tophat2 error: std out broken pipe

[ns_seqingAns]

Hello,

I am trying to use the latest versions of tophat2 (v2.1), bowtie2(v2.2.6) and samtools (v1.2).

I get an broken pipe error, that I do not quite understand. (this did appear to work when I changed only the tophat2 to v2.0.9)

My command:
tophat -r 100 --mate-std-dev 50 -p 4 --library-type fr-firststrand -o clean -G hg38/gencode.v23.annotation.gtf --transcriptome-index=hg38/clean_hg38/transcriptome_data/known hg38/clean_hg38/hg38_clean 1.fastq.gz 2.fastq.gz

(This worked with old versions: tophat2(v2.0.9), bowtie2(v2.1), samtools(v0.1.18))

cat logs/tophat.log

[2015-10-27 13:56:15] Beginning TopHat run (v2.1.0)
-----------------------------------------------
[2015-10-27 13:56:15] Checking for Bowtie
Bowtie version: 2.2.6.0
[2015-10-27 13:56:16] Checking for Bowtie index files (transcriptome)..
[2015-10-27 13:56:16] Checking for Bowtie index files (genome)..
[2015-10-27 13:56:16] Checking for reference FASTA file
[2015-10-27 13:56:16] Generating SAM header for ../../../Genomes/hg38/clean_hg38/hg38_clean
[2015-10-27 13:56:29] Reading known junctions from GTF file
[2015-10-27 13:57:07] Preparing reads
[FAILED]
Error running 'prep_reads'
gzip: stdout: Broken pipe

cat logs/prep_reads.log
prep_reads v2.1.0 (exported)
---------------------------

gzip: stdout: Broken pipe

gzip: stdout: Broken pipe

What is wrong here that I need to rectify? Any help and/or advice is much appreciated.

Many Thanks,
NS

[GenoMax]

TopHat was incompatible with new Samtools (v.1.x), which was why older samtools is included in the source. I would start by dropping samtools back to the older version and then running this command again.