Error in h(simpleError(msg, call))

[deb0612]

Dear sir, There are something wrong when I rumming freaser,

Is there anything wrong with bam file?

[vyepez88]

There might be. Did other bam files get counted? Make sure it is properly indexed. You can further check if it can get loaded by executing: Rsamtools::BamFile(path/to/yourbamfile.bam)

[deb0612]

Thanks, I found other bam files sometimes get counted and sometimes not.

Vicente Yepez @.***>於 2022年12月2日 週五，下午5:59寫道：

There might be. Did other bam files get counted? Make sure it is properly indexed. You can further check if it can get loaded by executing: Rsamtools::BamFile(path/to/yourbamfile.bam)

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[vyepez88]

can you rerun the pipeline with the -k option? In that way it will try to count all of them even if there was an error in the sample. Then, for the BAM files that didn't get counted, verify that they are indexed and that you can load them in R using the following command: Rsamtools::BamFile(path/to/yourbamfile.bam)

[deb0612]

Dear sir, I use -k option, however there is other error the log file was here: 2022-12-02T225702.748057.snakemake.log

The result of Rsamtools::BamFile(path/to/yourbamfile.bam):

[vyepez88]

of your 24 samples, can you check how many were counted the split reads? They should be in this folder: Output/processed_data/aberrant_splicing/datasets/cache/raw-local-normal/sample_tmp/splitCounts

[nickhsmith]

It seems to only fail for the split read counting. Could you please share the result of this command to check in detail the quality of your bam file, maybe we can see if things are split. Replacing <INPUT_BAM_FILE> with your bam. This will just look for the CIGAR string matching N which will hopefully show us split reads.

samtools view <INPUT_BAM_FILE>| cut -f6 |grep N |head -10

It should hopefully look something like this:

98M140N3M
96M140N5M
94M140N7M
94M140N7M
94M140N7M
94M140N7M
94M140N7M
93M140N8M
86M140N15M

[deb0612]

I got nothing in the folder.

Vicente Yepez @.***> 於 2022年12月3日 週六 凌晨12:08寫道：

of your 24 samples, can you check how many were counted the split reads? They should be in this folder:

Output/processed_data/aberrant_splicing/datasets/cache/raw-local-normal/sample_tmp/splitCounts

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[deb0612]

Here is not of the result [image: image.png]

nickhsmith @.***> 於 2022年12月3日 週六 凌晨1:44寫道：

It seems to only fail for the split read counting. Could you please share the result of this command to check in detail the quality of your bam file, maybe we can see if things are split. Replacing <INPUT_BAM_FILE> with your bam. This will just look for the CIGAR string matching N which will hopefully show us split reads.

samtools view <INPUT_BAM_FILE>| cut -f6 |grep N |head -10

It should hopefully look something like this:

98M140N3M 96M140N5M 94M140N7M 94M140N7M 94M140N7M 94M140N7M 94M140N7M 93M140N8M 86M140N15M

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[nickhsmith]

The image didn't get sent. Can you please share the results again?

[deb0612]

nickhsmith @.***>於 2022年12月4日 週日，上午5:06寫道：

The image didn't get sent. Can you please share the results again?

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[deb0612]

The output looked like this:

76M166846N13M1S 75M166846N15M 74M166840N16M 68M166846N16M6S 68M166846N13M9S 68M166846N17M5S 1S67M166846N17M5S 66M166846N17M7S 1S65M166846N17M7S 64M166846N14M12S

[nickhsmith]

Hmm. It seems like you do have split reads (this one is particularly large). @vyepez88 any thoughts?

[vyepez88]

hard to say. Can you share with us your config file?