When I run the tophat, the following error is given to me. How can I fix this error?

Question

[a.hasankhani74]

(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

[ATpoint]

How much memory do you have?

[a.hasankhani74]

200 gig storage and 8 gig Ram

[ATpoint]

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.

Answer 1

[swbarnes2]

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

Answer 2

[Antonio R. Franco]

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

[a.hasankhani74]

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

[GenoMax]

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.

Answer 3

[JC]

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.