Error running bowtie:

[sambhav2mishra]

Dear Daehwankimlab I'm using tophat2 (v.2.1.0) and tophat-fusion for circularRNA detection by circexplorer2 pipeline. tophat2 alignment ran well, but the problem lies in tophat-fusion, it gives the following error when i tried to run tophat fusion:

[2019-09-17 16:53:51] Beginning TopHat run (v2.1.0)

[2019-09-17 16:53:51] Checking for Bowtie Bowtie version: 1.2.3.0 [2019-09-17 16:53:51] Checking for Bowtie index files (genome).. [2019-09-17 16:53:51] Checking for reference FASTA file Warning: Could not find FASTA file /userdata/Dramaresh/fastq_dir/GMA_alignment/bowtie1_index/bowtie1_index.fa [2019-09-17 16:53:51] Reconstituting reference FASTA file from Bowtie index Executing: /userdata/Dramaresh/tools/bowtie-1.2.3-linux-x86_64/bowtie-inspect /userdata/Dramaresh/fastq_dir/GMA_alignment/bowtie1_index/bowtie1_index > /userdata/Dramaresh/fastq_dir/GMA_alignment/tophat_fusion/tmp/bowtie1_index.fa [2019-09-17 16:55:26] Generating SAM header for /userdata/Dramaresh/fastq_dir/GMA_alignment/bowtie1_index/bowtie1_index [2019-09-17 16:55:30] Preparing reads left reads: min. length=19, max. length=151, 12158285 kept reads (20688 discarded) Warning: short reads (<20bp) will make TopHat quite slow and take large amount of memory because they are likely to be mapped in too many places [2019-09-17 16:58:36] Mapping left_kept_reads to genome bowtie1_index with Bowtie [FAILED] Error running bowtie: Error while flushing and closing output terminate called after throwing an instance of 'int'

my command for tophat fusion: time tophat2 -o /userdata/Dramaresh/test_run/GMA/tophat_fusion -p 32 --fusion-search --keep-fasta-order --bowtie1 --no-coverage-search /userdata/Dramaresh/fastq_dir/bowtie1_index/bowtie1_index /userdata/Dramaresh/test_run/GMA/tophat/unmapped.fastq 2>/userdata/Dramaresh/test_run/GMA/tophat_fusion.log

Kindly help me, your help will surely be appreciated by our lab memebers. Thank you Sambhav

[muhammadharoon786]

did you find any solution of it? please respond!