Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • Bfast match abort error

    I have just started playing around with Bfast for single-end alignment of E. coli mutants to a reference genome. I got through all of the steps in making the reference and making the index files successfully, but now when I try to run the match command it aborts. I have found that I can run it successfully using a single index as the main index with no secondary indexes, but as soon as I try to use a secondary index it aborts (see below). Any ideas? I was trying to run the moderate accuracy mode described in the paper to see how it does with finding small indels.


    $ /usr/local/src/bfast-0.6.4e/bfast/bfast match -f Parent113010.fa -r /data/prior/Illumina/PEL2_nocode_qualfilt.fq -i 1 -I 3 -n 4 -t -w 0 -T Temp/ > bfast.matches.PEL2.bmf
    ************************************************************
    Checking input parameters supplied by the user ...
    Validating fastaFileName Parent113010.fa.
    Validating readsFileName /data/prior/Illumina/PEL2_nocode_qualfilt.fq.
    Validating tmpDir path Temp/.
    **** Input arguments look good!
    ************************************************************
    ************************************************************
    Printing Program Parameters:
    programMode: [ExecuteProgram]
    fastaFileName: Parent113010.fa
    mainIndexes 1
    secondaryIndexes 3
    readsFileName: /data/prior/Illumina/PEL2_nocode_qualfilt.fq
    offsets: [Using All]
    loadAllIndexes: [Not Using]
    compression: [Not Using]
    space: [NT Space]
    startReadNum: 1
    endReadNum: 2147483647
    keySize: [Not Using]
    maxKeyMatches: 8
    maxNumMatches: 384
    whichStrand: [Both Strands]
    numThreads: 4
    queueLength: 250000
    tmpDir: Temp/
    timing: [Using]
    ************************************************************
    Searching for main indexes...
    Found 1 index (1 file).
    Searching for secondary indexes...
    Found 1 index (1 file).
    ************************************************************
    Reading in reference genome from Parent113010.fa.nt.brg.
    In total read 1 contigs for a total of 4633479 bases
    ************************************************************
    Reading /data/prior/Illumina/PEL2_nocode_qualfilt.fq into a temp file.
    Will process 4625285 reads.
    ************************************************************
    Searching index file 1/1 (index #1, bin #1)...
    Reading index from Parent113010.fa.nt.1.1.bif.
    Read index from Parent113010.fa.nt.1.1.bif.
    Reads processed: 4625285
    Cleaning up index.
    Searching index file 1/1 (index #1, bin #1) complete...
    Found 4596991 matches.
    Found matches for 4596991 reads.
    Copying unmatched reads for secondary index search.
    Splitting unmatched reads into temp files.
    *** glibc detected *** /usr/local/src/bfast-0.6.4e/bfast/bfast: double free or corruption (!prev): 0x0000000013ab3670 ***
    ======= Backtrace: =========
    /lib64/libc.so.6[0x2aeabe14830f]
    /lib64/libc.so.6(cfree+0x4b)[0x2aeabe14876b]
    /lib64/libc.so.6(fclose+0x14b)[0x2aeabe136d5b]
    /usr/lib64/libz.so.1[0x33d6a030b4]
    /usr/local/src/bfast-0.6.4e/bfast/bfast[0x408c38]
    /usr/local/src/bfast-0.6.4e/bfast/bfast[0x4238a4]
    /usr/local/src/bfast-0.6.4e/bfast/bfast[0x424389]
    /usr/local/src/bfast-0.6.4e/bfast/bfast[0x42ad42]
    /lib64/libc.so.6(__libc_start_main+0xf4)[0x2aeabe0f3994]
    /usr/local/src/bfast-0.6.4e/bfast/bfast[0x401b59]
    ======= Memory map: ========
    00400000-0044b000 r-xp 00000000 fd:04 1344273 /usr/local/src/bfast-0.6.4e/bfast/bfast
    0064b000-0064d000 rw-p 0004b000 fd:04 1344273 /usr/local/src/bfast-0.6.4e/bfast/bfast
    13aaa000-196f4000 rw-p 13aaa000 00:00 0 [heap]
    41f22000-41f23000 ---p 41f22000 00:00 0
    41f23000-42923000 rw-p 41f23000 00:00 0
    42923000-42924000 ---p 42923000 00:00 0
