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[assembly] Trinity 第一部分的Chrysalis报错 求助

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发表于 2016-11-22 16:33:03 | 显示全部楼层 |阅读模式
anlan@ubuntu:~$ Trinity -seqType fq -left SRR031714/SRR031714_1_paired.fastq -right SRR031714/SRR031714_2_paired.fastq -min_kmer_cov 2  --CPU 2 -max_memory 4G
Trinity version: Trinity-v2.3.2
--------------------------------------------------------
-------------------- Chrysalis -------------------------
-- (Contig Clustering & de Bruijn Graph Construction) --
--------------------------------------------------------

inchworm_target: /home/anlan/trinity_out_dir/both.fa
bowite_reads_fa: /home/anlan/trinity_out_dir/both.fa
chrysalis_reads_fa: /home/anlan/trinity_out_dir/both.fa
-- Skipping CMD: /home/anlan/trinityrnaseq-Trinity-v2.3.2/util/misc/fasta_filter_by_min_length.pl /home/anlan/trinity_out_dir/inchworm.K25.L25.DS.fa 100 > /home/anlan/trinity_out_dir/chrysalis/inchworm.K25.L25.DS.fa.min100, checkpoint exists.
* Running CMD: bowtie2-build -o 3 /home/anlan/trinity_out_dir/chrysalis/inchworm.K25.L25.DS.fa.min100 /home/anlan/trinity_out_dir/chrysalis/inchworm.K25.L25.DS.fa.min100 1>/dev/null
Building a SMALL index
Segmentation fault
Error, cmd: bowtie2-build -o 3 /home/anlan/trinity_out_dir/chrysalis/inchworm.K25.L25.DS.fa.min100 /home/anlan/trinity_out_dir/chrysalis/inchworm.K25.L25.DS.fa.min100 1>/dev/null 2>tmp.7807.stderr died with ret 35584 at /home/anlan/trinityrnaseq-Trinity-v2.3.2/PerlLib/Pipeliner.pm line 166.
        Pipeliner::run(Pipeliner=HASH(0x55c8d027a2a8)) called at /usr/bin/Trinity line 1745
        main::run_chrysalis("/home/anlan/trinity_out_dir/inchworm.K25.L25.DS.fa", "/home/anlan/trinity_out_dir/both.fa", 200, 500, undef, "/home/anlan/trinity_out_dir/both.fa", "/home/anlan/trinity_out_dir/both.fa") called at /usr/bin/Trinity line 1590
        main::run_Trinity() called at /usr/bin/Trinity line 1257
        eval {...} called at /usr/bin/Trinity line 1256

Trinity run failed. Must investigate error above.

红色为错误信息,然后我将bowtie2-build -o 3 /home/anlan/trinity_out_dir/chrysalis/inchworm.K25.L25.DS.fa.min100 /home/anlan/trinity_out_dir/chrysalis/inchworm.K25.L25.DS.fa.min100 1重新运行,发现报错信息为:
anlan@ubuntu:~$ bowtie2-build -o 3 /home/anlan/trinity_out_dir/chrysalis/inchworm.K25.L25.DS.fa.min100 /home/anlan/trinity_out_dir/chrysalis/inchworm.K25.L25.DS.fa.min100 1
Settings:
  Output files: "/home/anlan/trinity_out_dir/chrysalis/inchworm.K25.L25.DS.fa.min100.*.bt2"
  Line rate: 6 (line is 64 bytes)
  Lines per side: 1 (side is 64 bytes)
  Offset rate: 3 (one in 8)
  FTable chars: 10
  Strings: unpacked
  Max bucket size: default
  Max bucket size, sqrt multiplier: default
  Max bucket size, len divisor: 4
  Difference-cover sample period: 1024
  Endianness: little
  Actual local endianness: little
  Sanity checking: disabled
  Assertions: disabled
  Random seed: 0
  Sizeofs: void*:8, int:4, long:8, size_t:8
Input files DNA, FASTA:
  /home/anlan/trinity_out_dir/chrysalis/inchworm.K25.L25.DS.fa.min100
Building a SMALL index
Reading reference sizes
  Time reading reference sizes: 00:00:00
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:00
bmax according to bmaxDivN setting: 925991
Using parameters --bmax 694494 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 694494 --dcv 1024
Constructing suffix-array element generator
Segmentation fault
bowtie2也重新安装了下,发现还是如此。
由于自身水平有限,折腾了好久还是没查出来是什么错误,希望大家能帮我看看是哪个或者哪些原因导致的了。

万分感谢!

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 楼主| 发表于 2016-11-22 20:29:24 | 显示全部楼层
刚刚解决了,在另外一台电脑上同样的数据和软件,正常出结果了。。因此上述问题还是系统或者软件安装不正确导致的。。。
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发表于 2016-11-23 10:02:28 | 显示全部楼层
很诡异,你报错是:Segmentation fault呀
这个是非常经典的垃圾篓,什么原因都有可能
你这个问题很复杂,需要打赏,请点击 http://www.bio-info-trainee.com/donate 进行打赏,谢谢
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