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ylab-hi / ScanNeo

A pipeline for identifying indel derived neoantigens using RNA-Seq data
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indel.bam not being created #4

Closed aditisk closed 2 years ago

aditisk commented 4 years ago

Hi @dolittle007,

I was able to get past the config file error in #3. But I am still getting an error because the indel.bam file is not being created. I am attaching the error file here. In the error file it says that the indel.bam generation is finished but the file is not created.

Begin building indel.bam using transIndel finished!

Could you please tell me what I need to fix ? Thanks. test.pbs.o1094071.txt

dolittle007 commented 4 years ago

Did the file "R_9080_N_ZAN174A16_S54_R1_001Aligned.sortedByCoord.out.bwa.bam" exist? If it did exist, it could be the problem of transIndel_build. For debugging purposes, we may have to comment the remove function in the ScanNeo.py by adding "#". Meanwhile I am running more tests on it.

aditisk commented 4 years ago

Hi @dolittle007, the .bwa.bam file exists.

I tried to comment the remove function and all calls of that function in the ScanNeo.py but I'm getting the same error again. Is there anything else I can try ?

Please let me know the outcome of your testing. Thanks.

dolittle007 commented 3 years ago

I tested using different BAM files. There is no problem in my end. It may be a bug in transIndel. Or you input the wrong GTF file, I am guessing. The GTF file and the BAM file should use the same coordinate system. For example, both chr1 ... chrY or both 1 ... Y. I have contacted the transIndel author, I will update ScanNeo along with transIndel soon. Thank you!