Question: When I run the tophat, the following error is given to me. How can I fix this error?
0
gravatar for a.hasankhani74
12 weeks ago by
a.hasankhani740 wrote:
(base) aliakbar@aliakbar-Lenovo-ideapad-320-15IKB:~/Desktop$ tophat2 -p8 --b2-very-sensitive  -G '/home/aliakbar/my data thesis & refrence genome/genome refrence/Apis_mellifera.Amel_4.5.43.gtf'   '/home/aliakbar/my data thesis & refrence genome/genome refrence/index bowtie2/Apis_mellifera.Amel_4.5.dna.toplevel'         '/home/aliakbar/my data thesis & refrence genome/SRR989675(scutellata).fastq/Scutellatatrim.fq'  

[2019-08-19 13:25:17] Beginning TopHat run (v2.1.1)
-----------------------------------------------
[2019-08-19 13:25:18] Checking for Bowtie
          Bowtie version:    2.3.4.1
[2019-08-19 13:25:19] Checking for Bowtie index files (genome)..
[2019-08-19 13:25:19] Checking for reference FASTA file
[2019-08-19 13:25:19] Generating SAM header for /home/aliakbar/my data thesis & refrence genome/genome refrence/index bowtie2/Apis_mellifera.Amel_4.5.dna.toplevel
[2019-08-19 13:25:22] Reading known junctions from GTF file
[2019-08-19 13:25:23] Preparing reads
     left reads: min. length=40, max. length=89, 3288354 kept reads (809 discarded)
[2019-08-19 13:26:03] Building transcriptome data files ./tophat_out/tmp/Apis_mellifera.Amel_4.5.43
[2019-08-19 13:26:08] Building Bowtie index from Apis_mellifera.Amel_4.5.43.fa
[2019-08-19 13:26:28] Mapping left_kept_reads to transcriptome Apis_mellifera.Amel_4.5.43 with Bowtie2 
[2019-08-19 13:32:08] Resuming TopHat pipeline with unmapped reads
[2019-08-19 13:32:08] Mapping left_kept_reads.m2g_um to genome Apis_mellifera.Amel_4.5.dna.toplevel with Bowtie2 
[2019-08-19 13:37:10] Mapping left_kept_reads.m2g_um_seg1 to genome Apis_mellifera.Amel_4.5.dna.toplevel with Bowtie2 (1/3)
[2019-08-19 13:37:53] Mapping left_kept_reads.m2g_um_seg2 to genome Apis_mellifera.Amel_4.5.dna.toplevel with Bowtie2 (2/3)
[2019-08-19 13:38:52] Mapping left_kept_reads.m2g_um_seg3 to genome Apis_mellifera.Amel_4.5.dna.toplevel with Bowtie2 (3/3)
[2019-08-19 13:40:33] Searching for junctions via segment mapping
[2019-08-19 13:41:10] Retrieving sequences for splices
[2019-08-19 13:41:17] Indexing splices
Building a SMALL index
[2019-08-19 13:41:21] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/3)
[2019-08-19 13:41:29] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/3)
[2019-08-19 13:41:40] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/3)
[2019-08-19 13:41:56] Joining segment hits
[2019-08-19 13:42:17] Reporting output tracks
-----------------------------------------------
[2019-08-19 13:43:55] A summary of the alignment counts can be found in ./tophat_out/align_summary.txt
[2019-08-19 13:43:55] Run complete: 00:18:37 elapsed
samtools view: samtools view: writing to standard output failed: Broken pipe
writing to standard output failed: Broken pipe
samtools view: error closing standard output: -1
samtools view: error closing standard output: -1
samtools view: writing to standard output failed: Broken pipe
samtools view: writing to standard output failed: Broken pipe
samtools view: error closing standard output: -1
samtools view: error closing standard output: -1
samtools view: writing to standard output failed: Broken pipe
samtools view: writing to standard output failed: Broken pipe
samtools view: error closing standard output: -1
samtools view: writing to standard output failedsamtools view: : Broken pipe
error closing standard output: -1
samtools view: error closing standard output: -1
samtools view: writing to standard output failed: Broken pipe
samtools view: writing to standard output failed: Broken pipe
samtools view: error closing standard output: -1
samtools view: error closing standard output: -1
samtools view: writing to standard output failed: Broken pipe
samtools view: samtools view: samtools view: writing to standard output failedwriting to standard output failed: Broken pipe
: Broken pipe
samtools view: samtools view: writing to standard output failed: Broken pipe
samtools view: writing to standard output failed: Broken pipe
error closing standard output: -1(base) aliakbar@aliakbar-Lenovo-ideapad-320-15IKB:~/Desktop$ 
samtools view: writing to standard output failed: Broken pipe
error closing standard output: -1
samtools view: error closing standard output: -1
samtools view: error closing standard output: -1
samtools view: error closing standard output: -1
samtools view: error closing standard output: -1
rna-seq software error • 264 views
ADD COMMENTlink modified 11 weeks ago by JC9.1k • written 12 weeks ago by a.hasankhani740
1

How much memory do you have?

ADD REPLYlink written 12 weeks ago by ATpoint26k

200 gig storage and 8 gig Ram

ADD REPLYlink written 12 weeks ago by a.hasankhani740

I would check memory usage as 8GB is not much for alignments. Maybe reduce the number of threads. Plus I suggest you follow the recommendations below, replace whitespace and & by e.g. underscores.

ADD REPLYlink modified 11 weeks ago • written 12 weeks ago by ATpoint26k
3
gravatar for swbarnes2
12 weeks ago by
swbarnes27.0k
United States
swbarnes27.0k wrote:

Why don't you start by getting rid of all those weird characters in your file names and folders. Especially the spaces.

ADD COMMENTlink written 12 weeks ago by swbarnes27.0k
2
gravatar for Antonio R. Franco
12 weeks ago by
Spain. Universidad de Córdoba
Antonio R. Franco4.2k wrote:

After reading the log, it is clear you don't have a problem with TopHat, This program ran the aligment All of the problem comes afterward, when using samtools

ADD COMMENTlink written 12 weeks ago by Antonio R. Franco4.2k

ok thanks for your help. So you think the mapping is done right for me?

ADD REPLYlink written 12 weeks ago by a.hasankhani740
1

I would recommend that you start over. Get rid of spaces and & etc from your directory/file names as recommended by others and re-run the analysis.

ADD REPLYlink written 11 weeks ago by genomax74k
2
gravatar for JC
11 weeks ago by
JC9.1k
Mexico
JC9.1k wrote:

Definitively the path used for your files is causing problems, the spaces are breaking the commands and the "&" is a symbol used to send a task to the background in Unix.

ADD COMMENTlink written 11 weeks ago by JC9.1k
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