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  • Error when using Cufflinks 2.0.1

    Hi,
    When running Cufflinks 2.0.1 it generates the error:

    *** glibc detected *** cufflinks: double free or corruption (!prev): 0x000000003f909d00 ***
    ======= Backtrace: =========
    /lib64/libc.so.6[0x3abc47245f]
    /lib64/libc.so.6(cfree+0x4b)[0x3abc4728bb]
    cufflinks[0x416f0c]
    cufflinks[0x416daf]
    cufflinks[0x416fdc]
    cufflinks[0x41703c]
    cufflinks[0x416daf]
    cufflinks[0x40d05b]
    cufflinks[0x4210fc]
    /lib64/libc.so.6(__libc_start_main+0xf4)[0x3abc41d994]
    cufflinks(sin+0xc1)[0x405bd9]
    ======= Memory map: ========
    00400000-00601000 r-xp 00000000 cfc:dd64c 311077305 /cufflinks-2.0.1.Linux_x86_64/cufflinks
    00801000-00805000 rwxp 00201000 cfc:dd64c 311077305 /cufflinks-2.0.1.Linux_x86_64/cufflinks
    00805000-00825000 rwxp 00805000 00:00 0
    15704000-409b7000 rwxp 15704000 00:00 0 [heap]
    409b7000-409b8000 ---p 409b7000 00:00 0
    409b8000-40bb8000 rwxp 409b8000 00:00 0
    41157000-41158000 ---p 41157000 00:00 0
    41158000-41358000 rwxp 41158000 00:00 0
    41743000-41744000 ---p 41743000 00:00 0
    41744000-41944000 rwxp 41744000 00:00 0
    41944000-41945000 ---p 41944000 00:00 0
    41945000-41b45000 rwxp 41945000 00:00 0
    41b45000-41b46000 ---p 41b45000 00:00 0
    41b46000-41d46000 rwxp 41b46000 00:00 0
    41d5f000-41d60000 ---p 41d5f000 00:00 0
    41d60000-41f60000 rwxp 41d60000 00:00 0
    41f60000-41f61000 ---p 41f60000 00:00 0
    41f61000-42161000 rwxp 41f61000 00:00 0
    42161000-42162000 ---p 42161000 00:00 0
    42162000-42362000 rwxp 42162000 00:00 0
    42362000-42363000 ---p 42362000 00:00 0
    42363000-42563000 rwxp 42363000 00:00 0
    3abc000000-3abc01c000 r-xp 00000000 00:13 23758096 /lib64/ld-2.5.so
    3abc21c000-3abc21d000 r-xp 0001c000 00:13 23758096 /lib64/ld-2.5.so
    3abc21d000-3abc21e000 rwxp 0001d000 00:13 23758096 /lib64/ld-2.5.so
    3abc400000-3abc54e000 r-xp 00000000 00:13 23758095 /lib64/libc-2.5.so
    3abc54e000-3abc74e000 ---p 0014e000 00:13 23758095 /lib64/libc-2.5.so
    3abc74e000-3abc752000 r-xp 0014e000 00:13 23758095 /lib64/libc-2.5.so
    3abc752000-3abc753000 rwxp 00152000 00:13 23758095 /lib64/libc-2.5.so
    3abc753000-3abc758000 rwxp 3abc753000 00:00 0
    3abcc00000-3abcc16000 r-xp 00000000 00:13 23758108 /lib64/libpthread-2.5.so
    3abcc16000-3abce15000 ---p 00016000 00:13 23758108 /lib64/libpthread-2.5.so
    3abce15000-3abce16000 r-xp 00015000 00:13 23758108 /lib64/libpthread-2.5.so
    3abce16000-3abce17000 rwxp 00016000 00:13 23758108 /lib64/libpthread-2.5.so
    3abce17000-3abce1b000 rwxp 3abce17000 00:00 0
    3abd000000-3abd082000 r-xp 00000000 00:13 23758249 /lib64/libm-2.5.so
    3abd082000-3abd281000 ---p 00082000 00:13 23758249 /lib64/libm-2.5.so
    3abd281000-3abd282000 r-xp 00081000 00:13 23758249 /lib64/libm-2.5.so
    3abd282000-3abd283000 rwxp 00082000 00:13 23758249 /lib64/libm-2.5.so
    3abdc00000-3abdc14000 r-xp 00000000 00:13 23665721 /usr/lib64/libz.so.1.2.3
    3abdc14000-3abde13000 ---p 00014000 00:13 23665721 /usr/lib64/libz.so.1.2.3
    3abde13000-3abde14000 rwxp 00013000 00:13 23665721 /usr/lib64/libz.so.1.2.3
    3abe400000-3abe40d000 r-xp 00000000 00:13 23758022 /lib64/libgcc_s-4.1.2-20080825.so.1
    3abe40d000-3abe60d000 ---p 0000d000 00:13 23758022 /lib64/libgcc_s-4.1.2-20080825.so.1
    3abe60d000-3abe60e000 rwxp 0000d000 00:13 23758022 /lib64/libgcc_s-4.1.2-20080825.so.1
    2aaaaaaab000-2aaaabc0e000 rwxp 2aaaaaaab000 00:00 0
    2aaaac000000-2aaaafe62000 rwxp 2aaaac000000 00:00 0
    2aaaafe62000-2aaab0000000 ---p 2aaaafe62000 00:00 0
    2aaab0000000-2aaab3c72000 rwxp 2aaab0000000 00:00 0
    2aaab3c72000-2aaab4000000 ---p 2aaab3c72000 00:00 0
    2aaab4000000-2aaab7ffd000 rwxp 2aaab4000000 00:00 0
    2aaab7ffd000-2aaab8000000 ---p 2aaab7ffd000 00:00 0
    2aaab8000000-2aaabbd75000 rwxp 2aaab8000000 00:00 0
    2aaabbd75000-2aaabc000000 ---p 2aaabbd75000 00:00 0
    2aaabc000000-2aaabf8d8000 rwxp 2aaabc000000 00:00 0
    2aaabf8d8000-2aaac0000000 ---p 2aaabf8d8000 00:00 0
    2aaac0000000-2aaac2e3d000 rwxp 2aaac0000000 00:00 0
    2aaac2e3d000-2aaac4000000 ---p 2aaac2e3d000 00:00 0
    2aaac4000000-2aaac7d6f000 rwxp 2aaac4000000 00:00 0
    2aaac7d6f000-2aaac8000000 ---p 2aaac7d6f000 00:00 0
    2aaac8600000-2aaac9421000 rwxp 2aaac8600000 00:00 0
    2aaacc000000-2aaacfee4000 rwxp 2aaacc000000 00:00 0
    2aaacfee4000-2aaad0000000 ---p 2aaacfee4000 00:00 0
    2aaad0000000-2aaad3ffb000 rwxp 2aaad0000000 00:00 0
    2aaad3ffb000-2aaad4000000 ---p 2aaad3ffb000 00:00 0
    2aaad4000000-2aaad6d63000 rwxp 2aaad4000000 00:00 0
    2b608771c000-2b608771d000 rwxp 2b608771c000 00:00 0
    2b608772a000-2b608792d000 rwxp 2b608772a000 00:00 0
    7fff7fffa000-7fff80010000 rw-p 7ffffffe8000 00:00 0 [stack]
    ffffffffff600000-ffffffffffe00000 ---p 00000000 00:00 0 [vdso]


    It seems to be creating all the necessary output files and they seem to be ok.
    The command I used was:
    cufflinks -o cuff_MB -p 8 -G mygenome.gtf -b newTHref.fa -u -N --no-update-check --compatible-hits-norm ./MB_C/accepted_hits.bam

    What is this error doing?
    Thanks

  • #2
    Hey there,
    Not that it helps you at all, but I get the same error. You aren't alone in this!


