tophat could not find bowtie index files - Page 2

GenoMax · 03-20-2015, 11:49 AM

Use this file instead of the GTF file you are using: /path_to/Drosophila_melanogaster/Ensembl/BDGP5.25/Annotation/Genes/genes.gtf

lupid · 03-20-2015, 12:48 PM

don't work u.u
tophat -p 2 -G ./genes.gtf -o ./C1_R1_thout_new ./genome ./GSM794483_C1_R1_1.fq ./GSM794483_C1_R1_2.fq

[2015-03-20 16:13:45] Beginning TopHat run (v2.0.13)
-----------------------------------------------
[2015-03-20 16:13:45] Checking for Bowtie
Bowtie version: 2.2.5.0
[2015-03-20 16:13:45] Checking for Bowtie index files (genome)..
[2015-03-20 16:13:45] Checking for reference FASTA file
Warning: Could not find FASTA file ./genome.fa
[2015-03-20 16:13:45] Reconstituting reference FASTA file from Bowtie index
Executing: /home/tomas/bin/bowtie2-inspect ./genome > ./C1_R1_thout_new/tmp/genome.fa
[2015-03-20 16:13:54] Generating SAM header for ./genome
[2015-03-20 16:13:55] Reading known junctions from GTF file
[2015-03-20 16:13:59] Preparing reads
left reads: min. length=75, max. length=75, 11607353 kept reads (0 discarded)
right reads: min. length=75, max. length=75, 11607353 kept reads (0 discarded)
[2015-03-20 16:18:58] Building transcriptome data files ./C1_R1_thout_new/tmp/genes
[2015-03-20 16:19:07] Building Bowtie index from genes.fa
[FAILED]
Error: Couldn't build bowtie index with err = 1
tomas@HP-Pavilion:~/bin/c1$

GenoMax · 03-20-2015, 01:03 PM

Can you show a current long listing of the files in directory?

Code:

$ ls -lh

As shown on page 570 of Nature protocols article it may be best to create at least this softlink in your current directory. I am assuming you have copied other files locally (will know from the listing above).

Code:

$ ln -s /path_to/Drosophila_melanogaster/Ensembl/BDGP5.25/Sequence/Bowtie2Index/genome.fa .

lupid · 03-20-2015, 01:10 PM

tomas@HP-Pavilion:~/bin/c1$ ls -lh
total 4,4G
drwxrwxr-x 4 tomas tomas 4,0K mar 20 10:32 C1_R1_thout
drwxrwxr-x 4 tomas tomas 4,0K mar 20 14:57 C1_R1_thout_new
drwxrwxr-x 3 tomas tomas 4,0K mar 20 15:54 Drosophila_melanogaster
-rwxrwxr-x 1 tomas tomas 117M mar 15 2012 genes.fa
-rwxrwxr-x 1 tomas tomas 54M may 23 2014 genes.gtf
-rwxrwxr-x 1 tomas tomas 43M abr 10 2012 genome.1.bt2
-rwxrwxr-x 1 tomas tomas 29M abr 10 2012 genome.2.bt2
-rwxrwxr-x 1 tomas tomas 143 abr 10 2012 genome.3.bt2
-rwxrwxr-x 1 tomas tomas 29M abr 10 2012 genome.4.bt2
lrwxrwxrwx 1 tomas tomas 29 mar 20 16:51 genome.fa -> ../WholeGenomeFasta/genome.fa
-rwxrwxr-x 1 tomas tomas 43M abr 10 2012 genome.rev.1.bt2
-rwxrwxr-x 1 tomas tomas 29M abr 10 2012 genome.rev.2.bt2
-rw-rw-r-- 1 tomas tomas 1,8G mar 20 10:34 GSM794483_C1_R1_1.fq
-rw-rw-r-- 1 tomas tomas 1,8G mar 20 10:35 GSM794483_C1_R1_2.fq
-rw-rw-r-- 1 tomas tomas 138M sep 13 2011 GSM794483_C1_R1_2.fq.gz
-rw-rw-r-- 1 tomas tomas 325M sep 9 2011 GSM794483_C1_R1.accepted_hits.bam
-rw-rw-r-- 1 tomas tomas 14M mar 20 11:02 GSM794483_C1_R1.transcripts.gff
tomas@HP-Pavilion:~/bin/c1$

