Warnings in cuffdiff subsequently killing the program

[konika]

Hi
I have run the command

cuffdiff -o /wrk/sushilth/analysis/differential_expression/all_samples_redo_cuffmerge2 \
-b /wrk/sushilth/MM_GFF/Mus_musculus/NCBI/build37.2/Sequence/WholeGenomeFasta/genome.fa \
-p 8 -L Scr,Lkb1,Nuak1,Nuak2 -u /wrk/sushilth/analysis/merged_asm/merged.gtf \
/wrk/sushilth/analysis/scr/br1/tophat_out_sbr1/sbr1_accepted_hits.bam,\
/wrk/sushilth/analysis/scr/br2/tophat_out_sbr2/sbr2_accepted_hits.bam,\
/wrk/sushilth/analysis/scr/br3/tophat_out_sbr3/sbr3_accepted_hits.bam \
/wrk/sushilth/analysis/lkb1/br1/tophat_out_lbr1/lbr1_accepted_hits.bam,\
/wrk/sushilth/analysis/lkb1/br2/tophat_out_lbr2/lbr2_accepted_hits.bam,\
/wrk/sushilth/analysis/lkb1/br3/tophat_out_lbr3/lbr3_accepted_hits.bam \
/wrk/sushilth/analysis/nuak1/br1/tophat_out_n1br1/n1br1_accepted_hits.bam,\
/wrk/sushilth/analysis/nuak1/br2/tophat_out_n1br2/n1br2_accepted_hits.bam,\
/wrk/sushilth/analysis/nuak1/br3/tophat_out_n1br3/n1br3_accepted_hits.bam \
/wrk/sushilth/analysis/nuak2/br1/tophat_out_n2br1/n2br1_accepted_hits.bam,\
/wrk/sushilth/analysis/nuak2/br2/tophat_out_n2br2/n2br2_accepted_hits.bam,\
/wrk/sushilth/analysis/nuak2/br3/tophat_out_n2br3/n2br3_accepted_hits.bam

This gives several warnings such as

Warning: couldn't find fasta record for '13|NT_110857.1'!
This contig will not be bias corrected.

And after some processing the program is killed :
cuffdiff_all_samples_redo.sh: line 26: 35440 Killed

Maybe anyone can help on what is going wrong.
Thanks