    ${CUFFLINKS} \
    -o out/$1/cufflinks_out \
    -p 4 \
    --multi-read-correct \
    --frag-bias-correct ${GENOME} \
    --library-type fr-unstranded \
    out/$1/tophat_out/accepted_hits.bam

    Is it wrong to use --frag-bias-correct when you also have an fr-unstranded RNA-seq library? Maybe that is causing the crash?

    Comment


    • #3
      Originally posted by jstjohn View Post

      Is it wrong to use --frag-bias-correct when you also have an fr-unstranded RNA-seq library? Maybe that is causing the crash?
      I didn't specify what my library type was so I don't think this is causing the error. Have you tried emailing the creators of Cufflinks?

      Comment


      • #4
        Hello,

        Same here, I don't have the answer but I seem to get the same error. I didn't have time to investigate it any further...

        Dario

        Code:
        cufflinks -o cufflinks_out/GTF/ds019 -p 1 --GTF /lustre/sblab/berald01/reference_data/genomes/iGenomes/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.gtf --multi-read-correct --upper-quartile-norm -b /lustre/sblab/berald01/reference_data/genomes/iGenomes/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.fa tophat_out/ds019/accepted_hits.bam
        
        You are using Cufflinks v2.0.1, which is the most recent release.
        [17:06:29] Loading reference annotation and sequence.
        Warning: couldn't find fasta record for 'chr17_ctg5_hap1'!
        This contig will not be bias corrected.
        Warning: couldn't find fasta record for 'chr17_gl000205_random'!
        This contig will not be bias corrected.
        Warning: couldn't find fasta record for 'chr19_gl000209_random'!
        This contig will not be bias corrected.
        Warning: couldn't find fasta record for 'chr1_gl000191_random'!
        This contig will not be bias corrected.
        Warning: couldn't find fasta record for 'chr4_ctg9_hap1'!
        This contig will not be bias corrected.
        Warning: couldn't find fasta record for 'chr4_gl000193_random'!
        This contig will not be bias corrected.
        Warning: couldn't find fasta record for 'chr4_gl000194_random'!
        This contig will not be bias corrected.
        Warning: couldn't find fasta record for 'chr6_apd_hap1'!
        This contig will not be bias corrected.
        Warning: couldn't find fasta record for 'chr6_cox_hap2'!
        This contig will not be bias corrected.
        Warning: couldn't find fasta record for 'chr6_dbb_hap3'!
        This contig will not be bias corrected.
        Warning: couldn't find fasta record for 'chr6_mann_hap4'!
        This contig will not be bias corrected.
        Warning: couldn't find fasta record for 'chr6_mcf_hap5'!
        This contig will not be bias corrected.
        Warning: couldn't find fasta record for 'chr6_qbl_hap6'!
        This contig will not be bias corrected.
        Warning: couldn't find fasta record for 'chr6_ssto_hap7'!
        This contig will not be bias corrected.
        Warning: couldn't find fasta record for 'chr7_gl000195_random'!
        This contig will not be bias corrected.
        Warning: couldn't find fasta record for 'chrUn_gl000211'!
        This contig will not be bias corrected.
        Warning: couldn't find fasta record for 'chrUn_gl000212'!
        This contig will not be bias corrected.
        Warning: couldn't find fasta record for 'chrUn_gl000218'!
        This contig will not be bias corrected.
        Warning: couldn't find fasta record for 'chrUn_gl000219'!
        This contig will not be bias corrected.
        Warning: couldn't find fasta record for 'chrUn_gl000220'!
        This contig will not be bias corrected.
        Warning: couldn't find fasta record for 'chrUn_gl000222'!
        This contig will not be bias corrected.
        Warning: couldn't find fasta record for 'chrUn_gl000223'!
        This contig will not be bias corrected.
        Warning: couldn't find fasta record for 'chrUn_gl000228'!
        This contig will not be bias corrected.
        [17:07:16] Inspecting reads and determining fragment length distribution.
        > Processed 20912 loci.                        [*************************] 100%
        > Map Properties:
        >	Upper Quartile: 2476.50
        >	Normalized Map Mass: 2476.50
        >	Raw Map Mass: 49549793.64
        >	Number of Multi-Reads: 1005158 (with 2421746 total hits)
        >	Fragment Length Distribution: Empirical (learned)
        >	              Estimated Mean: 177.23
        >	           Estimated Std Dev: 53.66
        [17:14:36] Learning bias parameters.
        > Processed 20912 loci.                        [*************************] 100%
        [18:13:09] Re-estimating abundances with bias and multi-read correction.
        > Processed 20912 loci.                        [*************************] 100%
        *** glibc detected *** cufflinks: double free or corruption (!prev): 0x000000001e1ec880 ***
        ======= Backtrace: =========
        /lib64/libc.so.6[0x30b067230f]
        /lib64/libc.so.6(cfree+0x4b)[0x30b067276b]
        cufflinks[0x416f0c]
        cufflinks[0x416daf]
        cufflinks[0x416fdc]
        cufflinks[0x41703c]
        cufflinks[0x416daf]
        cufflinks[0x40d05b]
        cufflinks[0x4210fc]
        /lib64/libc.so.6(__libc_start_main+0xf4)[0x30b061d994]
        cufflinks(sin+0xc1)[0x405bd9]
        ======= Memory map: ========
        00400000-00601000 r-xp 00000000 00:18 466076018                          /home/berald01/applications/cufflinks/cufflinks-2.0.1.Linux_x86_64/cufflinks
        00801000-00805000 rw-p 00201000 00:18 466076018                          /home/berald01/applications/cufflinks/cufflinks-2.0.1.Linux_x86_64/cufflinks
        00805000-00825000 rw-p 00805000 00:00 0 
        066e3000-1f21a000 rw-p 066e3000 00:00 0                                  [heap]
        40343000-40344000 ---p 40343000 00:00 0 
        40344000-40544000 rw-p 40344000 00:00 0 
        41a11000-41a12000 ---p 41a11000 00:00 0 
        41a12000-41c12000 rw-p 41a12000 00:00 0 
