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. # License file: # 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