I don't know if I did what you propouse, but when I try, this happend
tomas@HP-Pavilion:~/bin/c1$ ln -s /home/tomas/bin/c1/Drosophila_melanogaster/Ensembl/BDGP5.25/Sequence/Bowtie2Index/genome.fa .
ln: fallo al crear el enlace simbólico «./genome.fa»: El archivo ya existe
tomas@HP-Pavilion:~/bin/c1$

GenoMax · 03-20-2015, 01:15 PM

This link is not pointing to the right directory:

lrwxrwxrwx 1 tomas tomas 29 mar 20 16:51 genome.fa -> ../WholeGenomeFasta/genome.fa

So do this

Code:

$ unlink genome.fa

ONLY if above does not work then

Code:

$ rm -f genome.fa

Then create the soft link again

Code:

$ ln -s /home/tomas/bin/c1/Drosophila_melanogaster/Ensembl/BDGP5.25/Sequence/Bowtie2Index/genome.fa .

Try tophat.

lupid · 03-20-2015, 01:31 PM

after try both options still didn't work
here my console
tomas@HP-Pavilion:~/bin/c1$ rm -f genome.fa
tomas@HP-Pavilion:~/bin/c1$ ln -s /home/tomas/bin/c1/Drosophila_melanogaster/Ensembl/BDGP5.25/Sequence/Bowtie2Index/genome.fa .
tomas@HP-Pavilion:~/bin/c1$ ls -lh
total 4,4G
drwxrwxr-x 4 tomas tomas 4,0K mar 20 10:32 C1_R1_thout
drwxrwxr-x 4 tomas tomas 4,0K mar 20 14:57 C1_R1_thout_new
drwxrwxr-x 3 tomas tomas 4,0K mar 20 15:54 Drosophila_melanogaster
-rwxrwxr-x 1 tomas tomas 117M mar 15 2012 genes.fa
-rwxrwxr-x 1 tomas tomas 54M may 23 2014 genes.gtf
-rwxrwxr-x 1 tomas tomas 43M abr 10 2012 genome.1.bt2
-rwxrwxr-x 1 tomas tomas 29M abr 10 2012 genome.2.bt2
-rwxrwxr-x 1 tomas tomas 143 abr 10 2012 genome.3.bt2
-rwxrwxr-x 1 tomas tomas 29M abr 10 2012 genome.4.bt2
lrwxrwxrwx 1 tomas tomas 91 mar 20 17:23 genome.fa -> /home/tomas/bin/c1/Drosophila_melanogaster/Ensembl/BDGP5.25/Sequence/Bowtie2Index/genome.fa
-rwxrwxr-x 1 tomas tomas 43M abr 10 2012 genome.rev.1.bt2
-rwxrwxr-x 1 tomas tomas 29M abr 10 2012 genome.rev.2.bt2
-rw-rw-r-- 1 tomas tomas 1,8G mar 20 10:34 GSM794483_C1_R1_1.fq
-rw-rw-r-- 1 tomas tomas 1,8G mar 20 10:35 GSM794483_C1_R1_2.fq
-rw-rw-r-- 1 tomas tomas 138M sep 13 2011 GSM794483_C1_R1_2.fq.gz
-rw-rw-r-- 1 tomas tomas 325M sep 9 2011 GSM794483_C1_R1.accepted_hits.bam
-rw-rw-r-- 1 tomas tomas 14M mar 20 11:02 GSM794483_C1_R1.transcripts.gff
tomas@HP-Pavilion:~/bin/c1$ tophat -p 2 -G ./genes.gtf -o ./C1_R1_thout_new ./genome ./GSM794483_C1_R1_1.fq ./GSM794483_C1_R1_2.fq

[2015-03-20 17:24:20] Beginning TopHat run (v2.0.13)
-----------------------------------------------
[2015-03-20 17:24:20] Checking for Bowtie
Bowtie version: 2.2.5.0
[2015-03-20 17:24:20] Checking for Bowtie index files (genome)..
[2015-03-20 17:24:20] Checking for reference FASTA file
[2015-03-20 17:24:20] Generating SAM header for ./genome
[2015-03-20 17:24:21] Reading known junctions from GTF file
[2015-03-20 17:24:24] Preparing reads
left reads: min. length=75, max. length=75, 11607353 kept reads (0 discarded)
right reads: min. length=75, max. length=75, 11607353 kept reads (0 discarded)
[2015-03-20 17:29:19] Building transcriptome data files ./C1_R1_thout_new/tmp/genes
[2015-03-20 17:29:26] Building Bowtie index from genes.fa
[FAILED]
Error: Couldn't build bowtie index with err = 1
tomas@HP-Pavilion:~/bin/c1$