        30b0200000-30b021c000 r-xp 00000000 68:06 491836                         /lib64/ld-2.5.so
        30b041b000-30b041c000 r--p 0001b000 68:06 491836                         /lib64/ld-2.5.so
        30b041c000-30b041d000 rw-p 0001c000 68:06 491836                         /lib64/ld-2.5.so
        30b0600000-30b074e000 r-xp 00000000 68:06 491837                         /lib64/libc-2.5.so
        30b074e000-30b094d000 ---p 0014e000 68:06 491837                         /lib64/libc-2.5.so
        30b094d000-30b0951000 r--p 0014d000 68:06 491837                         /lib64/libc-2.5.so
        30b0951000-30b0952000 rw-p 00151000 68:06 491837                         /lib64/libc-2.5.so
        30b0952000-30b0957000 rw-p 30b0952000 00:00 0 
        30b0e00000-30b0e82000 r-xp 00000000 68:06 491843                         /lib64/libm-2.5.so
        30b0e82000-30b1081000 ---p 00082000 68:06 491843                         /lib64/libm-2.5.so
        30b1081000-30b1082000 r--p 00081000 68:06 491843                         /lib64/libm-2.5.so
        30b1082000-30b1083000 rw-p 00082000 68:06 491843                         /lib64/libm-2.5.so
        30b1200000-30b1216000 r-xp 00000000 68:06 491842                         /lib64/libpthread-2.5.so
        30b1216000-30b1415000 ---p 00016000 68:06 491842                         /lib64/libpthread-2.5.so
        30b1415000-30b1416000 r--p 00015000 68:06 491842                         /lib64/libpthread-2.5.so
        30b1416000-30b1417000 rw-p 00016000 68:06 491842                         /lib64/libpthread-2.5.so
        30b1417000-30b141b000 rw-p 30b1417000 00:00 0 
        30b1600000-30b1614000 r-xp 00000000 68:02 358643                         /usr/lib64/libz.so.1.2.3
        30b1614000-30b1813000 ---p 00014000 68:02 358643                         /usr/lib64/libz.so.1.2.3
        30b1813000-30b1814000 rw-p 00013000 68:02 358643                         /usr/lib64/libz.so.1.2.3
        30b2a00000-30b2a0d000 r-xp 00000000 68:06 491849                         /lib64/libgcc_s-4.1.2-20080825.so.1
        30b2a0d000-30b2c0d000 ---p 0000d000 68:06 491849                         /lib64/libgcc_s-4.1.2-20080825.so.1
        30b2c0d000-30b2c0e000 rw-p 0000d000 68:06 491849                         /lib64/libgcc_s-4.1.2-20080825.so.1
        30b4200000-30b4215000 r-xp 00000000 68:06 491714                         /lib64/libnsl-2.5.so
        30b4215000-30b4414000 ---p 00015000 68:06 491714                         /lib64/libnsl-2.5.so
        30b4414000-30b4415000 r--p 00014000 68:06 491714                         /lib64/libnsl-2.5.so
        30b4415000-30b4416000 rw-p 00015000 68:06 491714                         /lib64/libnsl-2.5.so
        30b4416000-30b4418000 rw-p 30b4416000 00:00 0 
        30b6e00000-30b6e11000 r-xp 00000000 68:06 491854                         /lib64/libresolv-2.5.so
        30b6e11000-30b7011000 ---p 00011000 68:06 491854                         /lib64/libresolv-2.5.so
        30b7011000-30b7012000 r--p 00011000 68:06 491854                         /lib64/libresolv-2.5.so
        30b7012000-30b7013000 rw-p 00012000 68:06 491854                         /lib64/libresolv-2.5.so
        30b7013000-30b7015000 rw-p 30b7013000 00:00 0 
        2aaaac000000-2aaab0000000 rw-p 2aaaac000000 00:00 0 
        2aaab4000000-2aaab7ffe000 rw-p 2aaab4000000 00:00 0 
        2aaab7ffe000-2aaab8000000 ---p 2aaab7ffe000 00:00 0 
        2ab8931a8000-2ab8931aa000 rw-p 2ab8931a8000 00:00 0 
        2ab8931bc000-2ab8931bf000 rw-p 2ab8931bc000 00:00 0 
        2ab8931bf000-2ab8931c9000 r-xp 00000000 68:06 491547                     /lib64/libnss_files-2.5.so
        2ab8931c9000-2ab8933c8000 ---p 0000a000 68:06 491547                     /lib64/libnss_files-2.5.so
        2ab8933c8000-2ab8933c9000 r--p 00009000 68:06 491547                     /lib64/libnss_files-2.5.so
        2ab8933c9000-2ab8933ca000 rw-p 0000a000 68:06 491547                     /lib64/libnss_files-2.5.so
        2ab8933ca000-2ab8933d3000 r-xp 00000000 68:06 491551                     /lib64/libnss_nis-2.5.so
        2ab8933d3000-2ab8935d3000 ---p 00009000 68:06 491551                     /lib64/libnss_nis-2.5.so
        2ab8935d3000-2ab8935d4000 r--p 00009000 68:06 491551                     /lib64/libnss_nis-2.5.so
        2ab8935d4000-2ab8935d5000 rw-p 0000a000 68:06 491551                     /lib64/libnss_nis-2.5.so
        2ab8935d5000-2ab8935d9000 r-xp 00000000 68:06 491545                     /lib64/libnss_dns-2.5.so
        2ab8935d9000-2ab8937d8000 ---p 00004000 68:06 491545                     /lib64/libnss_dns-2.5.so
        2ab8937d8000-2ab8937d9000 r--p 00003000 68:06 491545                     /lib64/libnss_dns-2.5.so
        2ab8937d9000-2ab8937da000 rw-p 00004000 68:06 491545                     /lib64/libnss_dns-2.5.so
        2ab8937da000-2ab8939da000 rw-p 2ab8937da000 00:00 0 
        7fffdba0a000-7fffdba20000 rw-p 7ffffffe8000 00:00 0                      [stack]
        7fffdbbfd000-7fffdbc00000 r-xp 7fffdbbfd000 00:00 0                      [vdso]
        ffffffffff600000-ffffffffffe00000 ---p 00000000 00:00 0                  [vsyscall]
        /home/berald01/.lsbatch/1340467579.346876: line 8: 31009 Aborted                 (core dumped) cufflinks -o cufflinks_out/GTF/ds019 -p 1 --GTF /lustre/sblab/berald01/reference_data/genomes/iGenomes/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.gtf --multi-read-correct --upper-quartile-norm -b /lustre/sblab/berald01/reference_data/genomes/iGenomes/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.fa tophat_out/ds019/accepted_hits.bam

        Comment


        • #5
          Yea, that looks like the same as mine. Seems like we all tried to use the -b bias correction option. Is there a final step with bias correction that is being missed with this, or are these runs all finishing?

          I emailed cufflinks help about this. I mentioned this thread and said that other people were having issues as well.

          Here is what my output looks like for one of my crashed runs (they all crashed like this in about the same way).


