Tophat - getQRead() failed

Question

[alexander.nash]

I am trying to align paired end read data to the zebrafish transcriptome and for each sample I encounter the following error in the tophat_reports step:

Error: singleton getQRead() failed for id# 1627678

(id# differs for each sample)

The command I used was:

/usr/bin/tophat --library-type fr-firststrand -p 8 -N 2 -o ../tophat_alignments/SRR372798 -G ../annotations/Danio_rerio.Zv9.75.gtf Zv9 SRR372798_1_val_1.fq SRR372798_2_val_2.fq

I can't seem to find any other reports of this error.

Does anyone have any idea what might be causing this?

[young yu]

hi, I also meet this problem, had you solve it

[davichen]

I also have the same problem, running tophat v2.0.13. This error seems to make my input into tophat really small, 100000 reads or so out of the 30 million in the fastq.

Anyone run into how to fix the problem? Does using less or 1 core help?

[davichen]

Pretty late to the game, but hope this helps anyone who comes by

I had the same problem using v2.0.13 of TopHat. Changing to the latest TopHat version fixed the issue. No idea why but it worked. Also updated Bowtie too and was able to avoid error.

Answer 1

[davichen]

Pretty late to the game, but hope this helps anyone who comes by

I had the same problem using v2.0.13 of TopHat. Changing to the latest TopHat version fixed the issue. No idea why but it worked. Also updated Bowtie too and was able to avoid error.