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baoe / AlignGraph

Algorithm for secondary de novo genome assembly guided by closely related references
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exit unexpectly #14

Open shenwei356 opened 9 years ago

shenwei356 commented 9 years ago

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 commented 9 years ago

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/baoe/AlignGraph/issues/14.