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humanlongevity / HLA

xHLA: Fast and accurate HLA typing from short read sequence data
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Error message #22

Open compbio opened 6 years ago

compbio commented 6 years ago

It would be great if you can take a look at what happened and give me some clue! Thanks!

2018-01-11T18:02:17.464782174Z processing FASTQ file 2018-01-11T18:02:17.474653029Z found 2796 reads 2018-01-11T18:02:17.474664030Z processing MSA file 2018-01-11T18:02:17.897350913Z found 26381 HLA exons 2018-01-11T18:02:17.897375302Z processing FASTQ file 2018-01-11T18:02:26.875431019Z matched to 9790 HLA exons 2018-01-11T18:02:26.875466077Z 262 reads matched to HLA types not in the MSA file 2018-01-11T18:02:26.944128389Z translating matches to MSA 2018-01-11T18:02:28.212725340Z Error in apply(mat2[, solution], 1, max) : 2018-01-11T18:02:28.212744859Z dim(X) must have a positive length 2018-01-11T18:02:28.212755739Z Execution halted 2018-01-11T18:02:28.221492161Z Traceback (most recent call last): 2018-01-11T18:02:28.221508050Z File "/opt/bin/run.py", line 64, in 2018-01-11T18:02:28.221514672Z check_call(bin_args) 2018-01-11T18:02:28.221517873Z File "/usr/lib/python2.7/subprocess.py", line 540, in check_call 2018-01-11T18:02:28.221525322Z raise CalledProcessError(retcode, cmd) 2018-01-11T18:02:28.221536499Z subprocess.CalledProcessError: Command '['/opt/bin/typer.sh', '/sbgenomics/Projects/11c7a09c-16a8-4ea2-a781-01709f9943c7/NA12878-Garvan-Vial1_R.bam', 'NA12878-Garvan-Vial1', 'delete', 'full']' returned non-zero exit status 1

teolmste commented 6 years ago

I am having the same error message. For some of my files, it appears to give a single HLA type, but then reads dim(X) must have a positive length.... as per above.