Open 3i-v opened 5 years ago
Hi, can you please share the input file that generates this error? That will help debugging.
thanks Best wishes, Claudia
Hi Claudia, Could you please sent me an eMail I can use to share the files with you ? Thank you so much, v.
Hi,
thanks for sending the files. This https://github.com/mitoNGS/MToolBox/commit/58f3db1b2d86715ae4fd56f014edd5b9dd212be1 should fix the issue now.
Best, Claudia
Thank you very much for the update Claudia. With the commit 58f3db1 you made, I was able to recover 5 on 8 analysis that previously failed. A bug is still persistent on 3 samples. The error messsage I obtain is this one:
##### ASSEMBLING MT GENOMES WITH ASSEMBLEMTGENOME...
WARNING: values of tail < 5 are deprecated and will be replaced with 5
[mpileup] 1 samples in 1 input files
Traceback (most recent call last):
File "(...)/MToolBox/assembleMTgenome.py", line 445, in <module>
mut_events = mtvcf_main_analysis(mt_table, sam_file, sample_name, tail=tail)
File "(...)/MToolBox/mtVariantCaller.py", line 563, in mtvcf_main_analysis
Refbase=mtDNAseq[int(i)-1]
IndexError: string index out of range
##### GENERATING VCF OUTPUT...
Traceback (most recent call last):
File "(...)/MToolBox/VCFoutput.py", line 36, in <module>
VCF_dict = ast.literal_eval(open('VCF_dict_tmp', 'r').read())
IOError: [Errno 2] No such file or directory: 'VCF_dict_tmp'
Thank you, v.
I am running the last MToolBox commit (MToolBox-f527c5c), but here is the error message I obtained on a sample that previously failed (with the older version); Thank you, v.
[Fri Feb 08 18:13:10 EST 2019] net.sf.picard.sam.SamFormatConverter done. Elapsed time: 0.09 minutes. Runtime.totalMemory()=602406912
ASSEMBLING MT GENOMES WITH ASSEMBLEMTGENOME...
WARNING: values of tail < 5 are deprecated and will be replaced with 5
[mpileup] 1 samples in 1 input files Traceback (most recent call last): File "xxx/MToolBox-f527c5c_20190206/MToolBox/assembleMTgenome.py", line 445, in
mut_events = mtvcf_main_analysis(mt_table, sam_file, sample_name, tail=tail)
File "xxx/MToolBox-f527c5c_20190206/MToolBox/mtVariantCaller.py", line 590, in mtvcf_main_analysis
Covbase.append(median(convert))
File "xxx/MToolBox-f527c5c_20190206/MToolBox/mtVariantCaller.py", line 65, in median
m1 = sorted(l)[(len(l)/2)+1-1]
IndexError: list index out of range