Tagged: Novoalign
This topic contains 0 replies, has 1 voice, and was last updated by Elisa 7 years, 2 months ago.
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August 31, 2017 at 3:54 pm #2296
Hello,
I was running novoalign and I got the following error.
I get this error with 4 samples consistently, but when I use the same command with other samples, then I don’t have any error.
I am trying to figure out what is causing the error.
Any help would be appreciated.
Thank you,
Elisa Lee# novoalign (V3.08.00 – Build Jul 14 2017 @ 12:08:36) – A short read aligner with qualities.
# (C) 2008-2016 Novocraft Technologies Sdn Bhd.
# License file: /DCEG/Resources/Tools/novocraft-new/novocraftV3.08.00/novocraft/novoalign.lic
# Licensed to Leidos
# novoalign -c 10 -d /DCEG/CGF/TempFileSwap/Elisa/primary_analysis_scripts/hg19.idx -f /CGF/Sequencing/Illumina/MiSeq/PostRun_Analysis/Data/170428_M01354_0048_000000000-B3R3J/CASAVA/L1/Project_RP0084-018/Sample_SC136945/SC136945_GAATTCGT_L001_R1_001_HQ_paired.fastq.gz /CGF/Sequencing/Illumina/MiSeq/PostRun_Analysis/Data/170428_M01354_0048_000000000-B3R3J/CASAVA/L1/Project_RP0084-018/Sample_SC136945/SC136945_GAATTCGT_L001_R2_001_HQ_paired.fastq.gz -F ILM1.8 -i +- 50-300 –amplicons /DCEG/CGF/Sequencing/Illumina/MiSeq/PostRun_Analysis/Staging/170428_M01354_0048_000000000-B3R3J/Panel_bed.bed 1 /CGF/Sequencing/Illumina/MiSeq/PostRun_Analysis/Data/170428_M01354_0048_000000000-B3R3J/target_novoalign_bed.bed -oSAM “@RG\tCN:CGR\tPL:ILLUMINA\tID:SC136945_GAATTCGT_L001_HQ_paired\tSM:SC136945\tPU:SC136945_GAATTCGT_L001_HQ_paired\tLB:N/A”
# Starting at Fri Aug 25 15:19:51 2017
# Interpreting input files as Illumina FASTQ, Casava Pipeline 1.8 & later.
# Index Build Version: 3.0
# Hash length: 14
# Step size: 2Interrupted..11
Stack Dump …
ip = 0x 495c1c, sp = 0x 2aac9c390a60
ip = 0x 40534d, sp = 0x 2aac9c391230
ip = 0x 5690e0, sp = 0x 2aac9c391240
ip = 0x 43922f, sp = 0x 2aac9c3917f0
ip = 0x 44431f, sp = 0x 2aac9c391850
ip = 0x 4469bf, sp = 0x 2aac9c391bf0
ip = 0x 406431, sp = 0x 2aac9c391e40
ip = 0x 436d37, sp = 0x 2aac9c391f40
ip = 0x 435aab, sp = 0x 2aac9c391f70
ip = 0x 563f9d, sp = 0x 2aac9c391f90
ip = 0x 5ca649, sp = 0x 2aac9c3920b0 -
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