Question: tophat2 "Broken pipe error"
2.4 years ago by
ahmad mousavi • 470
Royan Institute, Tehran, Iran
ahmad mousavi • 470 wrote:
I have downloaded the most recent versions of Samtools, Tophat2 and Bowtie2 on a Ubuntu 16.04 server.
I have got below error, How can I fix it?
[2017-09-07 16:20:09] Mapping right_kept_reads.m2g_um_seg4 to genome Homo_sapiens with Bowtie2 (4/5) [2017-09-07 16:22:09] Mapping right_kept_reads.m2g_um_seg5 to genome Homo_sapiens with Bowtie2 (5/5) [2017-09-07 16:25:34] Searching for junctions via segment mapping [2017-09-07 16:58:56] Retrieving sequences for splices [2017-09-07 17:25:39] Indexing splices [2017-09-07 17:26:39] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/5) gzip: stdout: Broken pipe [FAILED] Error running bowtie: Warning: gzbuffer added in zlib v22.214.171.124. Unable to change buffer size from default of 8192. Segmentation fault (core dumped) (ERR): bowtie2-align exited with value 139
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