaa commented 4 years ago

Hello, I was running minimap2 followed by racon, while minimap seems to work properly its output does not seem to be recognized by racon. The command line as follows:

minimap2 -t 31 -x map-ont s_reads3.srp.fa ../../Resources/raw.combined.fa > ula.mapping_1st.paf racon -t 31 -m 8 -x -6 -g -8 -w 500 ../../Resources/raw.combined.fa ula.mapping_1st.paf s_reads3.srp.fa > ula.racon_1st.fa

log file comes with a message like this: terminate called after throwing an instance of 'std::invalid_argument' what(): [bioparser::FastaParser] error: invalid file format! /var/spool/gridengine/execd/job_scripts/213619: line 10: 92317 Aborted What could be the problem and with which input file? Also most of the same files were utilized by minimap2 so they are unlikely to be damaged thank you

rvaser commented 4 years ago

Hello, which Racon version are you using? There is maybe something unusual in either of your fasta files, or there is a bug in the parser.

Best regards, Robert

astulaaa commented 4 years ago

racon version v1.4.7 Thanks

rvaser commented 4 years ago

Can you check if there is an empty sequence in either of the fasta files?

astulaaa commented 4 years ago

I have found the issue, wrong input file. Thanks!