Question: solution for SPades to assemble genome with low quality data
0
gravatar for StudentBio
13 months ago by
StudentBio0
StudentBio0 wrote:

hello the community when I run spades with this command:

inra@inra-VirtualBox:~/SPAdes-3.5.0-Linux/bin$ ./spades.py --sc -m 4 --iontorrent -k 21,33,55,77,99,127 -s /home/inra/share/outils/trimmed.fastq -o /home/inra/share/spades

i get this error, please any suggestions, i have single-reads from ion-torrent

=== Stack Trace ===
[0x405c5a]
[0x406d51]
[0x40fce0]
[0x4055f3]
[0x40fff7]
[0x40d4f7]
[0x403d9e]
[0x4517c1]
[0x589900]
[0x4001b9]
Verification of expression '(intptr_t)MappedRegion != -1L' failed in function 'void MMappedWriter::reserve(size_t)'. In file '/home/yasha/gitrep2/algorithmic-biology/assembler/src/include/io/mmapped_writer.hpp' on line 87. Message 'mmap(2) failed. Reason: Invalid argument. Error code: 22'.
Verification of expression '(intptr_t)MappedRegion != -1L' failed in function 'void MMappedWriter::reserve(size_t)'. In file '/home/yasha/gitrep2/algorithmic-biology/assembler/src/include/io/mmapped_writer.hpp' on line 87. Message 'mmap(2) failed. Reason: Invalid argument. Error code: 22'.
ionhammer: /home/yasha/gitrep2/algorithmic-biology/assembler/src/include/io/mmapped_writer.hpp:87: void MMappedWriter::reserve(size_t): Assertion `(intptr_t)MappedRegion != -1L' failed.


== Error ==  system call for: "['/home/inra/SPAdes-3.5.0-Linux/bin/ionhammer', '/home/inra/share/spades/corrected/configs/ionhammer.cfg']" finished abnormally, err code: -6

In case you have troubles running SPAdes, you can write to spades.support@bioinf.spbau.ru
Please provide us with params.txt and spades.log files from the output directory.
ADD COMMENTlink modified 13 months ago by Sej Modha4.2k • written 13 months ago by StudentBio0

Hello StudentBio,

Please use the formatting bar (especially the code option) to present your post better. I've done it for you this time.
code_formatting

Thank you!

ADD REPLYlink written 13 months ago by Sej Modha4.2k

How much memory is assigned to this VM instance? Are you acknowledging that this data is of low quality? If so in what way is it bad (not enough, bad Q scores)?

ADD REPLYlink written 13 months ago by genomax70k
1

Is this single-cell, iontorrent data? Why are you using --sc tag with --iontorrent? How big is your data file? Can you provide more memory for this process?

ADD REPLYlink written 13 months ago by Sej Modha4.2k

my file is 14 GB single-cell want mean it seems that i don t understand it

ADD REPLYlink written 13 months ago by StudentBio0

50 and quality score for position in reads are betweeen 28 and 20 after trimming

ADD REPLYlink written 13 months ago by StudentBio0

50 and quality score for position in reads are betweeen 28 and 20 after trimming

ADD REPLYlink written 13 months ago by StudentBio0

The SPAdes version you are using is really old - current version is SPAdes 3.12.0 - and many bugs were fixed in the meantime. Also, SPAdes is resource-hungry, and I wouldn't recommend using it under a VirtualBox unless your dataset is really small.

ADD REPLYlink written 13 months ago by h.mon26k
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