          + /hive/groups/genomeAssem/bin/cufflinks/cufflinks -o out/10_A_0d_X/cufflinks_out -p 4 --multi-read-correct --frag-bias-correct /hive/users/jstjohn/Alligator/Gator_Assem/AKHW01000000_sub1/aMiss_AKHW01000000_sub1.fa --library-type fr-unstranded out/10_A_0d_X/tophat_out/accepted_hits.bam
          You are using Cufflinks v2.0.1, which is the most recent release.
          [11:47:09] Inspecting reads and determining fragment length distribution.
          > Processed 202041 loci. [*************************] 100%
          > Map Properties:
          > Normalized Map Mass: 34357232.07
          > Raw Map Mass: 34357232.07
          > Number of Multi-Reads: 388396 (with 942238 total hits)
          > Fragment Length Distribution: Empirical (learned)
          > Estimated Mean: 221.25
          > Estimated Std Dev: 70.11
          [12:09:49] Assembling transcripts and initializing abundances for multi-read correction.
          > Processing Locus scaffold-14384:20845-20945 [****** ] 25%
          WARNING: Multi-Hit not found (953636,953778).
          > Processing Locus scaffold-3290:3025-3319 [*********** ] 44%
          WARNING: Multi-Hit not found (207023,207372).
          > Processing Locus scaffold-9514:13798-96850 [************************ ] 96%
          WARNING: Multi-Hit not found (1612340,1614129).
          > Processed 209036 loci. [*************************] 100%
          [14:06:01] Loading reference annotation and sequence.
          [14:11:20] Learning bias parameters.
          > Processed 28497 loci. [*************************] 100%
          [14:23:35] Re-estimating abundances with bias and multi-read correction.
          > Processed 28497 loci. [*************************] 100%
          *** glibc detected *** /hive/groups/genomeAssem/bin/cufflinks/cufflinks: double free or corruption (!prev): 0x00000000231fe180 ***
          ======= Backtrace: =========
          /lib64/libc.so.6[0x31a2c71ce2]
          /lib64/libc.so.6(cfree+0x8c)[0x31a2c7590c]
          /hive/groups/genomeAssem/bin/cufflinks/cufflinks[0x416f0c]
          /hive/groups/genomeAssem/bin/cufflinks/cufflinks[0x416daf]
          /hive/groups/genomeAssem/bin/cufflinks/cufflinks[0x416fdc]
          /hive/groups/genomeAssem/bin/cufflinks/cufflinks[0x41703c]
          /hive/groups/genomeAssem/bin/cufflinks/cufflinks[0x416daf]
          /hive/groups/genomeAssem/bin/cufflinks/cufflinks[0x40d05b]
          /hive/groups/genomeAssem/bin/cufflinks/cufflinks[0x4210fc]
          /lib64/libc.so.6(__libc_start_main+0xf4)[0x31a2c1d974]
          /hive/groups/genomeAssem/bin/cufflinks/cufflinks(sin+0xc1)[0x405bd9]
          ======= Memory map: ========
          00400000-00601000 r-xp 00000000 00:1a 390797415 /hive/groups/genomeAssem/src/cufflinks-2.0.1.Linux_x86_64/cufflinks
          00801000-00805000 rw-p 00201000 00:1a 390797415 /hive/groups/genomeAssem/src/cufflinks-2.0.1.Linux_x86_64/cufflinks
          00805000-00825000 rw-p 00805000 00:00 0
          1c5f9000-287ee000 rw-p 1c5f9000 00:00 0 [heap]
          43536000-43537000 ---p 43536000 00:00 0
          43537000-43f37000 rw-p 43537000 00:00 0
          44938000-44939000 ---p 44938000 00:00 0
          44939000-45339000 rw-p 44939000 00:00 0
          4673b000-4673c000 ---p 4673b000 00:00 0
          4673c000-4713c000 rw-p 4673c000 00:00 0
          31a2800000-31a281c000 r-xp 00000000 08:01 2050560 /lib64/ld-2.5.so
          31a2a1b000-31a2a1c000 r--p 0001b000 08:01 2050560 /lib64/ld-2.5.so
          31a2a1c000-31a2a1d000 rw-p 0001c000 08:01 2050560 /lib64/ld-2.5.so
          31a2c00000-31a2d4c000 r-xp 00000000 08:01 2050561 /lib64/libc-2.5.so
          31a2d4c000-31a2f4c000 ---p 0014c000 08:01 2050561 /lib64/libc-2.5.so
          31a2f4c000-31a2f50000 r--p 0014c000 08:01 2050561 /lib64/libc-2.5.so
          31a2f50000-31a2f51000 rw-p 00150000 08:01 2050561 /lib64/libc-2.5.so
          31a2f51000-31a2f56000 rw-p 31a2f51000 00:00 0
          31a3400000-31a3416000 r-xp 00000000 08:01 2050566 /lib64/libpthread-2.5.so
          31a3416000-31a3615000 ---p 00016000 08:01 2050566 /lib64/libpthread-2.5.so
          31a3615000-31a3616000 r--p 00015000 08:01 2050566 /lib64/libpthread-2.5.so
          31a3616000-31a3617000 rw-p 00016000 08:01 2050566 /lib64/libpthread-2.5.so
          31a3617000-31a361b000 rw-p 31a3617000 00:00 0
          31a3800000-31a3882000 r-xp 00000000 08:01 2050323 /lib64/libm-2.5.so
          31a3882000-31a3a81000 ---p 00082000 08:01 2050323 /lib64/libm-2.5.so
          31a3a81000-31a3a82000 r--p 00081000 08:01 2050323 /lib64/libm-2.5.so
          31a3a82000-31a3a83000 rw-p 00082000 08:01 2050323 /lib64/libm-2.5.so
          31a4400000-31a4414000 r-xp 00000000 08:01 495126 /usr/lib64/libz.so.1.2.3
          31a4414000-31a4613000 ---p 00014000 08:01 495126 /usr/lib64/libz.so.1.2.3
          31a4613000-31a4614000 rw-p 00013000 08:01 495126 /usr/lib64/libz.so.1.2.3
          37d4e00000-37d4e0d000 r-xp 00000000 08:01 2050331 /lib64/libgcc_s-4.1.2-20080825.so.1
          37d4e0d000-37d500d000 ---p 0000d000 08:01 2050331 /lib64/libgcc_s-4.1.2-20080825.so.1
          37d500d000-37d500e000 rw-p 0000d000 08:01 2050331 /lib64/libgcc_s-4.1.2-20080825.so.1
          2aaaaaaab000-2aaaaaaeb000 rw-p 2aaaaaaab000 00:00 0
          2aaaac000000-2aaab0000000 rw-p 2aaaac000000 00:00 0
          2aaab0000000-2aaab4000000 rw-p 2aaab0000000 00:00 0
          2aaab4000000-2aaab8000000 rw-p 2aaab4000000 00:00 0
          2aaab8000000-2aaabc000000 rw-p 2aaab8000000 00:00 0
          2aaac0000000-2aaac4000000 rw-p 2aaac0000000 00:00 0
          2aaac4000000-2aaac7ff5000 rw-p 2aaac4000000 00:00 0
          2aaac7ff5000-2aaac8000000 ---p 2aaac7ff5000 00:00 0
          2b02c551f000-2b02c5520000 rw-p 2b02c551f000 00:00 0
          2b02c552c000-2b02c552f000 rw-p 2b02c552c000 00:00 0
          2b02c552f000-2b02c5564000 r--s 00000000 08:01 3385625 /var/db/nscd/hosts
          2b02c5564000-2b02c55d1000 rw-p 2b02c5564000 00:00 0
          7fff029e2000-7fff029f8000 rw-p 7ffffffe9000 00:00 0 [stack]
          ffffffffff600000-ffffffffffe00000 ---p 00000000 00:00 0 [vdso]
          ./CuffLinksGenes.sh: line 20: 5564 Aborted ${CUFFLINKS} -o out/$1/cufflinks_out -p 4 --multi-read-correct --frag-bias-correct ${GENOME} --library-type fr-unstranded out/$1/tophat_out/accepted_hits.bam

