Help with using the multiBam Summary tool

Question: Help with using the multiBam Summary tool - error message

2.1 years ago by

alim • 10

United Kingdom

alim • 10 wrote:

Hello,

I have just aligned some reads using Bowtie2 and am wanting to look at correlation between my replicates using the plotCorrelation tool. However, this requires a matrix file to first be generated with the multiBamSummary tool. I tried running the latter to generate the matrix but this error message came up:

Fatal error: Exit code 1 () Traceback (most recent call last): File "/galaxy-repl/main/jobdir/014/048/14048548/conda-env/bin/multiBamSummary", line 7, in <module> main() File "/galaxy-repl/main/jobdir/014/048/14048548/conda-env/lib/python2.7/site-packages/deeptools/multiBamSummary.py", line 224, in main num_reads_per_bin = c.run(allArgs=args) File "/galaxy-repl/main/jobdir/014/048/14048548/conda-env/lib/python2.7/site-packages/deeptools/countReadsPerBin.py", line 263, in run raise ValueError("numberOfSamples has to be bigger than {} ".format(min_num_of_samples)) ValueError: numberOfSamples has to be bigger than 99567

Could anyone help this ?

Cheers, Alfred

rna-seq software error bam • 1.0k views

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modified 2.1 years ago • written 2.1 years ago by alim • 10

Which reference genome did you use?

ADD REPLY • link written 2.1 years ago by Devon Ryan • 1.9k

2.1 years ago by

Devon Ryan • 1.9k

Germany

Devon Ryan • 1.9k wrote:

More generally, try setting the "Bin Size in bp" to a smaller value. It needs to be larger than the average chromosome/contig length, which doesn't always happen by default if you have a lot of really small contigs.

ADD COMMENT • link written 2.1 years ago by Devon Ryan • 1.9k

hi Devon I am also getting error with multibamsummary. Reference genome is brassica juncea 1.5.

error: Fatal error: Exit code 1 () [bwHdrRead] There was an error while reading in the header! Traceback (most recent call last): File "/galaxy/main/deps/_conda/envs/mulled-v1-0fa290085c742a3ffee6a142d1fce47c178e1c289ff6f0c66023b506f3377842/bin/multiBamSummary", line 11, in <module> main(args) File "/galaxy/main/deps/_conda/envs/mulled-v1-0fa290085c742a3ffee6a142d1fce47c178e1c289ff6f0c66023b506f3377842/lib/python2.7/site-packages/deeptools/multiBamSummary.py", line 224, in main num_reads_per_bin = c.run(allArgs=args) File "/galaxy/main/deps/_conda/envs/mulled-v1-0fa290085c742a3ffee6a142d1fce47c178e1c289ff6f0c66023b506f3377842/lib/python2.7/site-packages/deeptools/countReadsPerBin.py", line 244, in run y = pyBigWig.open(x) RuntimeError: Received an error during file opening!

ADD REPLY • link written 9 months ago by xpna01t • 0

It looks like the bigWig file is corrupt or empty.

ADD REPLY • link written 9 months ago by Devon Ryan • 1.9k

2.1 years ago by

alim • 10

United Kingdom

alim • 10 wrote:

Hi Devon,

Many thanks for getting back to me. What sort of range of bin size would you suggest please and how can I estimate that? My reads are all 50-bp fragments, aligned to mouse mm10 genome.

ADD COMMENT • link written 2.1 years ago by alim • 10

For mm10 you shouldn't have to change anything and you shouldn't be getting that error message. Please submit a big report within Galaxy and, in the part of the report where you can type stuff in, put a link to this post and ask the site administrator to contact me. For reference, the 99567 number is the number of chromosomes/contigs in the BAM files, so either you're not using mm10 but rather some other assembly (e.g., a different strain from the Mouse Genomes Project) or something went wrong when comparing the chromosome names.

ADD REPLY • link written 2.1 years ago by Devon Ryan • 1.9k

Agree that the problem is likely a genome mismatch issue from the given info. Compare each input - data based on the same exact reference genome must be used for all steps. https://wiki.galaxyproject.org/Support#Reference_genomes

If you cannot find the issue but can replicate this at http://usegalaxy.org, this is how to send in the bug report: https://wiki.galaxyproject.org/Support#Reporting_tool_errors

Leave all inputs/outputs undeleted and include a link to this biostars post.

Thanks, Jen, Galaxy team

ADD REPLY • link written 2.1 years ago by Jennifer Hillman Jackson ♦ 25k

Thanks so much Devon and Jen - I will recheck my data and see if it was using the correct reference genome.

Cheers, Alfred

ADD REPLY • link written 2.1 years ago by alim • 10

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