GenoMax · 03-20-2015, 02:43 PM

Do this

Code:

$ head -5 genes.fa

and then move the genes.fa file to something else? I am not sure where that file came from

Code:

$ mv genes.fa genes.fa.BKP

lupid · 03-20-2015, 03:48 PM

Don't u.u
I changed the name of the gtf file, because I read that maybe has to have the same as the rest of the files, but don't work either, here my console
/bin/c1$ tophat -p 2 -G ./genome.gtf -o ./C1_R1_thout_new ./genome ./GSM794483_C1_R1_1.fq ./GSM794483_C1_R1_2.fq

[2015-03-20 19:36:20] Beginning TopHat run (v2.0.13)
-----------------------------------------------
[2015-03-20 19:36:20] Checking for Bowtie
Bowtie version: 2.2.5.0
[2015-03-20 19:36:20] Checking for Bowtie index files (genome)..
[2015-03-20 19:36:20] Checking for reference FASTA file
[2015-03-20 19:36:20] Generating SAM header for ./genome
[2015-03-20 19:36:20] Reading known junctions from GTF file
[2015-03-20 19:36:24] Preparing reads
left reads: min. length=75, max. length=75, 11607353 kept reads (0 discarded)
right reads: min. length=75, max. length=75, 11607353 kept reads (0 discarded)
[2015-03-20 19:41:34] Building transcriptome data files ./C1_R1_thout_new/tmp/genome
[2015-03-20 19:41:42] Building Bowtie index from genome.fa
[FAILED]
Error: Couldn't build bowtie index with err = 1
tomas@HP-Pavilion:~/bin/c1$ ls -lh
total 4,3G
-rw-rw-r-- 1 tomas tomas 22K mar 20 19:27 20.3.15
-rw-rw-r-- 1 tomas tomas 22K mar 20 19:27 20.3.15.txt
drwxrwxr-x 4 tomas tomas 4,0K mar 20 10:32 C1_R1_thout
drwxrwxr-x 4 tomas tomas 4,0K mar 20 14:57 C1_R1_thout_new
drwxrwxr-x 3 tomas tomas 4,0K mar 20 15:54 Drosophila_melanogaster
-rwxrwxr-x 1 tomas tomas 43M abr 10 2012 genome.1.bt2
-rwxrwxr-x 1 tomas tomas 29M abr 10 2012 genome.2.bt2
-rwxrwxr-x 1 tomas tomas 143 abr 10 2012 genome.3.bt2
-rwxrwxr-x 1 tomas tomas 29M abr 10 2012 genome.4.bt2
lrwxrwxrwx 1 tomas tomas 91 mar 20 17:23 genome.fa -> /home/tomas/bin/c1/Drosophila_melanogaster/Ensembl/BDGP5.25/Sequence/Bowtie2Index/genome.fa
-rwxrwxr-x 1 tomas tomas 54M may 23 2014 genome.gtf
-rwxrwxr-x 1 tomas tomas 43M abr 10 2012 genome.rev.1.bt2
-rwxrwxr-x 1 tomas tomas 29M abr 10 2012 genome.rev.2.bt2
-rw-rw-r-- 1 tomas tomas 1,8G mar 20 10:34 GSM794483_C1_R1_1.fq
-rw-rw-r-- 1 tomas tomas 1,8G mar 20 10:35 GSM794483_C1_R1_2.fq
-rw-rw-r-- 1 tomas tomas 138M sep 13 2011 GSM794483_C1_R1_2.fq.gz
-rw-rw-r-- 1 tomas tomas 325M sep 9 2011 GSM794483_C1_R1.accepted_hits.bam
-rw-rw-r-- 1 tomas tomas 14M mar 20 11:02 GSM794483_C1_R1.transcripts.gff

GenoMax · 03-20-2015, 05:07 PM

Did you download bowtie2 and tophat executables or compiled them yourself? Are you running 32-bit/64-bit Ubuntu?

