Hi Jen,
I have a similar problem as you can see below:
[2014-09-10 09:47:28] Beginning TopHat run (v2.0.8b)
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[2014-09-10 09:47:28] Checking for Bowtie
Bowtie version: 2.1.0.0
[2014-09-10 09:47:28] Checking for Samtools
Samtools version: 0.1.19.0
[2014-09-10 09:47:28] Checking for Bowtie index files
[2014-09-10 09:47:28] Checking for reference FASTA file
[2014-09-10 09:47:28] Generating SAM header for /home/xelcoro/Software/tophat-2.0.12.Linux_x86_64/mm10/mm10
format: fastq
quality scale: phred33 (default)
[2014-09-10 09:48:20] Reading known junctions from GTF file
[2014-09-10 09:48:24] Preparing reads
left reads: min. length=16, max. length=388, 133029181 kept reads (319 discarded)
Warning: short reads (<20bp) will make TopHat quite slow and take large amount of memory because they are likely to be mapped in too many places
[2014-09-10 10:32:23] Creating transcriptome data files..
[2014-09-10 10:33:01] Building Bowtie index from mm10.fa
[2014-09-10 10:45:05] Mapping left_kept_reads to transcriptome mm10 with Bowtie2
[2014-09-10 14:49:18] Resuming TopHat pipeline with unmapped reads
[2014-09-10 14:49:18] Mapping left_kept_reads.m2g_um to genome mm10 with Bowtie2
[2014-09-10 21:05:51] Mapping left_kept_reads.m2g_um_seg1 to genome mm10 with Bowtie2 (1/15)
[2014-09-10 23:20:33] Mapping left_kept_reads.m2g_um_seg2 to genome mm10 with Bowtie2 (2/15)
[2014-09-11 01:24:01] Mapping left_kept_reads.m2g_um_seg3 to genome mm10 with Bowtie2 (3/15)
[2014-09-11 03:36:15] Mapping left_kept_reads.m2g_um_seg4 to genome mm10 with Bowtie2 (4/15)
[2014-09-11 05:42:01] Mapping left_kept_reads.m2g_um_seg5 to genome mm10 with Bowtie2 (5/15)
[2014-09-11 07:31:05] Mapping left_kept_reads.m2g_um_seg6 to genome mm10 with Bowtie2 (6/15)
[2014-09-11 08:52:39] Mapping left_kept_reads.m2g_um_seg7 to genome mm10 with Bowtie2 (7/15)
[2014-09-11 09:30:02] Mapping left_kept_reads.m2g_um_seg8 to genome mm10 with Bowtie2 (8/15)
[2014-09-11 09:47:17] Mapping left_kept_reads.m2g_um_seg9 to genome mm10 with Bowtie2 (9/15)
[2014-09-11 09:53:55] Mapping left_kept_reads.m2g_um_seg10 to genome mm10 with Bowtie2 (10/15)
[2014-09-11 09:55:36] Mapping left_kept_reads.m2g_um_seg11 to genome mm10 with Bowtie2 (11/15)
[2014-09-11 09:55:48] Mapping left_kept_reads.m2g_um_seg12 to genome mm10 with Bowtie2 (12/15)
[2014-09-11 09:55:52] Mapping left_kept_reads.m2g_um_seg13 to genome mm10 with Bowtie2 (13/15)
[2014-09-11 09:55:56] Mapping left_kept_reads.m2g_um_seg14 to genome mm10 with Bowtie2 (14/15)
[2014-09-11 09:56:00] Mapping left_kept_reads.m2g_um_seg15 to genome mm10 with Bowtie2 (15/15)
[2014-09-11 09:56:04] Retrieving sequences for splices
[2014-09-11 10:00:03] Indexing splices
Building a SMALL index
[2014-09-11 10:00:28] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/15)
[2014-09-11 10:14:33] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/15)
[2014-09-11 10:27:41] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/15)
[2014-09-11 10:41:06] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/15)
[2014-09-11 10:53:45] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/15)
[2014-09-11 11:04:34] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/15)
[2014-09-11 11:12:10] Mapping left_kept_reads.m2g_um_seg7 to genome segment_juncs with Bowtie2 (7/15)
[2014-09-11 11:16:48] Mapping left_kept_reads.m2g_um_seg8 to genome segment_juncs with Bowtie2 (8/15)
[2014-09-11 11:19:08] Mapping left_kept_reads.m2g_um_seg9 to genome segment_juncs with Bowtie2 (9/15)
[2014-09-11 11:20:00] Mapping left_kept_reads.m2g_um_seg10 to genome segment_juncs with Bowtie2 (10/15)
[2014-09-11 11:20:17] Mapping left_kept_reads.m2g_um_seg11 to genome segment_juncs with Bowtie2 (11/15)
[2014-09-11 11:20:25] Mapping left_kept_reads.m2g_um_seg12 to genome segment_juncs with Bowtie2 (12/15)
[2014-09-11 11:20:33] Mapping left_kept_reads.m2g_um_seg13 to genome segment_juncs with Bowtie2 (13/15)
[2014-09-11 11:20:39] Mapping left_kept_reads.m2g_um_seg14 to genome segment_juncs with Bowtie2 (14/15)
[2014-09-11 11:20:45] Mapping left_kept_reads.m2g_um_seg15 to genome segment_juncs with Bowtie2 (15/15)
[2014-09-11 11:20:51] Joining segment hits
[FAILED]
Error running 'long_spanning_reads':Warning: 2476721 malformed closure
I'm not sure waht does it mean.
Can you help me?.
Best regards
Xabier
