No such file or directory at infer_bp_v4.pl line 13.

[lee duhee]

Hello Zechen.
I was trying to run novoBreak. but there were some error.

I using AWS because i dont have high-perfomance computer.

NovoBreak is in /home/ec2-user/novoBreak_distribution_v1.1.3. And i export the PATH too, but it didnt work well.

export $PATH
-bash: export: `/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/opt/aws/bin:/home/ec2-user/.local/bin:/home/ec2-user/bin:/home/ec2-user/novoBreak_distribution_v1.1.3': not a valid identifier

And i run by command 'sh run_novoBreak.sh ./ ucsc.hg19.fasta chr19.tumor.bam chr19.normal.bam 32 ./output1
' in novoBreak directory.

And following is running message

[Thu Aug 10 09:44:18 2017]
Building reference kmer...
Calculating number of paired reads ...
[fillin_bitvec] processed   21619126 reads
There are 139982732 reference kmers and 40891127 non-reference kmers
Finished reference kmer building
[Thu Aug 10 10:02:48 2017]
Freed reference hash and begin building reads hash table...
[Thu Aug 10 10:02:48 2017]
[build_readshash] processed   21619126 reads
[Thu Aug 10 10:04:03 2017]
 973100 kmers loaded

[Thu Aug 10 10:04:05 2017]
Calculating kmers from control...
[cal_ctrl_kmers] processed   21610684 reads
[Thu Aug 10 10:05:37 2017]
Loading sequences...
[Thu Aug 10 10:06:31 2017]61344 reads
Remove duplicate sequences...
[Thu Aug 10 10:07:18 2017]61344 reads

710301 kmers passed the minimum frequency cutoff in tumor (3) and maximum frequency cutoff in normal (3)
Program exit normally
[M::bam2fq_mainloop] processed 50944 reads
begin kmer2id ...
kmer2id takes 0 seconds
begin id2pair...
id2pair takes 4 seconds
begin sorting ids...
sorting ids takes 0 seconds
begin output results...
Outputting results takes 0 seconds
Finished
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[E::bwa_idx_load] fail to locate the index files
x??
No such file or directory at /home/ec2-user/novoBreak_distribution_v1.1.3/infer_bp_v4.pl line 13.

I have been trying to run this for 5 days. And i searched a lot on Google. But i cant run it. I thought that reason of error is OS, so i changed OS by ubuntu, Redhat, Amazon Linux. but all of them cant work well.

Would you give me some advice?