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YangLab / CIRCexplorer2

circular RNA analysis toolset
http://circexplorer2.readthedocs.org/
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Error in TopHat-Fusion #60

Closed smarhon closed 2 years ago

smarhon commented 2 years ago

The "CIRCexplorer2 align" crashes during tophat-fusion.

Any suggestion?

Here is the message Error: cannot map unmapped reads with TopHat-Fusion!

Log file message: [2022-02-19 19:04:04] Checking for reference FASTA file Warning: Could not find FASTA file HCT116_PBS/HCT116_PBS_CIRCexplorer2_2/bowtie1_index/hg38.fa.fa [2022-02-19 19:04:04] Reconstituting reference FASTA file from Bowtie index Executing: /cluster/tools/software/bowtie/1.1.2/bowtie-inspect HCT116_PBS/HCT116_PBS_CIRCexplorer2_2/bowtie1_index/hg38.fa > HCT116_PBS_CIRCexplorer2_2/tophat_fusion/tmp/hg38.fa.fa [FAILED] Error: bowtie-inspect returned an error bowtie-inspect: reference.h:549: int BitPairReference::getStretch(uint32_t*, size_t, size_t, sizet) const: Assertion `cumRefOff[i+1] == 0 || cumRefOff_[i+1] > toff' failed.

smarhon commented 2 years ago

This problem was solved by using bowtie/1.0.0.