Error running TopHat- "Warning: no input BAM records found"

[gkandoi]

I'm doing RNA-Seq analysis using TopHat and Cufflinks package on A. thaliana reads. When I run TopHat, I get the following error:

[2015-04-09 17:48:26] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2015-04-09 17:48:36] Joining segment hits
[2015-04-09 17:49:21] Reporting output tracks
[FAILED]
Error running /shared/software/bcb660/packages/TopHat/2.0.14/tophat_reports --min-anchor 8 --splice-mismatches 0 --min-report-intron 50 --max-report-intron 500000 --min-isoform-fraction 0.15 --output-dir SRR1020621/ --max-multihits 20 --max-seg-multihits 40 --segment-length 25 --segment-mismatches 2 --min-closure-exon 100 --min-closure-intron 50 --max-closure-intron 5000 --min-coverage-intron 50 --max-coverage-intron 20000 --min-segment-intron 50 --max-segment-intron 500000 --read-mismatches 2 --read-gap-length 2 --read-edit-dist 2 --read-realign-edit-dist 3 --max-insertion-length 3 --max-deletion-length 3 -z gzip -p32 --gtf-annotations TAIR10_GFF3_genes.gff --gtf-juncs SRR1020621/tmp/TAIR10_GFF3_genes.juncs --no-closure-search --no-coverage-search --no-microexon-search --sam-header SRR1020621/tmp/genome_genome.bwt.samheader.sam --report-discordant-pair-alignments --report-mixed-alignments --samtools=/shared/software/bcb660/packages/TopHat/2.0.14/samtools_0.1.18 --bowtie2-max-penalty 6 --bowtie2-min-penalty 2 --bowtie2-penalty-for-N 1 --bowtie2-read-gap-open 5 --bowtie2-read-gap-cont 3 --bowtie2-ref-gap-open 5 --bowtie2-ref-gap-cont 3 genome.fa SRR1020621/junctions.bed SRR1020621/insertions.bed SRR1020621/deletions.bed SRR1020621/fusions.out SRR1020621/tmp/accepted_hits SRR1020621/tmp/left_kept_reads.m2g.bam,SRR1020621/tmp/left_kept_reads.m2g_um.mapped.bam,SRR1020621/tmp/left_kept_reads.m2g_um.candidates SRR1020621/tmp/left_kept_reads.bam
Warning: no input BAM records found in SRR1020621/tmp/left_kept_reads.m2g_um.candidates31.bam (possibly due to wrong offset)

The software versions I'm using are:
Bowtie: 2.2.3
TopHat: 2.0.14

Can someone shed some light on what might be going wrong here?