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I have a text file which has been previously readable in linux, then I modified some names in it manually on windows and now when I am running it on linux (using samtools), it cannot find exactly those names that I have changed manually

[faidx] Failed to fetch sequence in Mariner-1_Dhyd-L#DNA/Tc1-Mariner

I suspect this is the windows to linux problem? the current encoding of the file is

file -i filname.lib
filename.lib: text/plain; charset=us-ascii

then I tried to change it to Utf8

iconv -i us-ascii -t UTF8 filename.lib > filname-encode.lib

though the file encoding has still remained the same and still same errors. how should I fix it

xyz0o
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  • It would be helpful to know what tool(s) you used to "modify some names manually on Windows", as well as the original encoding of the file. Some Windows editors add a Byte Order Mark (BOM) sequence to the beginning of the file, which can confuse other tools. If the file now contains a mix of encodings, you may need to go back to the original file, but I'm a little surprised everything isn't just ASCII. – Tom Morris Feb 22 '22 at 00:26
  • I used notepad for manual modification. I checked the whole encoding line by line in notepad++ in case there is windows characters in it or there is extra space...thought surprisingly I didn't find any encoding problem, just removing the headers that were complained about fixed it! – xyz0o Feb 22 '22 at 14:31

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