          Comment


          • #6
            Alright, Cole Trapnel has been working with me on this, and he identified and fixed the problem that was causing my crash at least. I believe a new version of cufflinks (2.0.2 or something) will be released soon reflecting the changes that fixed this issue for me. The error messages seem very similar though so I bet the new version will fix your problem as well.

            Comment


            • #7
              Originally posted by jstjohn View Post
              Alright, Cole Trapnel has been working with me on this, and he identified and fixed the problem that was causing my crash at least. I believe a new version of cufflinks (2.0.2 or something) will be released soon reflecting the changes that fixed this issue for me. The error messages seem very similar though so I bet the new version will fix your problem as well.
              Ok, thanks very much for letting me know. I'll keep an eye on the next release of cufflinks.

              Dario
              Last edited by dariober; 07-03-2012, 01:14 PM. Reason: wrong program name

              Comment


              • #8
                HI, I have had similar errors. The cufflinks output files still seem to be complete though. Did Cole mention if this bug would affect the final output?

                Comment


                • #9
                  cufflinks-2.0.2 can be downloaded now:


                  I have test this version successfully without previous mentioned errors.

                  Cheers!

                  Comment


                  • #10
                    Hi,

                    I am using cufflinks-2.0.2 and I am getting the warning messages:

                    Warning: couldn't find fasta record for 'chr17_ctg5_hap1'!
                    This contig will not be bias corrected.
                    Warning: couldn't find fasta record for 'chr17_gl000205_random'!
                    This contig will not be bias corrected.
                    Warning: couldn't find fasta record for 'chr19_gl000209_random'!
                    This contig will not be bias corrected.
                    Warning: couldn't find fasta record for 'chr1_gl000191_random'!
                    This contig will not be bias corrected.
                    Warning: couldn't find fasta record for 'chr4_ctg9_hap1'!
                    This contig will not be bias corrected.
                    Warning: couldn't find fasta record for 'chr4_gl000193_random'!
                    This contig will not be bias corrected.
                    Warning: couldn't find fasta record for 'chr4_gl000194_random'!
                    This contig will not be bias corrected.
                    Warning: couldn't find fasta record for 'chr6_apd_hap1'!
                    This contig will not be bias corrected.
                    Warning: couldn't find fasta record for 'chr6_cox_hap2'!
                    This contig will not be bias corrected.
                    Warning: couldn't find fasta record for 'chr6_dbb_hap3'!
                    This contig will not be bias corrected.
                    Warning: couldn't find fasta record for 'chr6_mann_hap4'!
                    This contig will not be bias corrected.
                    Warning: couldn't find fasta record for 'chr6_mcf_hap5'!
                    This contig will not be bias corrected.
                    Warning: couldn't find fasta record for 'chr6_qbl_hap6'!
                    This contig will not be bias corrected.
                    Warning: couldn't find fasta record for 'chr6_ssto_hap7'!
                    This contig will not be bias corrected.
                    Warning: couldn't find fasta record for 'chr7_gl000195_random'!
                    This contig will not be bias corrected.
                    Warning: couldn't find fasta record for 'chrUn_gl000211'!
                    This contig will not be bias corrected.
                    Warning: couldn't find fasta record for 'chrUn_gl000212'!
                    This contig will not be bias corrected.
                    Warning: couldn't find fasta record for 'chrUn_gl000218'!
                    This contig will not be bias corrected.
                    Warning: couldn't find fasta record for 'chrUn_gl000219'!
                    This contig will not be bias corrected.
                    Warning: couldn't find fasta record for 'chrUn_gl000220'!
                    This contig will not be bias corrected.
                    Warning: couldn't find fasta record for 'chrUn_gl000222'!
                    This contig will not be bias corrected.
                    Warning: couldn't find fasta record for 'chrUn_gl000223'!
                    This contig will not be bias corrected.

                    However, all the outputs look ok. Do you guys get these warnings with cufflinks-2.0.2?

                    Thanks
                    Pinki

                    Comment


                    • #11
                      same problem

                      I'm also getting very similar errors when running cuffmerge 2.0.2 with the following errors:
                      Code:
                      [Thu Dec 27 11:45:06 2012] Beginning transcriptome assembly merge
                      -------------------------------------------
                      
