Tophat Error

[ercfrtz]

I am trying to run Tophat with the simple basic command (using no options) and have done so successfully before but now when I try to run it, I get the following error:


[Mon Aug 16 10:59:32 2010] Mapping reads against b_taurus with Bowtie
[Mon Aug 16 11:34:47 2010] Mapping reads against b_taurus with Bowtie
[Mon Aug 16 12:06:51 2010] Searching for junctions via segment mapping
[Mon Aug 16 12:12:04 2010] Retrieving sequences for splices
[Mon Aug 16 12:14:18 2010] Indexing splices
[Mon Aug 16 12:14:19 2010] Mapping reads against segment_juncs with Bowtie
[Mon Aug 16 12:15:06 2010] Mapping reads against segment_juncs with Bowtie
[Mon Aug 16 12:15:53 2010] Joining segment hits
[FAILED]
Error: Segment join failed with err = 1
Traceback (most recent call last):
File "/raid/warehouse/tophat-1.0.13/bin/tophat", line 1635, in ?
sys.exit(main())
File "/raid/warehouse/tophat-1.0.13/bin/tophat", line 1595, in main
user_supplied_juncs)
File "/raid/warehouse/tophat-1.0.13/bin/tophat", line 1492, in spliced_alignment
mapped_reads)
File "/raid/warehouse/tophat-1.0.13/bin/tophat", line 1299, in join_mapped_segments
exit(1)
TypeError: 'str' object is not callable


Any help would be appreciated, thanks.

[tsucheta]

I also get the same tophat error. ANy help will be greatly appreciated.

Thanks

---- ERROR ----

tophat ends with the following errors:

--------
[Wed Sep 8 18:38:48 2010] Beginning TopHat run (v1.0.14)
-----------------------------------------------
[Wed Sep 8 18:38:48 2010] Preparing output location ./tophat_out/
[Wed Sep 8 18:38:48 2010] Checking for Bowtie index files
[Wed Sep 8 18:38:48 2010] Checking for reference FASTA file
Warning: Could not find FASTA file /home/data/bowtie-0.12.5/index/soj
aeV1.fa
[Wed Sep 8 18:38:48 2010] Reconstituting reference FASTA file from Bowtie index

[Wed Sep 8 18:39:07 2010] Checking for Bowtie
Bowtie version: 0.12.5.0
[Wed Sep 8 18:39:07 2010] Checking reads
seed length: 50bp
format: fastq
quality scale: phred33 (default)
[Wed Sep 8 18:43:08 2010] Reading known junctions from GFF file
Warning: TopHat did not find any junctions in GFF file
[Wed Sep 8 18:44:05 2010] Mapping reads against sojaeV1 with Bowtie
[Wed Sep 8 18:44:05 2010] Joining segment hits
Traceback (most recent call last):
File "/home/data/tophat-1.0.14.Linux_x86_64/tophat", line 1854, in <module>

sys.exit(main())
File "/home/data/tophat-1.0.14.Linux_x86_64/tophat", line 1814, in main
user_supplied_juncs)
File "/home/data/tophat-1.0.14.Linux_x86_64/tophat", line 1562, in spliced_
alignment
segment_len)
File "/home/data/tophat-1.0.14.Linux_x86_64/tophat", line 1229, in split_re
ads
reads_file = open(reads_filename)
IOError: [Errno 2] No such file or directory: './tophat_out/tmp//left_kept_reads
_missing.fq'

--
I am running the binary tophat distribution.

Many thanks

[kbushley]

I also get the same error. Puzzling as I have run a subset of my data and it completes fine which makes me think it may be an issue related to scaling up to a larger dataset but I am only trying to run about 7M reads...any solutions greatly appreciated.


quality scale: phred64 (reads generated with GA pipeline version >= 1\
.3)
[Fri Sep 10 13:20:51 2010] Mapping reads against MIRASEpPERef with Bowtie
[Fri Sep 10 14:16:28 2010] Joining segment hits
[FAILED]
Error: Segment join failed with err = 1
Traceback (most recent call last):
File "/local/cluster/spatafora/bin/tophat", line 1635, in ?
sys.exit(main())
File "/local/cluster/spatafora/bin/tophat", line 1595, in main
user_supplied_juncs)
File "/local/cluster/spatafora/bin/tophat", line 1370, in spliced_alignment
unspliced_sam)
File "/local/cluster/spatafora/bin/tophat", line 1299, in join_mapped_segment\
s
exit(1)
TypeError: 'str' object is not callable

[tsucheta]

I found that I was running tophat with colospace indexed reference. When I indexed them in regular sequence mode, tophat run was completed without much trouble. It may be worthwhile to check what type of index file you are running your data against.

[emucaki]

I'm having a similar problem:

...
[Thu Oct 28 15:46:49 2010] Searching for junctions via segment mapping
[FAILED]
Error: segment-based junction search failed with err = -6
Traceback (most recent call last):
File "tophat", line 1635, in ?
sys.exit(main())
File "tophat", line 1595, in main
user_supplied_juncs)
File "/tophat", line 1434, in spliced_alignment
ref_fasta)
File "tophat", line 1251, in junctions_from_segments
exit(1)
TypeError: 'str' object is not callable

In my case it isn't the index file as it is the one downloaded straight from the Bowtie website. I've run many alignments to this index without issue, but this pair of fastq files keeps giving me this error.

[kbushley]

Hi,

Yes, I think you are right. I had exactly the same problem...I had successfully run a test run on the index using sample fastq file but couldn't run larger files. I'm not sure I figured out the exact nature of the problem but I did find that when I increased memory for this job (I think up to around 12GB), I was able to finish the run without errors. Maybe that will help?

[emucaki]

This actually solved the problem! I wouldn't of guessed it was a memory issue. Thanks!

[ben.weisburd]

I was seeing this error also ("Error: Segment join failed with err = 1").
Turned out the problem was that I was running more than one tophat process simultaneously in the same directory (I wanted to process multiple fastq files in parallel). When I launched the processes in separate directories, everything worked fine.

-Ben

I am trying to run Tophat with the simple basic command (using no options) and have done so successfully before but now when I try to run it, I get the following error:


[Mon Aug 16 10:59:32 2010] Mapping reads against b_taurus with Bowtie
[Mon Aug 16 11:34:47 2010] Mapping reads against b_taurus with Bowtie
[Mon Aug 16 12:06:51 2010] Searching for junctions via segment mapping
[Mon Aug 16 12:12:04 2010] Retrieving sequences for splices
[Mon Aug 16 12:14:18 2010] Indexing splices
[Mon Aug 16 12:14:19 2010] Mapping reads against segment_juncs with Bowtie
[Mon Aug 16 12:15:06 2010] Mapping reads against segment_juncs with Bowtie
[Mon Aug 16 12:15:53 2010] Joining segment hits
[FAILED]
Error: Segment join failed with err = 1
Traceback (most recent call last):
File "/raid/warehouse/tophat-1.0.13/bin/tophat", line 1635, in ?
sys.exit(main())
File "/raid/warehouse/tophat-1.0.13/bin/tophat", line 1595, in main
user_supplied_juncs)
File "/raid/warehouse/tophat-1.0.13/bin/tophat", line 1492, in spliced_alignment
mapped_reads)
File "/raid/warehouse/tophat-1.0.13/bin/tophat", line 1299, in join_mapped_segments
exit(1)
TypeError: 'str' object is not callable


Any help would be appreciated, thanks.