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baoe / AlignGraph

Algorithm for secondary de novo genome assembly guided by closely related references
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BOWTIE2 CALL FAILED #30

Open jimmyjiming opened 7 years ago

jimmyjiming commented 7 years ago

Hello, When I run AlignGraph, I faced a problem that bowtie2 call failed. I have tried several methods, but can not solve it. Here are my scrips: PATH: /opt/smrtlink/smrtcmds/bin:/usr/lib64/qt-3.3/bin:/usr/kerberos/sbin:/usr/kerberos/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:$/home/Henry/bin/AlignGraph-master/AlignGraph:/home/Henry/bin/MUMmer3.23/scripts:/home/Henry/bin/MUMmer3.23/src/tigr:/home/Henry/bin/MUMmer3.23:/home/Henry/bin/AlignGraph-master/AlignGraph/bowtie2-2.2.3:$/home/Henry/bin/AlignGraph-master/bowtie2-2.2.3

AlignGraph --read1 S_trim30_pe1.fasta --read2 S_trim30_pe2.fasta --contig contigs.fasta --genome Ca_Brocadia_sp_40.fasta --distanceLow 550 --distanceHigh 1550 --fastMap --extendedContig S_extendedContigs.fa --remainingContig S_remainingContigs.fa AlignGraph: algorithm for secondary de novo genome assembly guided by closely related references By Ergude Bao, CS Department, UC-Riverside. All Rights Reserved

BOWTIE2 CALL FAILED!

I have no idea why bowtie2 call failed. I was wonder what is the reason? Thanks very much.

wiedenhoeft commented 7 years ago

I have the same issue using Bowtie2 v2.3.2-legacy :-(

baoe commented 6 years ago

Hi,

You should use "export" in your script to add Bowtie2 "executable" in your PATH.

Bao