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Hi everyone,
I am using tophat to analysis a RNA-seq library with read lenght=36. My command is:
tophat -p 4 --coverage-search -G TAIR10_GTF.gtf -o SRR074263.aln arabidopsis.index SRR074263.fastq
and I got an error like this:
[2013-02-22 00:46:14] Beginning TopHat run (v2.0.3)
-----------------------------------------------
[2013-02-22 00:46:14] Checking for Bowtie
Bowtie version: 2.0.0.7
[2013-02-22 00:46:14] Checking for Samtools
Samtools version: 0.1.18.0
[2013-02-22 00:46:14] Checking for Bowtie index files
[2013-02-22 00:46:14] Checking for reference FASTA file
[2013-02-22 00:46:14] Generating SAM header for arabidopsis.index
format: fastq
quality scale: phred33 (default)
[2013-02-22 00:46:14] Reading known junctions from GTF file
[2013-02-22 00:46:16] Preparing reads
left reads: min. length=36, max. length=36, 4126043 kept reads (73452 discarded)
[2013-02-22 00:46:57] Creating transcriptome data files..
[2013-02-22 00:47:02] Building Bowtie index from TAIR10_GTF.fa
[2013-02-22 00:50:19] Mapping left_kept_reads to transcriptome TAIR10_GTF with Bowtie2
[2013-02-22 00:53:05] Converting left_kept_reads.m2g to genomic coordinates (map2gtf)
[2013-02-22 00:53:43] Resuming TopHat pipeline with unmapped reads
Warning: you have only one segment per read.
If the read length is greater than or equal to 45bp,
we strongly recommend that you decrease --segment-length to about half the read length because TopHat will work better with multiple segments
[2013-02-22 00:53:48] Mapping left_kept_reads.m2g_um to genome arabidopsis.index with Bowtie2
[2013-02-22 00:54:40] Searching for junctions via segment mapping
Coverage-search algorithm is turned on, making this step very slow
Please try running TopHat again with the option (--no-coverage-search) if this step takes too much time or memory.
[FAILED]
Error: segment-based junction search failed with err =127
Can anyone help me?
I am using tophat to analysis a RNA-seq library with read lenght=36. My command is:
tophat -p 4 --coverage-search -G TAIR10_GTF.gtf -o SRR074263.aln arabidopsis.index SRR074263.fastq
and I got an error like this:
[2013-02-22 00:46:14] Beginning TopHat run (v2.0.3)
-----------------------------------------------
[2013-02-22 00:46:14] Checking for Bowtie
Bowtie version: 2.0.0.7
[2013-02-22 00:46:14] Checking for Samtools
Samtools version: 0.1.18.0
[2013-02-22 00:46:14] Checking for Bowtie index files
[2013-02-22 00:46:14] Checking for reference FASTA file
[2013-02-22 00:46:14] Generating SAM header for arabidopsis.index
format: fastq
quality scale: phred33 (default)
[2013-02-22 00:46:14] Reading known junctions from GTF file
[2013-02-22 00:46:16] Preparing reads
left reads: min. length=36, max. length=36, 4126043 kept reads (73452 discarded)
[2013-02-22 00:46:57] Creating transcriptome data files..
[2013-02-22 00:47:02] Building Bowtie index from TAIR10_GTF.fa
[2013-02-22 00:50:19] Mapping left_kept_reads to transcriptome TAIR10_GTF with Bowtie2
[2013-02-22 00:53:05] Converting left_kept_reads.m2g to genomic coordinates (map2gtf)
[2013-02-22 00:53:43] Resuming TopHat pipeline with unmapped reads
Warning: you have only one segment per read.
If the read length is greater than or equal to 45bp,
we strongly recommend that you decrease --segment-length to about half the read length because TopHat will work better with multiple segments
[2013-02-22 00:53:48] Mapping left_kept_reads.m2g_um to genome arabidopsis.index with Bowtie2
[2013-02-22 00:54:40] Searching for junctions via segment mapping
Coverage-search algorithm is turned on, making this step very slow
Please try running TopHat again with the option (--no-coverage-search) if this step takes too much time or memory.
[FAILED]
Error: segment-based junction search failed with err =127
Can anyone help me?
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