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bowhan / piPipes

piRNA pipeline collection developed in the Zamore Lab and ZLab in UMass Med School
GNU General Public License v3.0
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TRANSGENE_MAPPING_DIR not set in piPipes_GenomeSeq.sh #11

Closed blaiseli closed 9 years ago

blaiseli commented 9 years ago

Dear Bo Han,

I tried to run the piPipes dna pipeline and noticed the following in the output:

[bam_parse_region] fail to determine the sequence name.
[main_samview] region "chrXHet:-29-971" specifies an unknown reference name. Continue anyway.
[2015-09-17 11:49:00 CEST] Mapping transgene insertion by TEMP
piPipes_GenomeSeq.sh: line 291: /transgene.genome.bed: Permission denied
[samopen] SAM header is present: 15 sequences.
(ERR): bowtie2-align exited with value 141

Looking at piPipes_GenomeSeq.sh, it seems that the "Permission denied" error is due to the fact that line 109 (of current version) is commented:

# TRANSGENE_MAPPING_DIR=transgene_mapping && mkdir -p $TRANSGENE_MAPPING_DIR

This variable not being defined make it impossible for bedtools_piPipes bamtobed (line 291) to write its output: $TRANSGENE_MAPPING_DIR/transgene.genome.bed is just /transgene.genome.bed, and consequently not writeable.

bowhan commented 9 years ago

Hi, Thank you very much for reporting this bug. It has been fixed.