Since you have copied all other files to the current directory why don't we copy the genome file too

Code:

$ unlink genome.fa
$ cp /home/tomas/bin/c1/Drosophila_melanogaster/Ensembl/BDGP5.25/Sequence/WholeGenomeFasta/genome.fa .

lupid · 03-21-2015, 06:27 AM

I'm using Ubuntu 64 and download the executables
I try to put the file in the same directory as you suggest and nothing
/bin/c1$ ls -lh
total 4,4G
-rw-rw-r-- 1 tomas tomas 22K mar 20 19:27 20.3.15
-rw-rw-r-- 1 tomas tomas 22K mar 20 19:27 20.3.15.txt
drwxrwxr-x 4 tomas tomas 4,0K mar 20 10:32 C1_R1_thout
drwxrwxr-x 4 tomas tomas 4,0K mar 20 14:57 C1_R1_thout_new
drwxrwxr-x 3 tomas tomas 4,0K mar 20 15:54 Drosophila_melanogaster
-rwxrwxr-x 1 tomas tomas 54M mar 20 20:02 genes.gtf
-rwxrwxr-x 1 tomas tomas 43M abr 10 2012 genome.1.bt2
-rwxrwxr-x 1 tomas tomas 29M abr 10 2012 genome.2.bt2
-rwxrwxr-x 1 tomas tomas 143 abr 10 2012 genome.3.bt2
-rwxrwxr-x 1 tomas tomas 29M abr 10 2012 genome.4.bt2
-rwxrwxr-x 1 tomas tomas 117M mar 21 10:16 genome.fa
-rwxrwxr-x 1 tomas tomas 43M abr 10 2012 genome.rev.1.bt2
-rwxrwxr-x 1 tomas tomas 29M abr 10 2012 genome.rev.2.bt2
-rw-rw-r-- 1 tomas tomas 1,8G mar 20 10:34 GSM794483_C1_R1_1.fq
-rw-rw-r-- 1 tomas tomas 1,8G mar 20 10:35 GSM794483_C1_R1_2.fq
-rw-rw-r-- 1 tomas tomas 138M sep 13 2011 GSM794483_C1_R1_2.fq.gz
-rw-rw-r-- 1 tomas tomas 325M sep 9 2011 GSM794483_C1_R1.accepted_hits.bam
-rw-rw-r-- 1 tomas tomas 14M mar 20 11:02 GSM794483_C1_R1.transcripts.gff
tomas@HP-Pavilion:~/bin/c1$ tophat -p 2 -G ./genes.gtf -o ./C1_R1_thout_new ./genome ./GSM794483_C1_R1_1.fq ./GSM794483_C1_R1_2.fq

[2015-03-21 10:16:47] Beginning TopHat run (v2.0.13)
-----------------------------------------------
[2015-03-21 10:16:47] Checking for Bowtie
Bowtie version: 2.2.5.0
[2015-03-21 10:16:48] Checking for Bowtie index files (genome)..
[2015-03-21 10:16:48] Checking for reference FASTA file
[2015-03-21 10:16:48] Generating SAM header for ./genome
[2015-03-21 10:16:50] Reading known junctions from GTF file
[2015-03-21 10:16:54] Preparing reads
left reads: min. length=75, max. length=75, 11607353 kept reads (0 discarded)
right reads: min. length=75, max. length=75, 11607353 kept reads (0 discarded)
[2015-03-21 10:22:22] Building transcriptome data files ./C1_R1_thout_new/tmp/genes
[2015-03-21 10:22:29] Building Bowtie index from genes.fa
[FAILED]
Error: Couldn't build bowtie index with err = 1
tomas@HP-Pavilion:~/bin/c1$

lupid · 03-21-2015, 06:29 AM

I'll try to download all the files again maybe someone is corrupted

lupid · 03-21-2015, 07:29 AM

I think I find the problem, I cannot find the source of the .fq files, I have it but I don't know how xd, what is the oficial source?

GenoMax · 03-21-2015, 07:38 AM

Based on the file names tophat should be working. Well try doing a fresh download in a new directory.

GenoMax · 03-21-2015, 07:40 AM

Quote:

Originally Posted by lupid

I think I find the problem, I cannot find the source of the .fq files, I have it but I don't know how xd, what is the oficial source?

