Tophat2 Error gzip pipe broken? zipped file empty?

Question

[biogirl04]

Hi everyone,

I have the following error when using Tophat2:

readlink: illegal option -- f
usage: readlink [-n] [file ...]

[2018-07-06 11:36:32] Beginning TopHat run (v2.1.1)
-----------------------------------------------
[2018-07-06 11:36:32] Checking for Bowtie
  Bowtie version:    2.3.4.1
[2018-07-06 11:36:32] Checking for Bowtie index files (genome)..
[2018-07-06 11:36:32] Checking for reference FASTA file
Warning: Could not find FASTA file readsindex/readsFASTA.fa
[2018-07-06 11:36:32] Reconstituting reference FASTA file from Bowtie index
 Executing: /usr/local/bin/bowtie2-inspect readsindex/readsFASTA > orftp3_out/tmp/readsFASTA.fa
[2018-07-06 11:36:34] Generating SAM header for readsindex/readsFASTA
[2018-07-06 11:36:34] Preparing reads
left reads: min. length=75, max. length=10506, 15483 kept reads (0 discarded)
[2018-07-06 11:36:38] Mapping left_kept_reads to genome readsFASTA with Bowtie2 
Error: could not open writer pipe gzip -cf - < orftp3_out/tmp/left_kept_reads_seg124.fq.z

Apparently the left_kept_reads_seg124.fq.z file is empty. How can I get around this? Also when I tried exported gzip to path:

$export PATH=$PATH:/gzip
$echo PATH

PATH

That is what happens. I don't know what's going on. Any help would be greatly appreciated!!

Thank you!!

[h.mon]

There is a message (readlink: illegal option -- f) suggesting your command is wrong, but you didn'tshow us your command.

$export PATH=$PATH:/gzip $echo PATH PATH

This is essentially unreadable. Could you format the above snippet properly? And if the $ preceding the commands are just the shell prompt, please remove it from the commands. The way it stands now, I don't know if you are issuing echo or $echo, or export or $export - correct are without $. When assigning a value to the variable you don't use the $, but when referencing the variable, you do use the $. So it is:

export PATH=/some/path:$PATH
echo $PATH

Finally, what is /gzip in export PATH=$PATH:/gzip? The PATH variable should contain paths to where the executables are located, not the executables themselves.

[biogirl04]

Thanks for your help!

This is the command that I had run:

tophat2 -r 300 -o this1_out readsfastaindex/readsF orf.fastq

For some reason, no matter what I do, I keep getting the same error as above. Any ideas?

[WouterDeCoster]

How did you install tophat2?

[biogirl04]

I don't completely remember but I either did: sudo apt-get install tophat or I downloaded from https://ccb.jhu.edu/software/tophat/index.shtml

[WouterDeCoster]

You should know that the old 'Tuxedo' pipeline of Tophat(2) and Cufflinks is no longer the "advisable" tool for RNA-seq analysis. The software is deprecated/ in low maintenance and should be replaced by HISAT2, StringTie and ballgown. See this paper: Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown. There are also other alternatives, including alignment with STAR and bbmap, or pseudo-alignment using salmon followed by DESEq2 or edgeR.

Please stop using Tophat https://t.co/Es4ohxOEyx Cole and I developed the method in *2008*. It was greatly improved in TopHat2 then HISAT & HISAT2. There is no reason to use it anymore. I have been saying this for years yet it has more citations this year than last #methodsmatter

— Lior Pachter (@lpachter) December 2, 2017

[Jeffin Rockey]

Is the issue resolved?

Instead of $echo PATH

give $echo $PATH to get the path.

[1589537403]

Have you solved this problem? I met the same problem，thanks for your help。