Using long reads in MEGAHIT about megahit HOT 4 CLOSED

Hi Shaman,
How long is your "long reads" or contigs?

from megahit.

Well, for this particular data set, the longest read is: 11633. Also note that there are varying read lengths.

I actually made and attempts to run MEGAHIT on such data. Below is what I have to report at the moment. Here is the command issued:

megahit -o combined_assm --cpu-only -m 763000000000 --mem-flag 1 -l 11633 -r mixed_contigs-reads.fa -t 24

And This is the error received:

MEAGHIT v0.2.0-alpha
[Fri Feb 27 15:51:45 2015] Start assembly. Number of CPU threads 24.
[Fri Feb 27 15:51:45 2015] Extracting solid (k+1)-mers for k = 21
[Fri Feb 27 16:06:29 2015] Building graph for k = 21
sdbg_builder_cpu: io-utility.h:202: void ReadPackage::ReadBinaryReads(gzFile): Assertion `num_bytes % (words_per_read * sizeof(edge_word_t)) == 0' failed.
Error occurs when running "builder build" for k = 21
[Exit code -6]

As you can see, it was run on a high memory machine with 24 threads and ~720 GB of memory available. For the input, I concatenated contigs from a previous assembly with raw reads from an additional data set, thereby ending up with a file with all the contigs and reads (in fasta).

Do let me know if you require further information.

-Shaman-

from megahit.

Please send the log file in the output directory to me (voutcn gmail com) directly.

On 3 Mar, 2015, at 3:34 pm, Shaman [email protected] wrote:

Well, for this particular data set, the longest read is: 11633. Also note that there are varying read lengths.

I actually made and attempts to run MEGAHIT on such data. Below is what I have to report at the moment. Here is the command issued:

megahit -o MTpooledAssembledSequences-megahit-ALL_MG-reads_megahit --cpu-only -m 763000000000 --mem-flag 1 -l 11633 -r pooledAssembledSequences_MT-megahit_MT-megahit2_MG_reads.fa -t 24
And This is the error received:

MEAGHIT v0.2.0-alpha
[Fri Feb 27 15:51:45 2015] Start assembly. Number of CPU threads 24.
[Fri Feb 27 15:51:45 2015] Extracting solid (k+1)-mers for k = 21
[Fri Feb 27 16:06:29 2015] Building graph for k = 21
sdbg_builder_cpu: io-utility.h:202: void ReadPackage::ReadBinaryReads(gzFile): Assertion `num_bytes % (words_per_read * sizeof(edge_word_t)) == 0' failed.
Error occurs when running "builder build" for k = 21
[Exit code -6]
As you can see, it was run on a high memory machine with 24 threads and ~720 GB of memory available.

-Shaman-

—
Reply to this email directly or view it on GitHub #21 (comment).

from megahit.

Fixed 06f84d5

from megahit.