Get the data files from the GEO link: http://www.ncbi.nlm.nih.gov/geo/quer...i?acc=GSE32038 GSE32038_simulated_fastq_files.tar.gz

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03-20-2015, 01:03 PM	#23
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,080	Can you show a current long listing of the files in directory? Code: $ ls -lh As shown on page 570 of Nature protocols article it may be best to create at least this softlink in your current directory. I am assuming you have copied other files locally (will know from the listing above). Code: $ ln -s /path_to/Drosophila_melanogaster/Ensembl/BDGP5.25/Sequence/Bowtie2Index/genome.fa . Last edited by GenoMax; 03-20-2015 at 01:06 PM.

03-20-2015, 01:15 PM	#25
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,080	This link is not pointing to the right directory: lrwxrwxrwx 1 tomas tomas 29 mar 20 16:51 genome.fa -> ../WholeGenomeFasta/genome.fa So do this Code: $ unlink genome.fa ONLY if above does not work then Code: $ rm -f genome.fa Then create the soft link again Code: $ ln -s /home/tomas/bin/c1/Drosophila_melanogaster/Ensembl/BDGP5.25/Sequence/Bowtie2Index/genome.fa . Try tophat.

03-20-2015, 02:43 PM	#27
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,080	Do this Code: $ head -5 genes.fa and then move the genes.fa file to something else? I am not sure where that file came from Code: $ mv genes.fa genes.fa.BKP

03-20-2015, 05:07 PM	#29
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,080	Did you download bowtie2 and tophat executables or compiled them yourself? Are you running 32-bit/64-bit Ubuntu? Since you have copied all other files to the current directory why don't we copy the genome file too Code: $ unlink genome.fa $ cp /home/tomas/bin/c1/Drosophila_melanogaster/Ensembl/BDGP5.25/Sequence/WholeGenomeFasta/genome.fa .

03-20-2015, 11:49 AM	#21
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,080	Use this file instead of the GTF file you are using: /path_to/Drosophila_melanogaster/Ensembl/BDGP5.25/Annotation/Genes/genes.gtf

03-20-2015, 12:48 PM	#22
lupid Member Location: chile Join Date: Mar 2015 Posts: 54	don't work u.u tophat -p 2 -G ./genes.gtf -o ./C1_R1_thout_new ./genome ./GSM794483_C1_R1_1.fq ./GSM794483_C1_R1_2.fq [2015-03-20 16:13:45] Beginning TopHat run (v2.0.13) ----------------------------------------------- [2015-03-20 16:13:45] Checking for Bowtie Bowtie version: 2.2.5.0 [2015-03-20 16:13:45] Checking for Bowtie index files (genome).. [2015-03-20 16:13:45] Checking for reference FASTA file Warning: Could not find FASTA file ./genome.fa [2015-03-20 16:13:45] Reconstituting reference FASTA file from Bowtie index Executing: /home/tomas/bin/bowtie2-inspect ./genome > ./C1_R1_thout_new/tmp/genome.fa [2015-03-20 16:13:54] Generating SAM header for ./genome [2015-03-20 16:13:55] Reading known junctions from GTF file [2015-03-20 16:13:59] Preparing reads left reads: min. length=75, max. length=75, 11607353 kept reads (0 discarded) right reads: min. length=75, max. length=75, 11607353 kept reads (0 discarded) [2015-03-20 16:18:58] Building transcriptome data files ./C1_R1_thout_new/tmp/genes [2015-03-20 16:19:07] Building Bowtie index from genes.fa [FAILED] Error: Couldn't build bowtie index with err = 1 tomas@HP-Pavilion:~/bin/c1$

