mtVariantCaller issue (line 967) | IndexError: string index out of range

[3i-v]

@jich-MCTP, I open here a new issue in response of your comment in issue #38 Thank you very much for your help,

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

Set max per-file depth to 8000 Traceback (most recent call last): File "(...)/MToolBox/**assembleMTgenome.py", line 443**, in mut_events = mtvcf_main_analysis(mt_table, sam_file, sample_name, tail=tail) File "(...)/MToolBox/**mtVariantCaller.py", line 967**, in mtvcf_main_analysis deletions.append(mtDNAseq[delflank]) **IndexError: string index out of range** ##### GENERATING VCF OUTPUT... Traceback (most recent call last): File "(...)/MToolBox/VCFoutput.py", line 33, in VCF_dict = ast.literal_eval(open('VCF_dict_tmp', 'r').read()) IOError: [Errno 2] No such file or directory: 'VCF_dict_tmp'

[3i-v]

Hi, do you have any update ? (The same error is generated again on 2 new samples of a batch of 20). Thank you very much.

[3i-v]

I've run again MToolBox with the most recent version (commit 4ac8db7, 2017-10-23). The same error is obtained. The execution stops once the files OUT2.pileup && sampleXX-table.txt have been created. Do you have any update ? Thank you very much,

Here is the error described in the log file:

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

Set max per-file depth to 8000 Traceback (most recent call last): File "(...)/MToolBox/assembleMTgenome.py", line 443, in mut_events = mtvcf_main_analysis(mt_table, sam_file, sample_name, tail=tail) File "(...)/MToolBox/mtVariantCaller.py", line 950, in mtvcf_main_analysis Covbase.append(median(convert)) File "(...)/MToolBox/mtVariantCaller.py", line 402, in median m1 = sorted(l)[(len(l)/2)+1-1] IndexError: list index out of range ##### GENERATING VCF OUTPUT...

[clody23]

This issue should be now fixed with the latest changes. Please do git pull in your local installation of MToolBox and launch MToolBox again. See github issue #64 for further details.

best, Claudia