[mira_talk] Problem with assembly Illumina paired-end sequences
- From: "Camila M." <kamynz16@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Mon, 10 Feb 2014 11:44:42 -0200
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.
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