bug for the tophat 1.3 beta

[liuxq]

all my reads are 40bp single end reads.

it seems that there is something wrong with the junction mapping process

my tophat commands and error message are as follows

tophat --phred64-quals -o s_1_sequence ~/rd/work/rna_seq/genome_index/bowtie/mm9/mm9 s_1_sequence.txt

[Sat Jun 4 01:11:54 2011] Searching for junctions via segment mapping
Warning: junction database is empty!
[Sat Jun 4 01:13:23 2011] Processing bowtie hits
Traceback (most recent call last):
File "/home/liuxq/mybin/tools/tophat", line 2584, in <module>
sys.exit(main())
File "/home/liuxq/mybin/tools/tophat", line 2543, in main
user_supplied_deletions)
File "/home/liuxq/mybin/tools/tophat", line 2376, in spliced_alignment
os.remove(unspl_bwtfile)
UnboundLocalError: local variable 'unspl_bwtfile' referenced before assignment

[Francesc]

i have the same error.
did you figure out what it is?

[SEQguest]

Error connected to empty junction database?

Hello,

I encountered the same error as well:

[Thu Jun 9 17:47:43 2011] Searching for junctions via segment mapping
Warning: junction database is empty!
[Thu Jun 9 17:49:52 2011] Processing bowtie hits
Traceback (most recent call last):
File "./tophat", line 2584, in ?
sys.exit(main())
File "./tophat", line 2543, in main
user_supplied_deletions)
File "./tophat", line 2376, in spliced_alignment
os.remove(unspl_bwtfile)
UnboundLocalError: local variable 'unspl_bwtfile' referenced before assignment

Case 1: I ran TopHat v1.3.0 with these parameters/arguments:

./tophat -o C02_tophat_outSAM -r 150 -p 8 --mate-std-dev 38 --no-convert-bam ./../bowtie/indexes/hg19 C02_1_head.txt C02_2_head.txt

Content of the two files was as follows:

C02_1_head.txt:

@SRR057629.1_HWUSI-EAS230-R:2:1:2:1844#0/1
CAAAAAGTTGCAATCAAAGATCTCTTCATCTTATTG
+SRR057629.1_HWUSI-EAS230-R:2:1:2:1844#0/1
BCBCCBA:<@BBB?BBB@2B:B:B>>BB>A@5A948

C02_2_head.txt:

@SRR057629.1_HWUSI-EAS230-R:2:1:2:1844#0/2
TTGAGTCCNTTGCCTTTGCCCTCAACCTTGGCAATC
+SRR057629.1_HWUSI-EAS230-R:2:1:2:1844#0/2
82C=(:B=!=;BB?7':=ACBABAAC@-(7CCBA??

Case 2: The same happens when "--no-convert-bam" option is omitted.

Case 3: TopHat v1.2.0 finishes on the same data with no errors when identical command is used (option "--no-convert-bam" is not available in version 1.2.0, so the command is identical to Case 2).

- For each case a new, empty output folder was specified.

Maybe the error in v1.3.0 is connected to empty junction database? It was a circumstance in liuxq's analysis, too.

[gpertea]

This was indeed a small bug in the initial 1.3.0 release, the error appears for shorter reads (non-segmented). This has been fixed recently (with a silent update of the download packages), I also attached here the corrected tophat script.

However for reads shorter than 50 it's still a good idea to enforce segmented mapping by decreasing the segment length to about half the read length (using the ' --segment-length' option).

[SEQguest]

Yay

Thank you!