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unzip (installed on 20170823) failed at the task 0-phasing/012822F/blasr/task.json #93
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If one raw reads file is absent, it implies that the read tracking step didn't finish properly. There may also be other raw reads files missing. You can try re-running the read fetching step in track_reads.sh to ensure you've fetched all raw reads.
Comment out the first three python steps, and try re-running the final |
Thanks for your reply! By the way, I have a little question here: what does the value of row[3] mean? Because there is no 012822F_reads.fa, I think it must be caused by the failing of reaching some of your requirements. Therefore I have modified your code to output every values to make sure these values of the contig '012822F' satisfying your requirement of output, including:
Now I still haven't found the reason why there is no 012822F_reads.fa. Do you have any suggestion about where there would be a problem? |
I have found the reason. The content of the function is: The input of this function is pid and the output of this function is oid. Different pids could have the same oid with the transform of this function. I can show you some data. m54045_170723_035233/10158447/0_40972 000000296 m54045_170723_035233/11862691/0_23644 000000487 If we have lots of data, this problem will be ignored because there will be some subreads rest and the problem will not cause the unzip failing. |
@nottwy Due to the error rate and repeat genome content, it is possible that a subread can be used in correcting multiple preads. However, each pid read can be only trace to single subread (or one of the subreads from the ZMW, persumablly the all subreads from the same ZMW are from the same molecule). In your case, it is like not there is no unique track from a pid to a subread. But there are some better and worse error corrected reads, and all subreads are eventually be recurited by the better one. |
Let's start from a simple point. I have discover the reason completely. It's like this:
Wait for your reply! @cschin ,also @gconcepcion |
Again, please ask @pacbio for how they want to "officially" (if there is such thing) handle this for you. On the other hand, the design was the code will look for a list to see which config should be processed. You can remove the problematic config from the list. There is a way to hack through it as you have the source code. I simply have no resource to test any suggestion I make now. |
OK. Let's wait for @gconcepcion 's reply. |
Hi nottwy, It sounds like you have a good grasp on the problem, please feel free to submit a pull request and we can integrate a fix into the code. In the meantime, @cschin has provided a valid work around, simply remove that contig from the file 3-unzip/reads/ctg_list file and re-run the unzip pipeline. The offending contig should be ignored and you will be able to proceed with the pipeline. |
@gconcepcion , |
I find that there may exist an oid-rid match error. @gconcepcion |
@cschin @gconcepcion , |
Hi, Any progress? Any ideas? Bumped into similar issue. 22 contigs have no corresponding reads.fa |
Finally, I found that: |
Under the directory 3-unzip/reads/, there is a file called '012822F_ref.fa'. But there isn't the corresponding read file '012822F_reads.fa'. And it caused a task's (0-phasing/012822F/blasr/task.json) failure. It needs this read file.
I don't know how to generate this file manually. Can you tell me ?
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