Question: Error while mapping raw reads to genome using tophat2
0
gravatar for Bioinfonext
2.9 years ago by
Bioinfonext180
Korea
Bioinfonext180 wrote:

Deal All,

I getting error while mapping raw reads to genome using tophat2: Please suggest how to solve it.

[2017-01-15 05:09:52] Resuming TopHat pipeline with unmapped reads

[2017-01-15 05:09:52] Mapping left_kept_reads.m2g_um to genome genome_index with Bowtie2

[2017-01-15 06:32:14] Mapping left_kept_reads.m2g_um_seg1 to genome genome_index with Bowtie2 (1/5)

[2017-01-15 06:45:17] Mapping left_kept_reads.m2g_um_seg2 to genome genome_index with Bowtie2 (2/5)

[2017-01-15 06:59:09] Mapping left_kept_reads.m2g_um_seg3 to genome genome_index with Bowtie2 (3/5)

[2017-01-15 07:13:04] Mapping left_kept_reads.m2g_um_seg4 to genome genome_index with Bowtie2 (4/5)

[2017-01-15 07:26:16] Mapping left_kept_reads.m2g_um_seg5 to genome genome_index with Bowtie2 (5/5)

[2017-01-15 07:35:22] Mapping right_kept_reads.m2g_um to genome genome_index with Bowtie2

[2017-01-15 09:04:09] Mapping right_kept_reads.m2g_um_seg1 to genome genome_index with Bowtie2 (1/5)

[2017-01-15 09:20:25] Mapping right_kept_reads.m2g_um_seg2 to genome genome_index with Bowtie2 (2/5)

[2017-01-15 09:35:23] Mapping right_kept_reads.m2g_um_seg3 to genome genome_index with Bowtie2 (3/5)

[2017-01-15 09:50:10] Mapping right_kept_reads.m2g_um_seg4 to genome genome_index with Bowtie2 (4/5)

[2017-01-15 10:05:27] Mapping right_kept_reads.m2g_um_seg5 to genome genome_index with Bowtie2 (5/5)

[2017-01-15 10:17:04] Searching for junctions via segment mapping

[FAILED]

Error: segment-based junction search failed with err =127

/home/yog/software/tophat-2.1.1/src/segment_juncs: error while loading shared libraries: libboost_thread.so.1.62.0:

cannot open shared object file: No such file or directory

rna-seq • 1.2k views
ADD COMMENTlink written 2.9 years ago by Bioinfonext180
1

It appears that you don't have boost installed. But, I think it's probably faster and easier to install and run BBMap instead of TopHat.

ADD REPLYlink written 2.9 years ago by Brian Bushnell17k
1

Tophat is deprecated and instead you should use it's successor HISAT2 or alternative aligners such as STAR or BBMap.

ADD REPLYlink written 2.9 years ago by WouterDeCoster42k

Please share the link for HISAT2 and cammand line to install it on cento OS linux platform.

ADD REPLYlink written 2.9 years ago by Bioinfonext180
1

Please do some work/searching on your own. The manual is quite clear.

ADD REPLYlink written 2.9 years ago by WouterDeCoster42k

Thanks, I am able to install it.

ADD REPLYlink written 2.9 years ago by Bioinfonext180

See, wasn't so hard.

ADD REPLYlink written 2.9 years ago by WouterDeCoster42k

Where/how did you download/install TopHat?

ADD REPLYlink written 2.9 years ago by genomax75k

Now I am not sure from where I downloaded tophat2. Can you suggest how to uninstall it and is it possible to install boost library with tophat2?

If yes, please share the link and installation cammand line.

ADD REPLYlink written 2.9 years ago by Bioinfonext180

There should be no install needed if you download pre-compiled binary for TopHat. But that said you should consider switching to a newer program from ones suggested in this thread.

ADD REPLYlink modified 2.9 years ago • written 2.9 years ago by genomax75k
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