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3.8 years ago
maude • 0

I'm trying to map sequencing reads (fastq) to a reference genome that I obtained by the sequence of a plasmid. I'm using this version of Novoalign

  # novoalign (V3.07.00 - Build Feb  7 2017 @ 14:09:01) - A short read aligner with qualities.
# (C) 2008-2016 Novocraft Technologies Sdn Bhd.
# Licensed for evaluation, educational, and not-for-profit use only.


I've first constructed a index using novoindex:

'/home/Desktop/novocraft/novoindex' '/data_disk2/DNA/LacO.nix' '/data_disk2/Maude/DNA/LacO_plasmid.fa'


Then I'm trying to align my reads with novoalign

'/home/Desktop/novocraft/novoalign' -d '/data_disk2/DNA/LacO.nix' -f '/data_disk2/116_5m_b_L7_R1_001_3LdtqsRBoXl6.fastq' '/data_disk2/116_5m_b_L7_R2_001_IyVEjiInhBZo.fastq' -o SAM -r Random > '/data_disk2/5min_rep2.sam'


But after few minutes running I obtain the following error message

Interrupted..11
Stack  Dump ...
ip = 0x          4ab98f, sp = 0x    7ffc2f5d9a20
ip = 0x          409902, sp = 0x    7ffc2f5da1f0
ip = 0x          5e8cb0, sp = 0x    7ffc2f5da200
ip = 0x          417cc3, sp = 0x    7ffc2f5da788
ip = 0x          4402ec, sp = 0x    7ffc2f5da790
ip = 0x          444699, sp = 0x    7ffc2f5da7d0
ip = 0x          44684c, sp = 0x    7ffc2f5da940
ip = 0x          450a7a, sp = 0x    7ffc2f5daa10
ip = 0x          40a8f1, sp = 0x    7ffc2f5dad20
ip = 0x          4055fa, sp = 0x    7ffc2f5dae20
ip = 0x          5e9eaa, sp = 0x    7ffc2f60f350
ip = 0x          4097f1, sp = 0x    7ffc2f60f420


Do you have any idea about what could goes wrong? Thank you! Maude

novoalign • 1.2k views
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Has this install of novoalign worked for other jobs in past? What OS are you using this on?

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Yes it worked well with c.elegans genome before. I think the problem is coming from my new index file but I don't understand why...

I'm using Ubuntu

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Have you tried remaking the index?

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yes I tried few times and I always have the same error message. I'm now trying to align it on the C.elegans index that I know works to see if the problem is really coming from the index file.

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Are there any odd things with your fasta file? Like extra blank lines/non-ACTG characters etc? You may want to clean those out and try (if present).

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Hi, You might try a later version of Novoalign to see if that helps.

If not could you contact me at support@novocraft.com. I may ask you to share files so I can run in debug mode.

Best Regards, Colin Hercus, Novocraft