Hey everyone

So I've been trying to generate read counts from my sam files. So far I have converted the sam file to bam or sorted bam and tried using the line: /opt/biotools/cufflinks/bin/cufflinks -G /oasis/tscc/scratch/shagupta/L2AnnotatedGenome.02/gencode.vM10.long_noncoding_RNAs.gtf -o transcripts.gtf ./FF1_5_R.bam

I tried gdb to figure out the error and I get:

(gdb) backtrace

#0  0x00002aaaaaabf7a8 in boost::exception_ptr boost::exception_detail::get_static_exception_object<boost::exception_detail::bad_exception_>() ()
   from /opt/boost/gnu/lib/libboost_thread.so.1.55.0
#1  0x00002aaaaaac1451 in _GLOBAL__sub_I_thread.cpp ()
   from /opt/boost/gnu/lib/libboost_thread.so.1.55.0
#2  0x00002aaaaaac17c6 in __do_global_ctors_aux ()
   from /opt/boost/gnu/lib/libboost_thread.so.1.55.0
#3  0x00002aaaaaaba253 in _init ()
   from /opt/boost/gnu/lib/libboost_thread.so.1.55.0
#4  0x00002aaaab4619a0 in ?? ()
#5  0x00000036e720e625 in _dl_init_internal () from /lib64/ld-linux-x86-64.so.2
#6  0x00000036e7200b3a in _dl_start_user () from /lib64/ld-linux-x86-64.so.2
#7  0x0000000000000006 in ?? ()
#8  0x00007fffffffba5b in ?? ()
#9  0x00007fffffffba81 in ?? ()
#10 0x00007fffffffba84 in ?? ()
#11 0x00007fffffffbadb in ?? ()
#12 0x00007fffffffbade in ?? ()
#13 0x00007fffffffbaee in ?? ()
#14 0x0000000000000000 in ?? ()

which I don't really know what to do with. My head for the gtf file I used to map was:

##description: evidence-based annotation of the mouse genome (GRCm38), version M10 (Ensembl 85) - long non-coding RNAs                              
##provider: GENCODE                             
##contact: gencode-help@sanger.ac.uk                                
##format: gtf                               
##date: 2016-07-19                              
1   HAVANA  gene    3073253 3074322 .   +   .   gene_id "ENSMUSG00000102693.1"; gene_type "TEC"; gene_status "KNOWN"; gene_name "4933401J01Rik"; level 2; havana_gene "OTTMUSG00000049935.1";
1   HAVANA  transcript  3073253 3074322 .   +   .   gene_id "ENSMUSG00000102693.1"; transcript_id "ENSMUST00000193812.1"; gene_type "TEC"; gene_status "KNOWN"; gene_name "4933401J01Rik"; transcript_type "TEC"; transcript_status "KNOWN"; transcript_name "4933401J01Rik-001"; level 2; transcript_support_level "NA"; tag "basic"; havana_gene "OTTMUSG00000049935.1"; havana_transcript "OTTMUST00000127109.1";
1   HAVANA  exon    3073253 3074322 .   +   .   gene_id "ENSMUSG00000102693.1"; transcript_id "ENSMUST00000193812.1"; gene_type "TEC"; gene_status "KNOWN"; gene_name "4933401J01Rik"; transcript_type "TEC"; transcript_status "KNOWN"; transcript_name "4933401J01Rik-001"; exon_number 1; exon_id "ENSMUSE00001343744.1"; level 2; transcript_support_level "NA"; tag "basic"; havana_gene "OTTMUSG00000049935.1"; havana_transcript "OTTMUST00000127109.1";
1   HAVANA  gene    3365731 3368549 .   -   .   gene_id "ENSMUSG00000103377.1"; gene_type "TEC"; gene_status "KNOWN"; gene_name "Gm37180"; level 2; havana_gene "OTTMUSG00000049960.1";
1   HAVANA  transcript  3365731 3368549 .   -   .   gene_id "ENSMUSG00000103377.1"; transcript_id "ENSMUST00000195335.1"; gene_type "TEC"; gene_status "KNOWN"; gene_name "Gm37180"; transcript_type "TEC"; transcript_status "KNOWN"; transcript_name "Gm37180-001"; level 2; transcript_support_level "NA"; tag "basic"; havana_gene "OTTMUSG00000049960.1"; havana_transcript "OTTMUST00000127145.1";
1   HAVANA  exon    3365731 3368549 .   -   .   gene_id "ENSMUSG00000103377.1"; transcript_id "ENSMUST00000195335.1"; gene_type "TEC"; gene_status "KNOWN"; gene_name "Gm37180"; transcript_type "TEC"; transcript_status "KNOWN"; transcript_name "Gm37180-001"; exon_number 1; exon_id "ENSMUSE00001343189.1"; level 2; transcript_support_level "NA"; tag "basic"; havana_gene "OTTMUSG00000049960.1"; havana_transcript "OTTMUST00000127145.1";
1   HAVANA  gene    3375556 3377788 .   -   .   gene_id "ENSMUSG00000104017.1"; gene_type "TEC"; gene_status "KNOWN"; gene_name "Gm37363"; level 2; havana_gene "OTTMUSG00000049961.1";
1   HAVANA  transcript  3375556 3377788 .   -   .   gene_id "ENSMUSG00000104017.1"; transcript_id "ENSMUST00000192336.1"; gene_type "TEC"; gene_status "KNOWN"; gene_name "Gm37363"; transcript_type "TEC"; transcript_status "KNOWN"; transcript_name "Gm37363-001"; level 2; transcript_support_level "NA"; tag "basic"; havana_gene "OTTMUSG00000049961.1"; havana_transcript "OTTMUST00000127146.1";

Any help would be greatly appreciated!!