03-20-2015, 01:10 PM	#24
lupid Member Location: chile Join Date: Mar 2015 Posts: 54	tomas@HP-Pavilion:~/bin/c1$ ls -lh total 4,4G drwxrwxr-x 4 tomas tomas 4,0K mar 20 10:32 C1_R1_thout drwxrwxr-x 4 tomas tomas 4,0K mar 20 14:57 C1_R1_thout_new drwxrwxr-x 3 tomas tomas 4,0K mar 20 15:54 Drosophila_melanogaster -rwxrwxr-x 1 tomas tomas 117M mar 15 2012 genes.fa -rwxrwxr-x 1 tomas tomas 54M may 23 2014 genes.gtf -rwxrwxr-x 1 tomas tomas 43M abr 10 2012 genome.1.bt2 -rwxrwxr-x 1 tomas tomas 29M abr 10 2012 genome.2.bt2 -rwxrwxr-x 1 tomas tomas 143 abr 10 2012 genome.3.bt2 -rwxrwxr-x 1 tomas tomas 29M abr 10 2012 genome.4.bt2 lrwxrwxrwx 1 tomas tomas 29 mar 20 16:51 genome.fa -> ../WholeGenomeFasta/genome.fa -rwxrwxr-x 1 tomas tomas 43M abr 10 2012 genome.rev.1.bt2 -rwxrwxr-x 1 tomas tomas 29M abr 10 2012 genome.rev.2.bt2 -rw-rw-r-- 1 tomas tomas 1,8G mar 20 10:34 GSM794483_C1_R1_1.fq -rw-rw-r-- 1 tomas tomas 1,8G mar 20 10:35 GSM794483_C1_R1_2.fq -rw-rw-r-- 1 tomas tomas 138M sep 13 2011 GSM794483_C1_R1_2.fq.gz -rw-rw-r-- 1 tomas tomas 325M sep 9 2011 GSM794483_C1_R1.accepted_hits.bam -rw-rw-r-- 1 tomas tomas 14M mar 20 11:02 GSM794483_C1_R1.transcripts.gff tomas@HP-Pavilion:~/bin/c1$ I don't know if I did what you propouse, but when I try, this happend tomas@HP-Pavilion:~/bin/c1$ ln -s /home/tomas/bin/c1/Drosophila_melanogaster/Ensembl/BDGP5.25/Sequence/Bowtie2Index/genome.fa . ln: fallo al crear el enlace simbólico «./genome.fa»: El archivo ya existe tomas@HP-Pavilion:~/bin/c1$

03-20-2015, 01:31 PM	#26
lupid Member Location: chile Join Date: Mar 2015 Posts: 54	after try both options still didn't work here my console tomas@HP-Pavilion:~/bin/c1$ rm -f genome.fa tomas@HP-Pavilion:~/bin/c1$ ln -s /home/tomas/bin/c1/Drosophila_melanogaster/Ensembl/BDGP5.25/Sequence/Bowtie2Index/genome.fa . tomas@HP-Pavilion:~/bin/c1$ ls -lh total 4,4G drwxrwxr-x 4 tomas tomas 4,0K mar 20 10:32 C1_R1_thout drwxrwxr-x 4 tomas tomas 4,0K mar 20 14:57 C1_R1_thout_new drwxrwxr-x 3 tomas tomas 4,0K mar 20 15:54 Drosophila_melanogaster -rwxrwxr-x 1 tomas tomas 117M mar 15 2012 genes.fa -rwxrwxr-x 1 tomas tomas 54M may 23 2014 genes.gtf -rwxrwxr-x 1 tomas tomas 43M abr 10 2012 genome.1.bt2 -rwxrwxr-x 1 tomas tomas 29M abr 10 2012 genome.2.bt2 -rwxrwxr-x 1 tomas tomas 143 abr 10 2012 genome.3.bt2 -rwxrwxr-x 1 tomas tomas 29M abr 10 2012 genome.4.bt2 lrwxrwxrwx 1 tomas tomas 91 mar 20 17:23 genome.fa -> /home/tomas/bin/c1/Drosophila_melanogaster/Ensembl/BDGP5.25/Sequence/Bowtie2Index/genome.fa -rwxrwxr-x 1 tomas tomas 43M abr 10 2012 genome.rev.1.bt2 -rwxrwxr-x 1 tomas tomas 29M abr 10 2012 genome.rev.2.bt2 -rw-rw-r-- 1 tomas tomas 1,8G mar 20 10:34 GSM794483_C1_R1_1.fq -rw-rw-r-- 1 tomas tomas 1,8G mar 20 10:35 GSM794483_C1_R1_2.fq -rw-rw-r-- 1 tomas tomas 138M sep 13 2011 GSM794483_C1_R1_2.fq.gz -rw-rw-r-- 1 tomas tomas 325M sep 9 2011 GSM794483_C1_R1.accepted_hits.bam -rw-rw-r-- 1 tomas tomas 14M mar 20 11:02 GSM794483_C1_R1.transcripts.gff tomas@HP-Pavilion:~/bin/c1$ tophat -p 2 -G ./genes.gtf -o ./C1_R1_thout_new ./genome ./GSM794483_C1_R1_1.fq ./GSM794483_C1_R1_2.fq [2015-03-20 17:24:20] Beginning TopHat run (v2.0.13) ----------------------------------------------- [2015-03-20 17:24:20] Checking for Bowtie Bowtie version: 2.2.5.0 [2015-03-20 17:24:20] Checking for Bowtie index files (genome).. [2015-03-20 17:24:20] Checking for reference FASTA file [2015-03-20 17:24:20] Generating SAM header for ./genome [2015-03-20 17:24:21] Reading known junctions from GTF file [2015-03-20 17:24:24] Preparing reads left reads: min. length=75, max. length=75, 11607353 kept reads (0 discarded) right reads: min. length=75, max. length=75, 11607353 kept reads (0 discarded) [2015-03-20 17:29:19] Building transcriptome data files ./C1_R1_thout_new/tmp/genes [2015-03-20 17:29:26] Building Bowtie index from genes.fa [FAILED] Error: Couldn't build bowtie index with err = 1 tomas@HP-Pavilion:~/bin/c1$

