exit unexpectly

[shenwei356]

Hi, @baoe , I'm trying to assemble a bacteria genome of about 6.5M. Contigs was assembled by SPAdes. bowtie2 (v2.2.6) and blat (v. 35) were installed and added to $PATH.

AlignGraph exited with message below,

(0) Alignment finished

CHROMOSOME 0: 
(1) Chromosome loaded
(2) Contig alignment loaded

No wrong code appeared.

And adding option --resume seems not work, and no useful help message is given.

Besides, an option of --temp-dir could be useful when submitting multiple jobs to clusters from same work directory.

[baoe]

Hi, Wei Shen,

To resume the job, the command line is "./AlignGraph --resume" without anything else. Maybe you could try it again in this way?

Best,
Bao

---

From: Wei Shen [notifications@github.com]
Sent: Saturday, September 19, 2015 2:17 AM
To: baoe/AlignGraph
Cc: Bao
Subject: [AlignGraph] exit unexpectly (#14)

Hi, @baoehttps://github.com/baoe , I'm trying to assemble a bacteria genome of about 6.5M. Contigs was assembled by SPAdes. bowtie2 (v2.2.6) and blat (v. 35) were installed and added to $PATH.

AlignGraph exited with message below,

(0) Alignment finished

CHROMOSOME 0:
(1) Chromosome loaded
(2) Contig alignment loaded

No wrong code appeared.

And adding option --resume seems not work, and no useful help message is given.

Besides, an option of --temp-dir could be useful when submitting multiple jobs to clusters from same work directory.

—
Reply to this email directly or view it on GitHubhttps://github.com//issues/14.