Question: Cufflinks seg fault
0
gravatar for shg018
23 months ago by
shg0180
shg0180 wrote:

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!!

sequencing • 649 views
ADD COMMENTlink modified 23 months ago by Pierre Lindenbaum118k • written 23 months ago by shg0180

What OS is this on? Did you compile cufflinks yourself or downloaded the binary? If this was macOS then check into this option.

ADD REPLYlink modified 23 months ago • written 23 months ago by genomax64k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1410 users visited in the last hour