03-20-2015, 03:48 PM	#28
lupid Member Location: chile Join Date: Mar 2015 Posts: 54	Don't u.u I changed the name of the gtf file, because I read that maybe has to have the same as the rest of the files, but don't work either, here my console /bin/c1$ tophat -p 2 -G ./genome.gtf -o ./C1_R1_thout_new ./genome ./GSM794483_C1_R1_1.fq ./GSM794483_C1_R1_2.fq [2015-03-20 19:36:20] Beginning TopHat run (v2.0.13) ----------------------------------------------- [2015-03-20 19:36:20] Checking for Bowtie Bowtie version: 2.2.5.0 [2015-03-20 19:36:20] Checking for Bowtie index files (genome).. [2015-03-20 19:36:20] Checking for reference FASTA file [2015-03-20 19:36:20] Generating SAM header for ./genome [2015-03-20 19:36:20] Reading known junctions from GTF file [2015-03-20 19:36:24] Preparing reads left reads: min. length=75, max. length=75, 11607353 kept reads (0 discarded) right reads: min. length=75, max. length=75, 11607353 kept reads (0 discarded) [2015-03-20 19:41:34] Building transcriptome data files ./C1_R1_thout_new/tmp/genome [2015-03-20 19:41:42] Building Bowtie index from genome.fa [FAILED] Error: Couldn't build bowtie index with err = 1 tomas@HP-Pavilion:~/bin/c1$ ls -lh total 4,3G -rw-rw-r-- 1 tomas tomas 22K mar 20 19:27 20.3.15 -rw-rw-r-- 1 tomas tomas 22K mar 20 19:27 20.3.15.txt drwxrwxr-x 4 tomas tomas 4,0K mar 20 10:32 C1_R1_thout drwxrwxr-x 4 tomas tomas 4,0K mar 20 14:57 C1_R1_thout_new drwxrwxr-x 3 tomas tomas 4,0K mar 20 15:54 Drosophila_melanogaster -rwxrwxr-x 1 tomas tomas 43M abr 10 2012 genome.1.bt2 -rwxrwxr-x 1 tomas tomas 29M abr 10 2012 genome.2.bt2 -rwxrwxr-x 1 tomas tomas 143 abr 10 2012 genome.3.bt2 -rwxrwxr-x 1 tomas tomas 29M abr 10 2012 genome.4.bt2 lrwxrwxrwx 1 tomas tomas 91 mar 20 17:23 genome.fa -> /home/tomas/bin/c1/Drosophila_melanogaster/Ensembl/BDGP5.25/Sequence/Bowtie2Index/genome.fa -rwxrwxr-x 1 tomas tomas 54M may 23 2014 genome.gtf -rwxrwxr-x 1 tomas tomas 43M abr 10 2012 genome.rev.1.bt2 -rwxrwxr-x 1 tomas tomas 29M abr 10 2012 genome.rev.2.bt2 -rw-rw-r-- 1 tomas tomas 1,8G mar 20 10:34 GSM794483_C1_R1_1.fq -rw-rw-r-- 1 tomas tomas 1,8G mar 20 10:35 GSM794483_C1_R1_2.fq -rw-rw-r-- 1 tomas tomas 138M sep 13 2011 GSM794483_C1_R1_2.fq.gz -rw-rw-r-- 1 tomas tomas 325M sep 9 2011 GSM794483_C1_R1.accepted_hits.bam -rw-rw-r-- 1 tomas tomas 14M mar 20 11:02 GSM794483_C1_R1.transcripts.gff

