oushujun
commented
2 years ago Seems like your folder has write limitations. Can you enter the work directory and try this: touch test perl -i -nle 'print test' test
Thanks, Shujun
On Wed, Mar 2, 2022 at 10:14 PM wensulin93 @.***> wrote:
Thu Mar 3 10:47:04 CST 2022 Intact LTR-RT found: 5451
Cannot complete in-place edit of GCA_018127125.1_RGv1.1_genomic.fna.mod.ltrTE.pass.clust: failed to rename work file 'XXgZJrPD' to 'GCA_018127125.1_RGv1.1_genomic.fna.mod.ltrTE.pass.clust': Operation not permitted at -e line 1, <> line 8572. Thu Mar 3 11:02:25 CST 2022 Module 6: Start to analyze truncated LTR-RTs... Truncated LTR-RTs without the intact version will be retained in the LTR-RT library. Use -notrunc if you don't want to keep them.
Thu Mar 3 11:02:25 CST 2022 207 truncated LTR-RTs found Cannot complete in-place edit of GCA_018127125.1_RGv1.1_genomic.fna.mod.ltrTE.trunc: failed to rename work file 'XXpib7qa' to 'GCA_018127125.1_RGv1.1_genomic.fna.mod.ltrTE.trunc': Operation not permitted at -e line 1, <> line 828. ERROR: RepeatMasker is not running properly! Please check the file GCA_018127125.1_RGv1.1_genomic.fna.mod.ltrTE.mask.lib and GCA_018127125.1_RGv1.1_genomic.fna.mod.ltrTE.trunc and test run: RepeatMasker -e ncbi -q -pa 4 -no_is -norna -nolow -div 40 -lib GCA_018127125.1_RGv1.1_genomic.fna.mod.ltrTE.mask.lib -cutoff 225 GCA_018127125.1_RGv1.1_genomic.fna.mod.ltrTE.trunc Please report errors to https://github.com/oushujun/LTR_retriever/issues Program halt!
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Wenwen012345
Thu Mar 3 15:09:18 CST 2022 Intact LTR-RT found: 167
Cannot complete in-place edit of 1.fna.mod.ltrTE.pass.clust: failed to rename work file 'XXWfRHkf' to '1.fna.mod.ltrTE.pass.clust': Operation not permitted at -e line 1, <> line 520. Thu Mar 3 15:09:35 CST 2022 Module 6: Start to analyze truncated LTR-RTs... Truncated LTR-RTs without the intact version will be retained in the LTR-RT library. Use -notrunc if you don't want to keep them.
Thu Mar 3 15:09:35 CST 2022 46 truncated LTR-RTs found Cannot complete in-place edit of 1.fna.mod.ltrTE.trunc: failed to rename work file 'XXvwJG9h' to '1.fna.mod.ltrTE.trunc': Operation not permitted at -e line 1, <> line 190. ERROR: RepeatMasker is not running properly! Please check the file 1.fna.mod.ltrTE.mask.lib and 1.fna.mod.ltrTE.trunc and test run: RepeatMasker -e ncbi -q -pa 20 -no_is -norna -nolow -div 40 -lib 1.fna.mod.ltrTE.mask.lib -cutoff 225 1.fna.mod.ltrTE.trunc Please report errors to https://github.com/oushujun/LTR_retriever/issues Program halt!
manager@bl8vbox[ncbi-genomes-2022-02-28] RepeatMasker -e ncbi -q -pa 20 -no_is -norna -nolow -div 40 -lib 1.fna.mod.ltrTE.mask.lib -cutoff 225 1.fna.mod.ltrTE.trunc RepeatMasker version 4.1.2-p1 Search Engine: NCBI/RMBLAST [ 2.2.27+ ] Using Custom Repeat Library: 1.fna.mod.ltrTE.mask.lib
analyzing file 1.fna.mod.ltrTE.trunc FastaDB::_cleanIndexAndCompact(): Fasta file contains a sequence identifier which is too long ( max id length = 50 ) at /home/manager/miniconda3/bin/RepeatMasker line 739.