    42924000-43324000 rw-p 42924000 00:00 0
    48d2d000-48d2e000 ---p 48d2d000 00:00 0
    48d2e000-4972e000 rw-p 48d2e000 00:00 0
    33d6a00000-33d6a14000 r-xp 00000000 fd:04 1111537 /usr/lib64/libz.so.1.2.3
    33d6a14000-33d6c13000 ---p 00014000 fd:04 1111537 /usr/lib64/libz.so.1.2.3
    33d6c13000-33d6c14000 rw-p 00013000 fd:04 1111537 /usr/lib64/libz.so.1.2.3
    2aaaaaaac000-2aaaaaaad000 rw-p 2aaaaaaac000 00:00 0
    2aaaaaaae000-2aaaaaaaf000 rw-p 2aaaaaaae000 00:00 0
    2aaaaaacc000-2aaaaaad9000 r-xp 00000000 fd:04 10911746 /lib64/libgcc_s-4.1.2-20080825.so.1
    2aaaaaad9000-2aaaaacd9000 ---p 0000d000 fd:04 10911746 /lib64/libgcc_s-4.1.2-20080825.so.1
    2aaaaacd9000-2aaaaacda000 rw-p 0000d000 fd:04 10911746 /lib64/libgcc_s-4.1.2-20080825.so.1
    2aaaac000000-2aaaac021000 rw-p 2aaaac000000 00:00 0
    2aaaac021000-2aaab0000000 ---p 2aaaac021000 00:00 0
    2aaab0000000-2aaab0021000 rw-p 2aaab0000000 00:00 0
    2aaab0021000-2aaab4000000 ---p 2aaab0021000 00:00 0
    2aaab4000000-2aaab4121000 rw-p 2aaab4000000 00:00 0
    2aaab4121000-2aaab8000000 ---p 2aaab4121000 00:00 0
    2aaab8000000-2aaac0000000 rw-p 2aaab8000000 00:00 0
    2aeabd80a000-2aeabd826000 r-xp 00000000 fd:04 10916099 /lib64/ld-2.5.so
    2aeabd826000-2aeabd827000 rw-p 2aeabd826000 00:00 0
    2aeabd828000-2aeabd829000 rw-p 2aeabd828000 00:00 0
    2aeabd844000-2aeabd845000 rw-p 2aeabd844000 00:00 0
    2aeabda25000-2aeabda26000 r--p 0001b000 fd:04 10916099 /lib64/ld-2.5.so
    2aeabda26000-2aeabda27000 rw-p 0001c000 fd:04 10916099 /lib64/ld-2.5.so
    2aeabda27000-2aeabdaa9000 r-xp 00000000 fd:04 10915348 /lib64/libm-2.5.so
    2aeabdaa9000-2aeabdca8000 ---p 00082000 fd:04 10915348 /lib64/libm-2.5.so
    2aeabdca8000-2aeabdca9000 r--p 00081000 fd:04 10915348 /lib64/libm-2.5.so
    2aeabdca9000-2aeabdcaa000 rw-p 00082000 fd:04 10915348 /lib64/libm-2.5.so
    2aeabdcaa000-2aeabdcb9000 r-xp 00000000 fd:04 9240588 /usr/lib64/libbz2.so.1.0.3
    2aeabdcb9000-2aeabdeb8000 ---p 0000f000 fd:04 9240588 /usr/lib64/libbz2.so.1.0.3
    2aeabdeb8000-2aeabdeba000 rw-p 0000e000 fd:04 9240588 /usr/lib64/libbz2.so.1.0.3
    2aeabdeba000-2aeabdebb000 rw-p 2aeabdeba000 00:00 0
    2aeabdebb000-2aeabded1000 r-xp 00000000 fd:04 10911775 /lib64/libpthread-2.5.so
    2aeabded1000-2aeabe0d0000 ---p 00016000 fd:04 10911775 /lib64/libpthread-2.5.so
    2aeabe0d0000-2aeabe0d1000 r--p 00015000 fd:04 10911775 /lib64/libpthread-2.5.so
    2aeabe0d1000-2aeabe0d2000 rw-p 00016000 fd:04 10911775 /lib64/libpthread-2.5.so
    2aeabe0d2000-2aeabe0d6000 rw-p 2aeabe0d2000 00:00 0
    2aeabe0d6000-2aeabe224000 r-xp 00000000 fd:04 10911751 /lib64/libc-2.5.so
    2aeabe224000-2aeabe423000 ---p 0014e000 fd:04 10911751 /lib64/libc-2.5.so
    2aeabe423000-2aeabe427000 r--p 0014d000 fd:04 10911751 /lib64/libc-2.5.so
    2aeabe427000-2aeabe428000 rw-p 00151000 fd:04 10911751 /lib64/libc-2.5.so
    2aeabe428000-2aeabe665000 rw-p 2aeabe428000 00:00 0
    7fffc6c46000-7fffc6c5b000 rw-p 7ffffffe9000 00:00 0 [stack]
    ffffffffff600000-ffffffffffe00000 ---p 00000000 00:00 0 [vdso]
    Aborted

Latest Articles

Collapse

  • seqadmin
    Strategies for Sequencing Challenging Samples
    by seqadmin


    Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
    03-22-2024, 06:39 AM
  • seqadmin
    Techniques and Challenges in Conservation Genomics
    by seqadmin



    The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

    Avian Conservation
    Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
    03-08-2024, 10:41 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, Yesterday, 06:37 PM
0 responses
10 views
0 likes
Last Post seqadmin  
Started by seqadmin, Yesterday, 06:07 PM
0 responses
9 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-22-2024, 10:03 AM
0 responses
51 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-21-2024, 07:32 AM
0 responses
67 views
0 likes
Last Post seqadmin  
Working...
X