This topic contains 4 replies, has 2 voices, and was last updated by Colin Hercus 8 years, 11 months ago.
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February 24, 2016 at 8:24 pm #1834
New user, can’t seem to get this to work.
I created my own index (successfully, I think) using novoindex.
Now I’m trying this:
novoalign -d <index.nix> -f <file1.fastq> <file2.fastq>
and I’m getting this out:
Interrupted..11
Obtained 8 stack frames.
0 novoalign 0x000000010009f068 _ZNSt6vectorISsSaISsEE13_M_insert_auxEN9__gnu_cxx17__normal_iteratorIPSsS1_EERKSs + 1176
1 novoalign 0x00000001000058ba novoalign + 22714
2 libsystem_platform.dylib 0x00007fff8db0df1a _sigtramp + 26
3 ??? 0x00007fff6664c784 0x0 + 140734911268740
4 novoalign 0x0000000100034930 _ZStplIcSt11char_traitsIcESaIcEESbIT_T0_T1_EPKS3_RKS6_ + 8896
5 novoalign 0x0000000100030d60 _ZNK8iubcodes8iub2tonaEi + 6080
6 novoalign 0x0000000100005f29 novoalign + 24361
7 novoalign 0x0000000100005848 novoalign + 22600which is complete gibberish to me. What is going wrong?
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This topic was modified 8 years, 11 months ago by
top1214.
February 25, 2016 at 12:55 am #1836Hi,
That’s strange, I haven’t seen that before and the iub2tona routine shouldn’t be used by novoalign.
To help I’ll need some context…
1) What Linux flavour are you using? uname -a will do.
2) What novoalign did you download. There are several releases and builds for Linux2.6 and 3.0 kernels. Without this the stack dump isn’t much use.
3) What was the novoindex command you used to build the index? Do you have the log/stderr output from that?
4) The full stderr output from the novoalign run that includes any & all messages from novoalign rather than just the stack dump.
5) Did this happen right at the start of the run or after it had processed for some time? A wc -l of output file and the fastq files might show this.
6) If it happened at start then a head -100 of the two fastq files might be useful.Thanks, Colin
February 25, 2016 at 5:19 pm #1837Thanks
1) What Linux flavour are you using? uname -a will do.
It’s a mac, but here’s the output of uname -a:
Darwin sjlab-imac.wucon.wustl.edu 14.5.0 Darwin Kernel Version 14.5.0: Tue Sep 1 21:23:09 PDT 2015; root:xnu-2782.50.1~1/RELEASE_X86_64 x86_64
2) What novoalign did you download. There are several releases and builds for Linux2.6 and 3.0 kernels. Without this the stack dump isn’t much use.
Novoalign V3.04.01
3) What was the novoindex command you used to build the index? Do you have the log/stderr output from that?
sjlab-imac:RNA_seq johnsonlab$ novoindex D_rerio.nix Scott_RNA.fa # novoindex (3.4) - Universal k-mer index constructor. # (C) 2008 - 2011 NovoCraft Technologies Sdn Bhd # novoindex D_rerio.nix Scott_RNA.fa # Creating 4 indexing threads. # Building with 11-mer and step of 1 bp. # novoindex construction dT = 7.1s # Index memory size 0.239Gbyte. # Done.
4) The full stderr output from the novoalign run that includes any & all messages from novoalign rather than just the stack dump.
5) Did this happen right at the start of the run or after it had processed for some time? A wc -l of output file and the fastq files might show this.The output I posted happened immediately, and nothing else printed out to the terminal.
6) If it happened at start then a head -100 of the two fastq files might be useful.
And this is where I realize I idiotically picked 2 libraries where demultiplexing failed, and were empty files. I’m so sorry you wasted any time thinking about this, but thank you for pointing out my error. I’ll go hang my head in shame.
February 26, 2016 at 12:43 am #1838Hi,
Thanks for update. Novoalign shouldn’t do this when given empty files however recently I multi-threaded the class that reads the fastq files and it’s likely I never tested them on empty files so I’ll take a look at it and make it’s handled cleanly.
KR, Colin
February 26, 2016 at 1:29 am #1839Quick update
Linux versions give a meaningful error message
cat >r1.fq
^D
novoalign -d ssuis.nix -f r1.fq
Sequence file is empty: r1.fq
Error: Cannot open input sequence files. r1.fqwhile the Mac build crashes with the error you saw.
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