[mira_talk] Re: Problem with assembly Illumina paired-end sequences
- From: "Camila M." <kamynz16@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Mon, 10 Feb 2014 11:58:37 -0200
Sorry, I forget to mention that I'm using mira_4.0 in linux mint.
On Mon, Feb 10, 2014 at 11:44 AM, Camila M. <kamynz16@xxxxxxxxx> wrote:
> I'm doing a lot of Miras by groups of 500 Miras. I have 500 manifest
> files, which means one manifest file for each contig.
>
> One of those manifest looks like this:
>
> project = comp4715_c0_seq1.mira
> job = est,denovo,accurate
> parameters = -GE:not=1 -NW:cmrnl=no -OUTPUT:output_result_html=yes
>
> readgroup = comp4715_c0_seq1._library_1
> data =
> /home/ABTLUS/maria.villa/RNASeq_Pseudozyma/read_by_contig/comp4715_c0_seq1_Glicose_1_ACTTGA_merge_R1_001.fastq
> /home/ABTLUS/maria.villa/RNASeq_Pseudozyma/read_by_contig/comp4715_c0_seq1_Glicose_1_ACTTGA_merge_R2_001.fastq
> technology = solexa
> strain = pseudozyma
> segment_placement= ---> <---
>
> readgroup = comp4715_c0_seq1._library_2
> data =
> /home/ABTLUS/maria.villa/RNASeq_Pseudozyma/read_by_contig/comp4715_c0_seq1_Xilano_1_AGTCAA_merge_R1_001.fastq
> /home/ABTLUS/maria.villa/RNASeq_Pseudozyma/read_by_contig/comp4715_c0_seq1_Xilano_1_AGTCAA_merge_R2_001.fastq
> technology = solexa
> strain = pseudozyma
> segment_placement= ---> <---
>
> readgroup = comp4715_c0_seq1._library_3
> data =
> /home/ABTLUS/maria.villa/RNASeq_Pseudozyma/read_by_contig/comp4715_c0_seq1_Xilose_1_GGCTAC_merge_R1_001.fastq
> /home/ABTLUS/maria.villa/RNASeq_Pseudozyma/read_by_contig/comp4715_c0_seq1_Xilose_1_GGCTAC_merge_R2_001.fastq
> technology = solexa
> strain = pseudozyma
> segment_placement= ---> <---
>
>
> MIRA worked well with the first 1500 assemblies, but now it gives the
> following error message:
>
>
>
> ********************************************************************************
> * Expected to read 4428 elements in file
> *
> * comp4715_c0_seq1.mira_assembly/comp4715_c0_seq1.mira_d_tmp/stattmp0.bin
> but *
> * read less. Was the file deleted? Disk full?
> *
>
> ********************************************************************************
> ->Thrown: size_t HashStatistics::createHashStatisticsFile(string &
> hashstatfilename, vector<string> & hashfilenames, vector<size_t> &
> elementsperfile, ReadPool & rp, bool onlyagainstrails, const string &
> directory)
> ->Caught: main
>
> What can I do to fix it?
>
> --
> Camila M.
>
--
Camila M.
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