tophat2 "Broken pipe error"

Question

[ahmad mousavi]

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

[Satyajeet Khare]

What is the command that you used?

[ahmad mousavi]

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

[Satyajeet Khare]

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.

[ahmad mousavi]

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

[Satyajeet Khare]

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.