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I am not getting any alignments when using DALIGNER as a mapper. It works great when I align PacBio reads among themselves, but when I try to align them to a DAM built from the human reference sequen…
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I have been experiencing and issue where during the raw read error correction phase, when the initial d_\* (daligner) jobs are running, the vast majority will complete without issue, but some small nu…
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For example consider adding here: https://github.com/thegenemyers/DALIGNER/blob/709c02d74a1baea248a64eb0e8ea1cd7b5733d2b/daligner.c#L189:
``` diff
diff --git a/daligner.c b/daligner.c
index 399218b..…
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Hello,
We have sequenced 80x Pacbio Reads of Rice Genome , but the Quality of these data is relatively low ( Low alignment identity compared to Ecoli Test Data , Fruitfly Data etc. ) .
Then I trie…
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We are trying to align two smaller genomes (160Mb) to each other:
**\* glibc detected **\* /ebio/abt6/fbemm/software/dazzler/daligner/daligner: munmap_chunk(): invalid pointer: 0x00007fff77201010 ***…
fbemm updated
9 years ago
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Hi,
I was wondering how job recovery works.
Currently Falcon runs the DAligner Step and I like to stop/kill the process and change the SGE parameters.
Can I just run fc_run.py and it will restart th…
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see: https://github.com/thegenemyers/DALIGNER/blob/8edd180ba7b5302c6f1fc859eef5c646db99fd87/README#L307
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Hello
I was just curious why the option -o "optimal" for LAshow disappeared . I liked the idea behind it , used it in a few scripts and am now curious whether the concept did not hold up or whether it…
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See: https://github.com/thegenemyers/DALIGNER/blob/8edd180ba7b5302c6f1fc859eef5c646db99fd87/README#L321
Should likely be:
``` bash
LAshow -c -a -w50 G G.1 | more
```
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Dear Dr. Chin,
Is there a way in Falcon to estimate running time? We are running Falcon on a large data set for several days. I think it should have been done based on previous analyses, but it's sti…