gff2bed fails with "Non-numeric start coordinate. "
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14 months ago

I am running gff2bed 2.4.41 and get the error:

Warning: If your Wiggle data is a significant portion of available system memory, use the --max-mem and --sort-tmpdir options, or use --do-not-sort to disable post-conversion sorting. See --help for more information.
Non-numeric start coordinate.  See line 1085469 in -.
(remember that chromosome names should not contain spaces.)
Error: Stage [Sorted BED to stdout] failed -- exit status [256 | 1]

This line is no different from every other line is this GFF file. It is tab delimited and generated by AUGUSTUS. It is specifically:

Camer_chr1 AUGUSTUS tts 23621380 23621380 . - . transcript_id "g2302.t1"; gene_id "g2302";

Any suggestions appreciated

bedops • 651 views
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Any reason why you can't use awk or cut to extract a BED-formatted file?

awk '{print $1 "\t" $4 "\t" $5}' file.gff > file.bed
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