ddRAD analysis pipelines

Question

[Jeffin Rockey]

I have a Fish ddRAD data, 50 samples.

In dDocent I am getting very low alignment ~30%.

In STACKS the issue is "Error: Failed to find any matching paired-end reads in" though reads are indeed paired.

In ipyard the error is "TypeError(Can't broadcast (100, 1130, 133) -> (100, 187, 133)) in Step 6 "

Request advise on the above errors. Also please suggest other recommended tool or pipeline for ddRAD data.

[GenoMax]

How did you run STACKS? You need to ensure that you choose the right index scheme. Examples are described well in STACKS manual.

[Jeffin Rockey]

I went to manual again and index seems to be the barcodes. However the data I have is already demultiplexed. Many steps ran fine also.

From the log

ustacks is done.
cstacks is done.
sstacks is done.

but below tsv2bam the below error is there.

denovo_map.pl: Aborted because the last command failed (1); see log file.

In tsv2bam & denovo_map.log logfiles error is like below

Failed to find any matching paired-end reads in ..

Looks like some naming issue. (I had to rename _R1s to .1 and R2s to .2 earlier based on a requirement raised by the tool.)

It is like the files were identifiable in the beginning but not now at tsv2bam. Trying to identify the cause.

[h.mon]

ipyrad issue opened here: TypeError Can't broadcast. @Jeffin Rockey: could you update your post if the issue gets resolved there?

[Jeffin Rockey]

I am still working with Isaac on this specific ipyrad error, going through the error logs and all. From the ipyrad group discussions it do not appear to be a generic issue. I tried in Redhat and Ubuntu servers,but error persists.

Very sad to see that it is getting lost at the 6th step.

Anyways I shall update here if resolved.

[felipe_o_torquato]

Hi Jeffin,

I've been having the same problem with single-digest and paired-end data.

Which program did you use to solve the problem??

Thanks in advance

[h.mon]

Please do not use ADD ANSWER to post comments and questions, use the ADD COMMENT button instead.

He didn't use any program to solve the issue, he used the correct cut-site sequence:

The enzyme cut-site sequence I provided was incorrect.

And:

Once I gave the correct cut-site it worked as expected.

[Jeffin Rockey]

Stacks issue I could not resolve.

ipyrad issue root cause was wrong cut site information given which I corrected.

Answer 1

[Jeffin Rockey]

Resolved now.

The reason was completely unexpected.

The enzyme cut-site sequence I provided was incorrect. So in filtering step most of the reads did not pass(zero for all most all samples). This caused the error downstream at step6.

Once I gave the correct cut-site it worked as expected.Took almost a month to identify the root cause.