Question: Tophat 2 alignment error
0
gravatar for cjvegame
3.2 years ago by
cjvegame0
United States
cjvegame0 wrote:

Hello everyone, I am trying to aligned a paired end sequences using tophat2. Everything works fine with the practice data I am using, but when I used it with my real data it gives me the error below. Has anybody encountered this problem before?

Code:

tophat2 -p 12 -r 60 --library-type fr-firststrand --rg-id=PQ_3_day_1_Abdomen --rg-sample=BSTRES_02-3d15_PQ_3_day_1_Abdomen_CGATGT_L001 -o /media/ubuntu/"TOSHIBA EXT"/Rna_Seq_2_attempts/trimmed/PQ_3_day_1_Abdomen -G /media/ubuntu/"TOSHIBA EXT"/Rna_Seq_2_attempts/refs/Apis/fasta/gene_Apis.gtf --transcriptome-index /media/ubuntu/"TOSHIBA EXT"/Rna_Seq_2_attempts/tophat/index /media/ubuntu/"TOSHIBA EXT"/Rna_Seq_2_attempts/bwt/Apis/Apis /media/ubuntu/"TOSHIBA EXT"/Rna_Seq_2_attempts/trimmed/BSTRES_02-3d15_PQ_3_day_1_Abdomen_CGATGT_L001__1.fastq.gz /media/ubuntu/"TOSHIBA EXT"/Rna_Seq_2_attempts/trimmed/BSTRES_02-3d15_PQ_3_day_1_Abdomen_CGATGT_L001__2.fastq.gz

Input

[2015-12-28 10:15:53] Beginning TopHat run (v2.1.0)
-----------------------------------------------
[2015-12-28 10:15:53] Checking for Bowtie
          Bowtie version:     2.2.6.0
[2015-12-28 10:15:53] Checking for Bowtie index files (transcriptome)..
[2015-12-28 10:15:53] Checking for Bowtie index files (genome)..
[2015-12-28 10:15:53] Checking for reference FASTA file
[2015-12-28 10:15:53] Generating SAM header for /media/ubuntu/TOSHIBA EXT/Rna_Seq_2_attempts/bwt/Apis/Apis
[2015-12-28 10:15:53] Reading known junctions from GTF file
[2015-12-28 10:15:54] Preparing reads
     left reads: min. length=25, max. length=112, 14848766 kept reads (26376 discarded)
    right reads: min. length=25, max. length=112, 14871677 kept reads (3465 discarded)
[2015-12-28 10:25:39] Using pre-built transcriptome data..
[2015-12-28 10:25:39] Mapping left_kept_reads to transcriptome gene_Apis with Bowtie2
    [FAILED]
Error running bowtie:
Warning: Output file '-' was specified without -S.  This will not work in future Bowtie 2 versions.  Please use -S instead.
Warning: Could not open read file "EXT/Rna_Seq_2_attempts/tophat/index/gene_Apis" for reading; skipping...
Error: No input read files were valid
(ERR): bowtie2-align exited with value 1

 

This is also my first post in this forum so not sure if I gave as much information as possible. So please tell me if you need more.

 

rna-seq alignment assembly • 1.4k views
ADD COMMENTlink modified 3.2 years ago • written 3.2 years ago by cjvegame0
0
gravatar for vivekbhr
3.2 years ago by
vivekbhr510
Germany
vivekbhr510 wrote:

Hi

Most probably it's because you have a space in the file name "TOSHIBA EXT"..Remove it and try again ..

ADD COMMENTlink written 3.2 years ago by vivekbhr510
0
gravatar for Antonio R. Franco
3.2 years ago by
Spain. Universidad de Córdoba
Antonio R. Franco4.0k wrote:

Try the using of the TAB key to introduce the PATH at the time of defining the files and archives, and you will avoid many problems

ADD COMMENTlink written 3.2 years ago by Antonio R. Franco4.0k
0
gravatar for cjvegame
3.2 years ago by
cjvegame0
United States
cjvegame0 wrote:

Hahaha.. I knew it was something that trivial. I appreciate the input from both of you. This problem is fixed.

ADD COMMENTlink written 3.2 years ago by cjvegame0
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