Hi,
I am running your program to detect haplotype frequency across 20 samples with a malaria gene. In every case, my amplicon can vary from 120 bp to 1100 bp (it is length polymorphic), and I performed a sequencing process with Illumina MiSeq in pair-end mode using 2x250, so as you can see I have shorter reads than my amplicon. First I did mapping to my reference, then sorted every sam file, and tried running the local analysis using dec.py. However, after I run it using dec.py -b s11msp1.mapped.bam.sam.bam -f pf_msp1.fasta -w 300 -k, the output I get is:
/gpfs/home/kbaral/anaconda3/envs/shorah/bin/diri_sampler/gpfs/home/kbaral/anaconda3/envs/shorah/bin/diri_sampler: error while loading shared libraries: libopenblas.so.0: error while loading shared libraries: libopenblas.so.0: cannot open shared object file: No such file or directory
/gpfs/home/kbaral/anaconda3/envs/shorah/bin/diri_sampler: error while loading shared libraries: libopenblas.so.0: cannot open shared object file: No such file or directory
: cannot open shared object file: No such file or directory
{0: 1756}
Traceback (most recent call last):
File "/home/kbaral/anaconda3/envs/shorah/bin/dec.py", line 78, in <module>
args.region, args.max_coverage, args.alpha, args.keep_files, args.seed)
File "/home/kbaral/anaconda3/envs/shorah/lib/python3.5/site-packages/shorah_dec.py", line 582, in main
(kp, proposed[kp][0] / proposed[kp][1]))
TypeError: unsupported operand type(s) for /: 'str' and 'int'
Hi, I am running your program to detect haplotype frequency across 20 samples with a malaria gene. In every case, my amplicon can vary from 120 bp to 1100 bp (it is length polymorphic), and I performed a sequencing process with Illumina MiSeq in pair-end mode using 2x250, so as you can see I have shorter reads than my amplicon. First I did mapping to my reference, then sorted every sam file, and tried running the local analysis using
dec.py
. However, after I run it usingdec.py -b s11msp1.mapped.bam.sam.bam -f pf_msp1.fasta -w 300 -k
, the output I get is:Do you know what could be happening here?
Thanks in advance,
Kabita