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kyizhak / RNA_MUTECT_1.0

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Error in the final filterbasedonDuplicateReads step #1

Open xiongssg opened 5 years ago

xiongssg commented 5 years ago

Hi, I get the following error when running the final filterbasedonDuplicateReads step. Can you please help me fix this?

load MAF file convert_chr: assuming human for chrX/chrY Remove sites supported by duplicate reads

i =

 1

Warning: Found invalid tag in header type: 'PG'. Ignoring tag 'PN:STAR'.

In saminfo (line 186) In baminfo (line 74) In bamread (line 131) In FilterRNAMutationsBasedOnDuplicateReads (line 65) Warning: Found invalid tag in header type: 'PG'. Ignoring tag 'PN:MarkDuplicates'. In saminfo (line 186) In baminfo (line 74) In bamread (line 131) In FilterRNAMutationsBasedOnDuplicateReads (line 65)

Error using cigar2align (line 57) Input sequences must be in a cell array of strings.

Error in removeCallsBasedOnDuplicateReadsV2 (line 12)

Error in FilterRNAMutationsBasedOnDuplicateReads (line 66)

bioinfo:cigar2align:InvalidSequenceInput

My full code is : ./run_FilterRNAMutationsBasedOnDuplicateReads.sh ~/PIPELINE/Matlab2016a LZY-10-AZX_RNA_vs_DNA_somatic LZY-10-AZX.sort.markDup.bam LZY-10-AZX_RNA_vs_DNA_somatic.post_filtering_no_pon.txt 3

I used the RNA bam file generated from STAR, and then sort and MarkDuplicates by picard. The post_filtering_MAF_file is uploaded here. LZY-10-AZX_RNA_vs_DNA_somatic.post_filtering_no_pon.txt

Thank you for your help! xiong

xiongssg commented 5 years ago

I also extract the first 40000+ reads from the RNA bam file.

tmp.txt

longqh3 commented 4 years ago

Hi, I get the following error when running the final filterbasedonDuplicateReads step. Can you please help me fix this?

load MAF file convert_chr: assuming human for chrX/chrY Remove sites supported by duplicate reads

i =

 1

Warning: Found invalid tag in header type: 'PG'. Ignoring tag 'PN:STAR'.

In saminfo (line 186) In baminfo (line 74) In bamread (line 131) In FilterRNAMutationsBasedOnDuplicateReads (line 65) Warning: Found invalid tag in header type: 'PG'. Ignoring tag 'PN:MarkDuplicates'. In saminfo (line 186) In baminfo (line 74) In bamread (line 131) In FilterRNAMutationsBasedOnDuplicateReads (line 65)

Error using cigar2align (line 57) Input sequences must be in a cell array of strings.

Error in removeCallsBasedOnDuplicateReadsV2 (line 12)

Error in FilterRNAMutationsBasedOnDuplicateReads (line 66)

bioinfo:cigar2align:InvalidSequenceInput

My full code is : ./run_FilterRNAMutationsBasedOnDuplicateReads.sh ~/PIPELINE/Matlab2016a LZY-10-AZX_RNA_vs_DNA_somatic LZY-10-AZX.sort.markDup.bam LZY-10-AZX_RNA_vs_DNA_somatic.post_filtering_no_pon.txt 3

I used the RNA bam file generated from STAR, and then sort and MarkDuplicates by picard. The post_filtering_MAF_file is uploaded here. LZY-10-AZX_RNA_vs_DNA_somatic.post_filtering_no_pon.txt

Thank you for your help! xiong

Hi, I also encountered your problem which display error info just like yours. I tried using Picard's ValidateSamFile to make sure the bam file was intact, but it still failed even it passed the validation test. I also dive into cigar2align.m program file and found the sequence from bam file failed cellstr test to raise error. 图片 I'm wondering whether the "FilterRNAMutationsBasedOnDuplicateReads " codes had some bugs. Hope you or the author can tip me out, thanks!