DiscordantPairs

[MarineBergot]

Hi! I'm trying to run TEfinder but unfortunatly i can't succeed, i always have this error message, do you have any idea what is wrong?
thanks!

TEfinder -alignment OC1F1X6_aln_ref_v6_bwa2.mark.RG.bam -fa /data/Home/CM248032/Maureen/CreinhardtiiCC_4532/v6.1/assembly/CreinhardtiiCC_4532_707_v6.0.fa -gtf /data/Home/CM248032/Maureen/CreinhardtiiCC_4532/v6.1/assembly/all_TEs.gff -te List_of_TEs.txt -out GTF -intermed yes
[bam_sort_core] merging from 15 files and 1 in-memory blocks...
ven. mars 3 16:56:02 CET 2023 Alignment file sorted successfully.

ven. mars 3 17:02:32 CET 2023 Alignments are filtered - secondary and supplementary alignments have been removed.

ven. mars 3 17:02:32 CET 2023 Transposon analysis for Bill has started

ven. mars 3 17:02:32 CET 2023 Transposon analysis for Gulliver has started

ven. mars 3 17:02:32 CET 2023 Transposon analysis for MRC1 has started

/data/Home/CM248032/TEfinder/TEfinder: ligne62: ${currdir}/${line}_TE.gff : redirection ambiguë
ven. mars 3 17:02:32 CET 2023 Transposon analysis for Pioneer1 has started

ven. mars 3 17:02:32 CET 2023 Transposon analysis for Tcr3 has started

/data/Home/CM248032/TEfinder/TEfinder: ligne62: ${currdir}/${line}_TE.gff : redirection ambiguë
/data/Home/CM248032/TEfinder/TEfinder: ligne62: ${currdir}/${line}_TE.gff : redirection ambiguë
ven. mars 3 17:02:32 CET 2023 Transposon analysis for Tcr1 has started

ven. mars 3 17:02:32 CET 2023 Transposon analysis for TOC1 has started

/data/Home/CM248032/TEfinder/TEfinder: ligne62: ${currdir}/${line}_TE.gff : redirection ambiguë
/data/Home/CM248032/TEfinder/TEfinder: ligne62: ${currdir}/${line}_TE.gff : redirection ambiguë
ven. mars 3 17:02:32 CET 2023 Transposon analysis for REM1 has started

ven. mars 3 17:02:32 CET 2023 Transposon analysis for TOC2 has started

/data/Home/CM248032/TEfinder/TEfinder: ligne62: ${currdir}/${line}_TE.gff : redirection ambiguë
/data/Home/CM248032/TEfinder/TEfinder: ligne62: ${currdir}/${line}_TE.gff : redirection ambiguë
/data/Home/CM248032/TEfinder/TEfinder: ligne62: ${currdir}/${line}_TE.gff : redirection ambiguë
ven. mars 3 17:02:32 CET 2023 Individual TE GFF has been created for TOC2

/data/Home/CM248032/TEfinder/TEfinder: ligne65: bedtools : commande introuvable
ven. mars 3 17:02:32 CET 2023 All transposons are processed. Finalizing...

[E::hts_open_format] Failed to open file "TEfinder_20230303164719//_DiscordantPairs.bam" : No such file or directory
samtools merge: fail to open "TEfinder_20230303164719//_DiscordantPairs.bam": No such file or directory