                      [Thu Dec 27 11:45:06 2012] Preparing output location cuffmergeallmskgucsc/
                      [Thu Dec 27 11:46:34 2012] Converting GTF files to SAM
                      [11:46:34] Loading reference annotation.
                      [11:46:51] Loading reference annotation.
                      [11:47:08] Loading reference annotation.
                      [11:47:24] Loading reference annotation.
                      [11:47:42] Loading reference annotation.
                      [11:48:02] Loading reference annotation.
                      [11:48:18] Loading reference annotation.
                      [11:48:35] Loading reference annotation.
                      [11:48:54] Loading reference annotation.
                      [11:49:09] Loading reference annotation.
                      [11:49:27] Loading reference annotation.
                      [11:49:46] Loading reference annotation.
                      [Thu Dec 27 11:50:13 2012] Quantitating transcripts
                      You are using Cufflinks v2.0.2, which is the most recent release.
                      Command line:
                      cufflinks -o cuffmergeallmskgucsc/ -F 0.05 -g ucscknowngenes.gtf -q --overhang-tolerance 200 --library-type=transfrags -A 0.0 --min-frags-per
                      -transfrag 0 --no-5-extend -p 8 cuffmergeallmskgucsc/tmp/mergeSam_fileueEsu4
                      [bam_header_read] EOF marker is absent. The input is probably truncated.
                      [bam_header_read] invalid BAM binary header (this is not a BAM file).
                      File cuffmergeallmskgucsc/tmp/mergeSam_fileueEsu4 doesn't appear to be a valid BAM file, trying SAM...
                      [11:50:13] Loading reference annotation.
                      [11:50:22] Inspecting reads and determining fragment length distribution.
                      Processed 31407 loci.
                      > Map Properties:
                      >       Normalized Map Mass: 1291061.00
                      >       Raw Map Mass: 1291061.00
                      >       Fragment Length Distribution: Truncated Gaussian (default)
                      >                     Default Mean: 200
                      >                  Default Std Dev: 80
                      [11:50:52] Assembling transcripts and estimating abundances.
                      Processed 31407 loci.
                      [Thu Dec 27 12:15:29 2012] Comparing against reference file ucscknowngenes.gtf
                      You are using Cufflinks v2.0.2, which is the most recent release.
                      Warning: couldn't find fasta record for 'chr17_ctg5_hap1'!
                      Warning: couldn't find fasta record for 'chr17_gl000204_random'!
                      Warning: couldn't find fasta record for 'chr17_gl000205_random'!
                      Warning: couldn't find fasta record for 'chr19_gl000209_random'!
                      Warning: couldn't find fasta record for 'chr1_gl000191_random'!
                      Warning: couldn't find fasta record for 'chr1_gl000192_random'!
                      Warning: couldn't find fasta record for 'chr4_ctg9_hap1'!
                      Warning: couldn't find fasta record for 'chr4_gl000193_random'!
                      Warning: couldn't find fasta record for 'chr4_gl000194_random'!
                      Warning: couldn't find fasta record for 'chr6_apd_hap1'!
                      Warning: couldn't find fasta record for 'chr6_cox_hap2'!
                      Warning: couldn't find fasta record for 'chr6_dbb_hap3'!
                      Warning: couldn't find fasta record for 'chr6_mann_hap4'!
                      Warning: couldn't find fasta record for 'chr6_mcf_hap5'!
                      Warning: couldn't find fasta record for 'chr6_qbl_hap6'!
                      Warning: couldn't find fasta record for 'chr6_ssto_hap7'!
                      Warning: couldn't find fasta record for 'chr7_gl000195_random'!
                      Warning: couldn't find fasta record for 'chr9_gl000201_random'!
                      Warning: couldn't find fasta record for 'chrUn_gl000211'!
                      Warning: couldn't find fasta record for 'chrUn_gl000212'!
                      Warning: couldn't find fasta record for 'chrUn_gl000213'!
                      Warning: couldn't find fasta record for 'chrUn_gl000214'!
                      Warning: couldn't find fasta record for 'chrUn_gl000217'!
                      Warning: couldn't find fasta record for 'chrUn_gl000218'!
                      Warning: couldn't find fasta record for 'chrUn_gl000219'!
                      Warning: couldn't find fasta record for 'chrUn_gl000220'!
                      Warning: couldn't find fasta record for 'chrUn_gl000221'!
                      Warning: couldn't find fasta record for 'chrUn_gl000222'!
                      Warning: couldn't find fasta record for 'chrUn_gl000223'!
                      Warning: couldn't find fasta record for 'chrUn_gl000227'!
                      Warning: couldn't find fasta record for 'chrUn_gl000228'!
                      Warning: couldn't find fasta record for 'chrUn_gl000229'!
                      Warning: couldn't find fasta record for 'chrUn_gl000237'!
                      Warning: couldn't find fasta record for 'chrUn_gl000238'!
                      Warning: couldn't find fasta record for 'chrUn_gl000241'!
                      Warning: couldn't find fasta record for 'chrUn_gl000242'!
                      Warning: couldn't find fasta record for 'chrUn_gl000243'!
                      Warning: couldn't find fasta record for 'chrUn_gl000247'!
                      [Thu Dec 27 12:17:17 2012] Comparing against reference file ucscknowngenes.gtf
                      You are using Cufflinks v2.0.2, which is the most recent release.
                      Warning: couldn't find fasta record for 'chr17_ctg5_hap1'!
                      Warning: couldn't find fasta record for 'chr17_gl000204_random'!
                      Warning: couldn't find fasta record for 'chr17_gl000205_random'!
                      Warning: couldn't find fasta record for 'chr19_gl000209_random'!
                      Warning: couldn't find fasta record for 'chr1_gl000191_random'!
                      Warning: couldn't find fasta record for 'chr1_gl000192_random'!
                      Warning: couldn't find fasta record for 'chr4_ctg9_hap1'!
                      Warning: couldn't find fasta record for 'chr4_gl000193_random'!
                      Warning: couldn't find fasta record for 'chr4_gl000194_random'!
                      Warning: couldn't find fasta record for 'chr6_apd_hap1'!
                      Warning: couldn't find fasta record for 'chr6_cox_hap2'!
                      Warning: couldn't find fasta record for 'chr6_dbb_hap3'!
                      Warning: couldn't find fasta record for 'chr6_mann_hap4'!
                      Warning: couldn't find fasta record for 'chr6_mcf_hap5'!
                      Warning: couldn't find fasta record for 'chr6_qbl_hap6'!
                      Warning: couldn't find fasta record for 'chr6_ssto_hap7'!
                      Warning: couldn't find fasta record for 'chr7_gl000195_random'!
                      Warning: couldn't find fasta record for 'chr9_gl000201_random'!
                      Warning: couldn't find fasta record for 'chrUn_gl000211'!
                      Warning: couldn't find fasta record for 'chrUn_gl000212'!
                      Warning: couldn't find fasta record for 'chrUn_gl000213'!
                      Warning: couldn't find fasta record for 'chrUn_gl000214'!
                      Warning: couldn't find fasta record for 'chrUn_gl000217'!
                      Warning: couldn't find fasta record for 'chrUn_gl000218'!
                      Warning: couldn't find fasta record for 'chrUn_gl000219'!
                      Warning: couldn't find fasta record for 'chrUn_gl000220'!
                      Warning: couldn't find fasta record for 'chrUn_gl000221'!
                      Warning: couldn't find fasta record for 'chrUn_gl000222'!
                      Warning: couldn't find fasta record for 'chrUn_gl000223'!
                      Warning: couldn't find fasta record for 'chrUn_gl000227'!
                      Warning: couldn't find fasta record for 'chrUn_gl000228'!
                      Warning: couldn't find fasta record for 'chrUn_gl000229'!
                      Warning: couldn't find fasta record for 'chrUn_gl000237'!
                      Warning: couldn't find fasta record for 'chrUn_gl000238'!
                      Warning: couldn't find fasta record for 'chrUn_gl000241'!
                      Warning: couldn't find fasta record for 'chrUn_gl000242'!
                      Warning: couldn't find fasta record for 'chrUn_gl000243'!
                      Warning: couldn't find fasta record for 'chrUn_gl000247'!
                      However, I still receive all the output files. Are they OK to use? Is there a solution to this problem?

                      Thanks

                      Comment


                      • #12
                        Warning: couldn't find fasta record for 'chr17_ctg5_hap1'!

                        I have the same error.
                        Is there any solution
                        ????


                        Originally posted by dariober View Post
                        Hello,

                        Same here, I don't have the answer but I seem to get the same error. I didn't have time to investigate it any further...

