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write temporary bam files #8
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Hi Dario, I agree that it is probably not tigmint that caused the crash, since it was just bwa mem running at that stage. Using additional threads would speed up the You could:
Hope that helps! |
Hi Lauren, Thanks for the suggestion, I will go for it. Dario |
Hi Dario, Yes, you can partition the fq.gz (post-Longranger basic) file the same as you would any other interleaved fastq file. The only special thing about the longranger basic output as opposed to another fastq file is the chromium barcode information encoded in the read header. Ex:
So as long as your partitioning approach keeps the R1/R2 pairs together, and keeps the "BX:Z" comment in the read header, you will be fine! Running Hope that helps -- let me know if you have any other questions! |
@dcopetti - I'll close this for now, but feel free to re-open if you have further questions! |
Hello,
I am not sure how else I should compose the command to use the bam as an input instead. |
Hi Dario, First off, you can just use the master branch -- the logic in the tigmint-span branch used to look for spanning molecules to identify misassemblies has been incorporated into the master branch. Also, no need to comment out commands to ensure that the Makefile starts at the step that you want. You just need to ensure that your BAM file is named It appears that tigmint detects that the target files of the pipeline are already present in your directory. Could you note the other files in your working directory, as well as what you named the BAM file? |
Hi, I installed the newest version, but it is giving me an error, same as the older installation (both attempts are here below:
Also adding --dry-run gives me the same error.
I am not sure what else I should do. Dario |
Looks like you misspelled |
Dang! With the --dry-run looks like this:
Then I run it and I get this error:
so I updated pysam:
move to a new terminal and I get this:
as if it is not recognizing the bam file? |
Just checking -- are you in the same working directory as before? It looks like it can't see the file named |
You are right, the links were not activated.
should I maybe redownlaod tigmint after having updated pysam? |
I just downloaded again tigmint, same error |
Can you double check that the python3 that you want to use is being found (ie. in your PATH)? |
Nope, it is the one in |
No problem! Let me know if you encounter any other issues. |
Hi, |
Hello,
I was running tigmint-span and the sever crashed (I am pretty sure it is not due to tigmint, unless it required a huge amount of memory all of a sudden).
I have now a bunch of *.bam.tmp.0628.bam files - I guess it died during the sorting of this command:
bwa mem -t$t -pC $(draft).fa $< | samtools view -h -F4 | samtools sort -@$t -tBX -o $@
I am thinking of two alternative options:
Would it be possible to implement any of the options, or any other that will help deal with long computation time?
Thanks,
Dario
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