$ clear_quant -1 206_1.fq.gz -2 206_2.fq.gz -g /library/hg19.fa -i /library/hg19.fa -j /library/hg19.fa -G /library/hg19.genes.gtf -o 206 -p 40
###Parameters:
Namespace(bowtie1='/library/hg19.fa', genome='/library/hg19.fa', gtf='/library/hg19.genes.gtf', hisat='/library/hg19.fa', m1='206_1.fq.gz', m2='206_2.fq.gz', output='206', thread='40')
###Parameters
###Start hisat2 mapping
# start to get sp sites for hisat mapping
# start to align to genome by hisat
# get mapped and unmapped reads
# sort bam file
# index bam file
###End hisat2 mapping
###Start tophat-fusion mapping
Traceback (most recent call last):
File "/software/anaconda2/bin/clear_quant", line 11, in <module>
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 "/software/anaconda2/lib/python2.7/subprocess.py", line 223, in check_output
raise CalledProcessError(retcode, cmd, output=output)
subprocess.CalledProcessError: Command '['tophat2', '-o', '206/fusion', '-p', '40', '--fusion-search', '--keep-fasta-order', '--bowtie1', '--no-coverage-search', '/library/hg19.fa', '206/hisat/unmapped.fq']' returned non-zero exit status 1
Hi,
In the mapping with tophat-fusion step, I get the below error:
I am not sure what the error says and how to fix it. Can you help?
@xingma