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malonge / RagTag

Tools for fast and flexible genome assembly scaffolding and improvement
MIT License
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Error in patch command #139

Open akhtarmzn2010 opened 2 years ago

akhtarmzn2010 commented 2 years ago

Hi Sir,

I got the same error after run both patch command (A & B): please suggest how i can solve the problem.

A. ragtag.py patch scaffold_RE2/ragtag.scaffold.fasta /media/d/D1/GBS_analysis/NGSEP/reference/AABB_BrapaZ1_BnI100/AABB_BrapaZ1_BnI100.fasta B. ragtag.py patch scaffold_RE2/ragtag.scaffold.fasta reference/AABB_BrapaZ1_BnI100.fasta --aligner nucmer -o ragtag_output2 --debug -d 200000

[E::fai_retrieve] Failed to retrieve block: unexpected end of file Traceback (most recent call last): File "/home/d/anaconda3/bin/ragtag_rename.py", line 70, in main() File "/home/d/anaconda3/bin/ragtag_rename.py", line 61, in main print(fai.fetch(reference)) File "pysam/libcfaidx.pyx", line 319, in pysam.libcfaidx.FastaFile.fetch ValueError: failure when retrieving sequence on 'B8'

adriludwig commented 1 month ago

Hi! I'm wondering if you find and remember what the problem was. I'm getting the same message. Thanks