Question: tophat2 "Broken pipe error"
0
gravatar for ahmad mousavi
2.4 years ago by
ahmad mousavi470
Royan Institute, Tehran, Iran
ahmad mousavi470 wrote:

Dear all,

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?

Thanks

[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 v1.2.3.5. Unable to change buffer size from default of 8192.
Segmentation fault (core dumped)
(ERR): bowtie2-align exited with value 139
rna-seq ngs • 1.3k views
ADD COMMENTlink written 2.4 years ago by ahmad mousavi470

What is the command that you used?

ADD REPLYlink written 2.4 years ago by Satyajeet Khare1.5k

for f in *_1.fastq; do tophat2 -p 4 -G Homo_sapiens.gtf -o ${f/_1.fastq/} Homo_sapiens $f ${f/_1/_2}; done

ADD REPLYlink modified 2.4 years ago • written 2.4 years ago by ahmad mousavi470

Can you print the output of this loop to make sure that files are recognized properly? That will make it easy for others to troubleshoot.

P.S. If you are providing GTF file, you might want to build transcriptome index first.

ADD REPLYlink modified 2.4 years ago • written 2.4 years ago by Satyajeet Khare1.5k

tophat2 -p 4 -G Homo_sapiens.gtf -o sample Homo_sapiens s1.fastq s2.fastq

ADD REPLYlink written 2.4 years ago by ahmad mousavi470

Can you confirm availability of space and threads and that there are not issues with reading writing privileges?

On a related note, if you are starting from scratch, you might want to start with HiSAT2, STAR etc.

ADD REPLYlink written 2.4 years ago by Satyajeet Khare1.5k
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