ucagenomix/sicelore

null sequence and quality in consensus sequence

defendant602 opened this issue · 4 comments

defendant602 commented

Sorry to bother you. When I run "compute consensus sequence" in quickrun.v2.sh, I have found quite a lot of null sequence in the ouput consensus.fq, and for the molecures which have normal sequence, all the quality value in the quality line are "$" symbol. I want to know if it is normal for this step?

The consensus.fq looks like this:
image

My version of spoa and racon is v3.0.2 and v1.3.3, respectively.

Thnaks!

defendant602 commented

and in the stderr of "compute consensus sequence" step, I got many exceptions of "java.lang.NullPointerException".

java.lang.NullPointerException
        at org.ipmc.sicelore.utils.ConsensusMsa.process(ConsensusMsa.java:51)
        at org.ipmc.sicelore.utils.ConsensusMsa.<init>(ConsensusMsa.java:40)
        at org.ipmc.sicelore.utils.Consensus.call(Consensus.java:225)
        at org.ipmc.sicelore.utils.Consensus.call(Consensus.java:14)
        at java.util.concurrent.FutureTask.run(FutureTask.java:266)
        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
        at java.lang.Thread.run(Thread.java:748)
ucagenomix commented

Hi,
consensus sequence is computed when you got at least 3 reads per UMI. The null values obtained when you have >2 reads per UMI mean that spoa is not working properly, you should look at the tmp directory rights permission and the spoa output files from cmd line 'spoa -r 2 /tmp/molecule_reads.fa > /tmp/molecule.msa'
You can set DEBUG=true to keep tmp files to debug whats not going well in your environnement.

best,

defendant602 commented

Hi, Thanks for your reply! The cmd "spoa -r 2 /tmp/molecule_reads.fa > /tmp/molecule.msa" work just fine, no error message occurred. The ouput msa file looks like this:

image

Should I try the jar files in the dev_versions directory?

ucagenomix commented

Are you sure to submit the jar file with a valid TMPDIR, that exists and where you have read/write permissions ?
You can try the jar files in the dev version, but it should not change this error.