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YangLab / CLEAR

direct comparison of circular and linear RNA expression
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Error in run clear_quant when "start tophat-fusion mapping" #3

Closed Scathacheng closed 4 years ago

Scathacheng commented 4 years ago

Hi. Here is the bug, Traceback (most recent call last): File "/zs32/home/jcdai/zouhan/ChIP/miniconda2/bin/clear_quant", line 9, in load_entry_point('CLEAR==1.0.0', 'console_scripts', 'clear_quant')() File "build/bdist.linux-x86_64/egg/src/run.py", line 256, in main File "build/bdist.linux-x86_64/egg/src/run.py", line 159, in fusion_align File "/zs32/home/jcdai/zouhan/ChIP/miniconda2/lib/python2.7/subprocess.py", line 223, in check_output raise CalledProcessError(retcode, cmd, output=output) subprocess.CalledProcessError: Command '['tophat2', '-o', '/hw2600/JcDai/02ChineseBrain/01CLEAR/fusion', '-p', '5', '--fusion-search', '--keep-fasta-order', '--bowtie1', '--no-coverage-search', '/zs32/home/jcdai/04circRNA/03database/bowtie1hg38index/hg38.bowtie1_index', '/hw2600/JcDai/02ChineseBrain/01CLEAR/hisat/unmapped.fq']' returned non-zero exit status 1

I think the problem is that unmapped.fq have no map with index. How do you have any idea to solve this problem? thanks!

xingma commented 4 years ago

It may be related to compatibility of different tools. bowtie (v0.12.9), tophat2 (v2.0.12) and hisat2 (v2.0.5) works well. You may try these versions.