                        Dario

                        Code:
                        cufflinks -o cufflinks_out/GTF/ds019 -p 1 --GTF /lustre/sblab/berald01/reference_data/genomes/iGenomes/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.gtf --multi-read-correct --upper-quartile-norm -b /lustre/sblab/berald01/reference_data/genomes/iGenomes/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.fa tophat_out/ds019/accepted_hits.bam
                        
                        You are using Cufflinks v2.0.1, which is the most recent release.
                        [17:06:29] Loading reference annotation and sequence.
                        Warning: couldn't find fasta record for 'chr17_ctg5_hap1'!
                        This contig will not be bias corrected.
                        Warning: couldn't find fasta record for 'chr17_gl000205_random'!
                        This contig will not be bias corrected.
                        Warning: couldn't find fasta record for 'chr19_gl000209_random'!
                        This contig will not be bias corrected.
                        Warning: couldn't find fasta record for 'chr1_gl000191_random'!
                        This contig will not be bias corrected.
                        Warning: couldn't find fasta record for 'chr4_ctg9_hap1'!
                        This contig will not be bias corrected.
                        Warning: couldn't find fasta record for 'chr4_gl000193_random'!
                        This contig will not be bias corrected.
                        Warning: couldn't find fasta record for 'chr4_gl000194_random'!
                        This contig will not be bias corrected.
                        Warning: couldn't find fasta record for 'chr6_apd_hap1'!
                        This contig will not be bias corrected.
                        Warning: couldn't find fasta record for 'chr6_cox_hap2'!
                        This contig will not be bias corrected.
                        Warning: couldn't find fasta record for 'chr6_dbb_hap3'!
                        This contig will not be bias corrected.
                        Warning: couldn't find fasta record for 'chr6_mann_hap4'!
                        This contig will not be bias corrected.
                        Warning: couldn't find fasta record for 'chr6_mcf_hap5'!
                        This contig will not be bias corrected.
                        Warning: couldn't find fasta record for 'chr6_qbl_hap6'!
                        This contig will not be bias corrected.
                        Warning: couldn't find fasta record for 'chr6_ssto_hap7'!
                        This contig will not be bias corrected.
                        Warning: couldn't find fasta record for 'chr7_gl000195_random'!
                        This contig will not be bias corrected.
                        Warning: couldn't find fasta record for 'chrUn_gl000211'!
                        This contig will not be bias corrected.
                        Warning: couldn't find fasta record for 'chrUn_gl000212'!
                        This contig will not be bias corrected.
                        Warning: couldn't find fasta record for 'chrUn_gl000218'!
                        This contig will not be bias corrected.
                        Warning: couldn't find fasta record for 'chrUn_gl000219'!
                        This contig will not be bias corrected.
                        Warning: couldn't find fasta record for 'chrUn_gl000220'!
                        This contig will not be bias corrected.
                        Warning: couldn't find fasta record for 'chrUn_gl000222'!
                        This contig will not be bias corrected.
                        Warning: couldn't find fasta record for 'chrUn_gl000223'!
                        This contig will not be bias corrected.
                        Warning: couldn't find fasta record for 'chrUn_gl000228'!
                        This contig will not be bias corrected.
                        [17:07:16] Inspecting reads and determining fragment length distribution.
                        > Processed 20912 loci.                        [*************************] 100%
                        > Map Properties:
                        >	Upper Quartile: 2476.50
                        >	Normalized Map Mass: 2476.50
                        >	Raw Map Mass: 49549793.64
                        >	Number of Multi-Reads: 1005158 (with 2421746 total hits)
                        >	Fragment Length Distribution: Empirical (learned)
                        >	              Estimated Mean: 177.23
                        >	           Estimated Std Dev: 53.66
                        [17:14:36] Learning bias parameters.
                        > Processed 20912 loci.                        [*************************] 100%
                        [18:13:09] Re-estimating abundances with bias and multi-read correction.
                        > Processed 20912 loci.                        [*************************] 100%
                        *** glibc detected *** cufflinks: double free or corruption (!prev): 0x000000001e1ec880 ***
                        ======= Backtrace: =========
                        /lib64/libc.so.6[0x30b067230f]
                        /lib64/libc.so.6(cfree+0x4b)[0x30b067276b]
                        cufflinks[0x416f0c]
                        cufflinks[0x416daf]
                        cufflinks[0x416fdc]
                        cufflinks[0x41703c]
                        cufflinks[0x416daf]
                        cufflinks[0x40d05b]
                        cufflinks[0x4210fc]
                        /lib64/libc.so.6(__libc_start_main+0xf4)[0x30b061d994]
                        cufflinks(sin+0xc1)[0x405bd9]
                        ======= Memory map: ========
                        00400000-00601000 r-xp 00000000 00:18 466076018                          /home/berald01/applications/cufflinks/cufflinks-2.0.1.Linux_x86_64/cufflinks
                        00801000-00805000 rw-p 00201000 00:18 466076018                          /home/berald01/applications/cufflinks/cufflinks-2.0.1.Linux_x86_64/cufflinks
                        00805000-00825000 rw-p 00805000 00:00 0 
                        066e3000-1f21a000 rw-p 066e3000 00:00 0                                  [heap]
                        40343000-40344000 ---p 40343000 00:00 0 
                        40344000-40544000 rw-p 40344000 00:00 0 
                        41a11000-41a12000 ---p 41a11000 00:00 0 
                        41a12000-41c12000 rw-p 41a12000 00:00 0 
                        30b0200000-30b021c000 r-xp 00000000 68:06 491836                         /lib64/ld-2.5.so
                        30b041b000-30b041c000 r--p 0001b000 68:06 491836                         /lib64/ld-2.5.so
                        30b041c000-30b041d000 rw-p 0001c000 68:06 491836                         /lib64/ld-2.5.so
                        30b0600000-30b074e000 r-xp 00000000 68:06 491837                         /lib64/libc-2.5.so
                        30b074e000-30b094d000 ---p 0014e000 68:06 491837                         /lib64/libc-2.5.so
                        30b094d000-30b0951000 r--p 0014d000 68:06 491837                         /lib64/libc-2.5.so
                        30b0951000-30b0952000 rw-p 00151000 68:06 491837                         /lib64/libc-2.5.so
                        30b0952000-30b0957000 rw-p 30b0952000 00:00 0 
                        30b0e00000-30b0e82000 r-xp 00000000 68:06 491843                         /lib64/libm-2.5.so
                        30b0e82000-30b1081000 ---p 00082000 68:06 491843                         /lib64/libm-2.5.so
                        30b1081000-30b1082000 r--p 00081000 68:06 491843                         /lib64/libm-2.5.so
                        30b1082000-30b1083000 rw-p 00082000 68:06 491843                         /lib64/libm-2.5.so
                        30b1200000-30b1216000 r-xp 00000000 68:06 491842                         /lib64/libpthread-2.5.so
                        30b1216000-30b1415000 ---p 00016000 68:06 491842                         /lib64/libpthread-2.5.so
                        30b1415000-30b1416000 r--p 00015000 68:06 491842                         /lib64/libpthread-2.5.so
                        30b1416000-30b1417000 rw-p 00016000 68:06 491842                         /lib64/libpthread-2.5.so
                        30b1417000-30b141b000 rw-p 30b1417000 00:00 0 
                        30b1600000-30b1614000 r-xp 00000000 68:02 358643                         /usr/lib64/libz.so.1.2.3
                        30b1614000-30b1813000 ---p 00014000 68:02 358643                         /usr/lib64/libz.so.1.2.3
                        30b1813000-30b1814000 rw-p 00013000 68:02 358643                         /usr/lib64/libz.so.1.2.3
                        30b2a00000-30b2a0d000 r-xp 00000000 68:06 491849                         /lib64/libgcc_s-4.1.2-20080825.so.1
                        30b2a0d000-30b2c0d000 ---p 0000d000 68:06 491849                         /lib64/libgcc_s-4.1.2-20080825.so.1
                        30b2c0d000-30b2c0e000 rw-p 0000d000 68:06 491849                         /lib64/libgcc_s-4.1.2-20080825.so.1
                        30b4200000-30b4215000 r-xp 00000000 68:06 491714                         /lib64/libnsl-2.5.so
                        30b4215000-30b4414000 ---p 00015000 68:06 491714                         /lib64/libnsl-2.5.so
                        30b4414000-30b4415000 r--p 00014000 68:06 491714                         /lib64/libnsl-2.5.so
                        30b4415000-30b4416000 rw-p 00015000 68:06 491714                         /lib64/libnsl-2.5.so
                        30b4416000-30b4418000 rw-p 30b4416000 00:00 0 
                        30b6e00000-30b6e11000 r-xp 00000000 68:06 491854                         /lib64/libresolv-2.5.so
                        30b6e11000-30b7011000 ---p 00011000 68:06 491854                         /lib64/libresolv-2.5.so
                        30b7011000-30b7012000 r--p 00011000 68:06 491854                         /lib64/libresolv-2.5.so
                        30b7012000-30b7013000 rw-p 00012000 68:06 491854                         /lib64/libresolv-2.5.so
                        30b7013000-30b7015000 rw-p 30b7013000 00:00 0 
                        2aaaac000000-2aaab0000000 rw-p 2aaaac000000 00:00 0 
                        2aaab4000000-2aaab7ffe000 rw-p 2aaab4000000 00:00 0 
                        2aaab7ffe000-2aaab8000000 ---p 2aaab7ffe000 00:00 0 
                        2ab8931a8000-2ab8931aa000 rw-p 2ab8931a8000 00:00 0 
                        2ab8931bc000-2ab8931bf000 rw-p 2ab8931bc000 00:00 0 
                        2ab8931bf000-2ab8931c9000 r-xp 00000000 68:06 491547                     /lib64/libnss_files-2.5.so
                        2ab8931c9000-2ab8933c8000 ---p 0000a000 68:06 491547                     /lib64/libnss_files-2.5.so
                        2ab8933c8000-2ab8933c9000 r--p 00009000 68:06 491547                     /lib64/libnss_files-2.5.so
                        2ab8933c9000-2ab8933ca000 rw-p 0000a000 68:06 491547                     /lib64/libnss_files-2.5.so
                        2ab8933ca000-2ab8933d3000 r-xp 00000000 68:06 491551                     /lib64/libnss_nis-2.5.so
                        2ab8933d3000-2ab8935d3000 ---p 00009000 68:06 491551                     /lib64/libnss_nis-2.5.so
                        2ab8935d3000-2ab8935d4000 r--p 00009000 68:06 491551                     /lib64/libnss_nis-2.5.so
                        2ab8935d4000-2ab8935d5000 rw-p 0000a000 68:06 491551                     /lib64/libnss_nis-2.5.so
                        2ab8935d5000-2ab8935d9000 r-xp 00000000 68:06 491545                     /lib64/libnss_dns-2.5.so
                        2ab8935d9000-2ab8937d8000 ---p 00004000 68:06 491545                     /lib64/libnss_dns-2.5.so
                        2ab8937d8000-2ab8937d9000 r--p 00003000 68:06 491545                     /lib64/libnss_dns-2.5.so
                        2ab8937d9000-2ab8937da000 rw-p 00004000 68:06 491545                     /lib64/libnss_dns-2.5.so
                        2ab8937da000-2ab8939da000 rw-p 2ab8937da000 00:00 0 
                        7fffdba0a000-7fffdba20000 rw-p 7ffffffe8000 00:00 0                      [stack]
                        7fffdbbfd000-7fffdbc00000 r-xp 7fffdbbfd000 00:00 0                      [vdso]
                        ffffffffff600000-ffffffffffe00000 ---p 00000000 00:00 0                  [vsyscall]
                        /home/berald01/.lsbatch/1340467579.346876: line 8: 31009 Aborted                 (core dumped) cufflinks -o cufflinks_out/GTF/ds019 -p 1 --GTF /lustre/sblab/berald01/reference_data/genomes/iGenomes/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.gtf --multi-read-correct --upper-quartile-norm -b /lustre/sblab/berald01/reference_data/genomes/iGenomes/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.fa tophat_out/ds019/accepted_hits.bam

