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
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
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