Analyzing primers for their specificity... IndexError: string index out of range #29
Comments
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@ARVINDEN Thank you for the question and sorry for such a delay with an answer. I think the problem may be with the BWA. Possibly it was terminated due to low memory with a "Segmentation fault" error, and this type of error cannot be caught. Could you check your SAM-file with less? |
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Dear Dr.aakechin: Total number of different constructed primers: 502178Analyzing primers for their specificity... |
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When the input bed region was big, and the designed primer number excess 1 million, this error seems to be always occured, could there be any advices? thank you very much! |
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@realgoldace Thank you for the question. Did you use the last version of the NGS-PrimerPlex? Some bugs were fixed since 2022. And which NGS-PrimerPlex version (gui or command-line, with or without docker) and with which OS did you use the program? And what was the reference genome? |
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Dear Dr.Andrey Kechin:
Thank you for your kindly answers,
I used the docker of the latest version which was downloaded at April this year, and the command was
dockerrun-it--entrypoint'bash'--namengs_primerplex_ref--rm-v/data10/luqin/multiplex:/multiplexaakechin/ngs-primerplex:latest
'python3NGS_primerplex.py--regions-file/multiplex/inter_neuron.bed--max-amplicon-length275--optimal-amplicon-length220--optimal-primer-melting-temp60--min-primer-melting-temp58-refhg19/ucsc.hg19.fasta-blast-snps-dbsnphg19/common_all_20180423_hg19.vcf.gz--threads20--skip-uncovered--min-primer-end-gc0--opt-primer-end-gc3'
The reference and snp file was preseted in the docker, and the reference version was hg19, the program was ran on the following OS:Linux version 3.10.0-1160.83.1.el7.x86_64 ***@***.***)(gcc version 4.8.5 20150623 (Red Hat 4.8.5-44) (GCC) ) #1 SMP Wed Jan 25 16:41:43 UTC 2023 Jan 25 16:41:43 UTC 2023.
And the bed was attached as appendix.
Sincerely yours
Qin Lu
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发送时间:2023-06-05 16:23:26 (星期一)
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主题: Re: [aakechin/NGS-PrimerPlex] Analyzing primers for their specificity... IndexError: string index out of range (Issue #29)
@realgoldace Thank you for the question. Did you use the last version of the NGS-PrimerPlex? Some bugs were fixed since 2022. And which NGS-PrimerPlex version (gui or command-line, with or without docker) and with which OS did you use the program? And what was the reference genome?
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Hi,
I am trying to read from draft file and trying to make multiplex primer with -blast option but failed in checking for checking non specific region step, I have pasted error message below, please help me resolve this error.
Reading input file...
Total number of input point regions: 5627
Number of unique input point regions: 5627
Reading file with draft primers and checking them for interactions...
Number of primer pairs from draft file: 65535
That do not form secondary structures: 65535
Getting positions that uncovered by draft primers...
Total number of uncovered positions: 0
Analyzing primers for their specificity...
Running BWA...
Processing SAM-file...
[E::fai_retrieve] Failed to retrieve block: unexpected end of file
File "/NGS-PrimerPlex/NGS_primerplex.py", line 3291, in
args.maxNonSpecLen,args.maxPrimerNonspec,False,'',args.blastNum)
File "/NGS-PrimerPlex/NGS_primerplex.py", line 1310, in checkPrimersSpecificity
res=res.get()
File "/usr/lib/python3.5/multiprocessing/pool.py", line 608, in get
raise self._value
File "/usr/lib/python3.5/multiprocessing/pool.py", line 119, in worker
result = (True, func(*args, **kwds))
File "/NGS-PrimerPlex/NGS_primerplex.py", line 1543, in readBwaFile
regionSeq[-2]==primerSeq[-2]):
IndexError: string index out of range
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