03-21-2015, 06:27 AM	#30
lupid Member Location: chile Join Date: Mar 2015 Posts: 54	I'm using Ubuntu 64 and download the executables I try to put the file in the same directory as you suggest and nothing /bin/c1$ ls -lh total 4,4G -rw-rw-r-- 1 tomas tomas 22K mar 20 19:27 20.3.15 -rw-rw-r-- 1 tomas tomas 22K mar 20 19:27 20.3.15.txt drwxrwxr-x 4 tomas tomas 4,0K mar 20 10:32 C1_R1_thout drwxrwxr-x 4 tomas tomas 4,0K mar 20 14:57 C1_R1_thout_new drwxrwxr-x 3 tomas tomas 4,0K mar 20 15:54 Drosophila_melanogaster -rwxrwxr-x 1 tomas tomas 54M mar 20 20:02 genes.gtf -rwxrwxr-x 1 tomas tomas 43M abr 10 2012 genome.1.bt2 -rwxrwxr-x 1 tomas tomas 29M abr 10 2012 genome.2.bt2 -rwxrwxr-x 1 tomas tomas 143 abr 10 2012 genome.3.bt2 -rwxrwxr-x 1 tomas tomas 29M abr 10 2012 genome.4.bt2 -rwxrwxr-x 1 tomas tomas 117M mar 21 10:16 genome.fa -rwxrwxr-x 1 tomas tomas 43M abr 10 2012 genome.rev.1.bt2 -rwxrwxr-x 1 tomas tomas 29M abr 10 2012 genome.rev.2.bt2 -rw-rw-r-- 1 tomas tomas 1,8G mar 20 10:34 GSM794483_C1_R1_1.fq -rw-rw-r-- 1 tomas tomas 1,8G mar 20 10:35 GSM794483_C1_R1_2.fq -rw-rw-r-- 1 tomas tomas 138M sep 13 2011 GSM794483_C1_R1_2.fq.gz -rw-rw-r-- 1 tomas tomas 325M sep 9 2011 GSM794483_C1_R1.accepted_hits.bam -rw-rw-r-- 1 tomas tomas 14M mar 20 11:02 GSM794483_C1_R1.transcripts.gff tomas@HP-Pavilion:~/bin/c1$ tophat -p 2 -G ./genes.gtf -o ./C1_R1_thout_new ./genome ./GSM794483_C1_R1_1.fq ./GSM794483_C1_R1_2.fq [2015-03-21 10:16:47] Beginning TopHat run (v2.0.13) ----------------------------------------------- [2015-03-21 10:16:47] Checking for Bowtie Bowtie version: 2.2.5.0 [2015-03-21 10:16:48] Checking for Bowtie index files (genome).. [2015-03-21 10:16:48] Checking for reference FASTA file [2015-03-21 10:16:48] Generating SAM header for ./genome [2015-03-21 10:16:50] Reading known junctions from GTF file [2015-03-21 10:16:54] Preparing reads left reads: min. length=75, max. length=75, 11607353 kept reads (0 discarded) right reads: min. length=75, max. length=75, 11607353 kept reads (0 discarded) [2015-03-21 10:22:22] Building transcriptome data files ./C1_R1_thout_new/tmp/genes [2015-03-21 10:22:29] Building Bowtie index from genes.fa [FAILED] Error: Couldn't build bowtie index with err = 1 tomas@HP-Pavilion:~/bin/c1$

03-21-2015, 06:29 AM	#31
lupid Member Location: chile Join Date: Mar 2015 Posts: 54	I'll try to download all the files again maybe someone is corrupted

03-21-2015, 07:29 AM	#32
lupid Member Location: chile Join Date: Mar 2015 Posts: 54	I think I find the problem, I cannot find the source of the .fq files, I have it but I don't know how xd, what is the oficial source?

03-21-2015, 07:38 AM	#33
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,080	Based on the file names tophat should be working. Well try doing a fresh download in a new directory.