                        Comment


                        • #13
                          Charitra: The original thread is referring to an older version of cufflinks. Are you getting this error with a more current version of cufflinks (now in at v.2.1.1)?

                          Comment


                          • #14
                            Yes and thanks for your concern. I am using cufflinks-2.0.2.Linux_x86_64
                            However, a new cufflinks has been release few days before and didnt update cos I was stuckup in the middle of cuffdiff.

                            What you think I should ?
                            I have just continued with with warnings.. and lets see if it can give me something in R then I will try with new release....

                            I am confused which genome is to be used.. there are different in UCSC (I have downloaded the whole .gz) there are also genome.fa and on other folder chr.fa

                            ???

                            Comment


                            • #15
                              Thanks GenoMax
                              As you advised, I have followed but still I got this error. I am using cufflinks 2.1.1 and also downloaded all the files from ensembl hg19.

                              why do I have error
                              Warning: couldn't find fasta record for 'GL000191.1'!
                              Warning: couldn't find fasta record for 'GL000192.1'!
                              Warning: couldn't find fasta record for 'GL000193.1'!
                              Warning: couldn't find fasta record for 'GL000194.1'!
                              Warning: couldn't find fasta record for 'GL000195.1'!
                              Warning: couldn't find fasta record for 'GL000196.1'!
                              Warning: couldn't find fasta record for 'GL000199.1'!
                              Warning: couldn't find fasta record for 'GL000201.1'!
                              Warning: couldn't find fasta record for 'GL000204.1'!
                              Warning: couldn't find fasta record for 'GL000205.1'!
                              Warning: couldn't find fasta record for 'GL000209.1'!
                              Warning: couldn't find fasta record for 'GL000211.1'!
                              Warning: couldn't find fasta record for 'GL000212.1'!
                              Warning: couldn't find fasta record for 'GL000213.1'!
                              Warning: couldn't find fasta record for 'GL000215.1'!
                              Warning: couldn't find fasta record for 'GL000216.1'!
                              Warning: couldn't find fasta record for 'GL000218.1'!
                              Warning: couldn't find fasta record for 'GL000219.1'!
                              Warning: couldn't find fasta record for 'GL000220.1'!
                              Warning: couldn't find fasta record for 'GL000221.1'!
                              Warning: couldn't find fasta record for 'GL000222.1'!
                              Warning: couldn't find fasta record for 'GL000223.1'!

                              Please guide me

                              Comment

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