Error on running splitBam

Question

Error on running splitBam

hchetia opened this issue 4 years ago · comments

While running the command
objs <- splitBam(bamfile, tags=tags, outPath=outPath,
txs=txs, genome=genome,
conservation=phastCons100way.UCSC.hg38)
I get the following error-
Error in asMethod(object) :
cannot coerce a non-logical 'Rle' or a logical 'Rle' with NAs to an IRanges object

JIANHONG OU · Answer 1 · Fri Sep 18 2020 19:53:50 GMT+0800 (China Standard Time)

Thank you for reporting this. Could you share a subset of your data for me to debug?

Hasnahana Chetia · Answer 2 · Fri Sep 18 2020 22:13:58 GMT+0800 (China Standard Time)

Hi Jian,
Pls let me know which file format would you like me to share?

JIANHONG OU · Answer 3 · Sun Sep 20 2020 23:01:08 GMT+0800 (China Standard Time)

It will be great if you can share the mimimal size of bamfile which can repeat the error.
Thank you.

Hasnahana Chetia · Answer 4 · Thu Sep 24 2020 23:33:36 GMT+0800 (China Standard Time)

Please see attachment

sample.bam.zip

JIANHONG OU · Answer 5 · Fri Sep 25 2020 20:13:02 GMT+0800 (China Standard Time)

Thank you for sharing. However, I can not index the file. It report error: is not a BAM file.

Hasnahana Chetia · Answer 6 · Mon Oct 05 2020 23:34:34 GMT+0800 (China Standard Time)

Shall I share index and bam?

Hasnahana Chetia · Answer 7 · Thu Oct 08 2020 03:17:26 GMT+0800 (China Standard Time)

Hi Jian, check out if this works.

Archive.zip

JIANHONG OU · Answer 8 · Thu Oct 08 2020 04:13:08 GMT+0800 (China Standard Time)

Thank you. I will take a look soon. Best! Your sincerely, Jianhong Ou

…

On Oct 7, 2020, at 3:17 PM, hchetia ***@***.***> wrote: Hi Jian, check out if this works. Archive.zip — You are receiving this because you commented. Reply to this email directly, view it on GitHub, or unsubscribe.

JIANHONG OU · Answer 9 · Fri Oct 16 2020 22:53:56 GMT+0800 (China Standard Time)

I found the bug. It is caused by not enough nucleosome free reads for training. So please try without conservation score.

Hasnahana Chetia · Answer 10 · Sat Oct 17 2020 09:03:58 GMT+0800 (China Standard Time)

Hi Jian,
DO you think the bug you found was actually because I shared only a snippet of my whole dataset?

Meanwhile, I will try without conservation score.

JIANHONG OU · Answer 11 · Sun Oct 18 2020 05:07:19 GMT+0800 (China Standard Time)

I don't think it is caused by a small bam file. Just try without conservation score.

…

On Fri, Oct 16, 2020 at 9:04 PM hchetia ***@***.***> wrote: Hi Jian, DO you think the bug you found was actually because I shared only a snippet of my whole dataset? Meanwhile, I will try without conservation score. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#32 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABLBEAYTQWAKEJLSZYWG353SLDUQVANCNFSM4RRIV6SA> .

-- Yours sincerely, Jianhong Ou

Hasnahana Chetia · Answer 12 · Sat Oct 24 2020 01:11:04 GMT+0800 (China Standard Time)

Hi Jian,
How many nucleosome free reads are typically required for generating a conservations score?

JIANHONG OU · Answer 13 · Tue Nov 03 2020 06:11:45 GMT+0800 (China Standard Time)

typically it should be more than 15% of your total reads.