Open ChiragNepal opened 5 years ago
I think I had a similar error when I ran it, it could be because you are running seq2hla on python 2.7 + while the script is written in 2.6.8. You can make the changes to seq2hla.py suggested here to get it running - https://bitbucket.org/sebastian_boegel/seq2hla/pull-requests/2/run-on-posix-like-environments/diff
totalreads=float(linecache.getline(logfile,1).split(':')[1])
the total reads not exists in logfile line1 , but exists in line2.
use python 2.7+ , the logfile is
Setting the index via positional argument will be deprecated in a future release. Please use -x option instead.
reads processed: 580
# reads with at least one alignment: 580 (100.00%) # reads that failed to align: 0 (0.00%) Reported 35847 paired-end alignments Now running seq2HLA version 2.3! Input is a gipped file .....
I am running seq2HLA for the first time, the program runs fine up to this stage and throws the error.
The digital haplotype is written into runName-ClassI-class.digitalhaplotype2 2nd iteration done. -----------2 digit typing results-------------
Locus Allele 1 Confidence Allele 2 Confidence
A A68 0 A01 0.01747313 B B51 0.0009102886 B57 0.0002627386 C C15 3.922862e-12 C06 0.01667079 Calculation of locus-specific expression ...
runName-ClassI-class.bowtielog Traceback (most recent call last): File "/NextGenSeqData/project-data/chirag/unixTools/seq2HLA/seq2HLA.py", line 769, in
File "/NextGenSeqData/project-data/chirag/unixTools/seq2HLA/seq2HLA.py", line 123, in main
File "/NextGenSeqData/project-data/chirag/unixTools/seq2HLA/seq2HLA.py", line 195, in mainHLA expression(locus_list,length_dict,map,runName,readFile1) File "/NextGenSeqData/project-data/chirag/unixTools/seq2HLA/seq2HLA.py", line 623, in expression totalreads=float(linecache.getline(logfile,1).split(':')[1])
ValueError: could not convert string to float: Skipping pair D00620