Ok thanks for your replies. I tried with new fastq files, and still got the problem, only one sample passed through to the complete SAM file. I also tried mapping without any preprocessing, and same error BWA stops at sampe.
I want to run it in command line outside of Galaxy, but Im not super-familiar with linux. Right now Im indexing the genome. Should all indexing files be in the same directory as my input fastqs and reference? Or can I specify the location somehow? I just installed bwa by apt-get on a clean Ubuntu disk image. But where exactly does it install? Only thing I know, is that bwa is in the PATH.
And my apologies for such basic linux questions.
Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
X
-
As mentioned above, you need to make sure that your processed paired end reads are paired correctly in read 1 and read 2 files. I had BWA stall forever when my reads weren't paired properly after preprocessing (filtering by quality will get rid of different reads in read 1 and read 2 file if you don't use the appropriate software or re-pair after processing).
Leave a comment:
-
What does bwa sample tell you are the approximate insert sizes? If they are crazy huge, it can take the software a long time to decide that, and move on.
But no, it should not hang. It should be outputting its progress every couple of seconds.
Leave a comment:
-
With the latter scenario I would have expected BWA to "hang" for several hours/days? Im currently running an alignment with newly transferred fastqs, and will report back if that doesnt solve the issue.
Leave a comment:
-
Pasting the output when it goes bad might help.
Is it possible that the fastqs got corrupted part-way through?
Renaming and trimming shouldn't hurt things, as long as the millionth read in fastq 1 really is the mate of the millionth read of fastq 2, and so on.
Leave a comment:
-
BWA PE Problem
Dear forum,
I am experiencing problems during BWA paired-end mapping on my local setup. I have two fastq files for each sample. BWA aln step seems okay, but then at sampe the alignment may fail after outputting 1 Mb or even 1 Gb of SAM data. Could this happen to be a pre-processing issue? Fastq --> rename --> trimming ?
BWA is executed under Galaxy platform and I dont see the log file, so I may try to run it on command line. I see it fails at sampe via htop command.
I have also indexed the reference.Tags: None
Latest Articles
Collapse
-
by seqadmin
Next-generation sequencing (NGS) and quantitative polymerase chain reaction (qPCR) are essential techniques for investigating the genome, transcriptome, and epigenome. In many cases, choosing the appropriate technique is straightforward, but in others, it can be more challenging to determine the most effective option. A simple distinction is that smaller, more focused projects are typically better suited for qPCR, while larger, more complex datasets benefit from NGS. However,...-
Channel: Articles
10-18-2024, 07:11 AM -
-
by seqadmin
Non-coding RNAs (ncRNAs) do not code for proteins but play important roles in numerous cellular processes including gene silencing, developmental pathways, and more. There are numerous types including microRNA (miRNA), long ncRNA (lncRNA), circular RNA (circRNA), and more. In this article, we discuss innovative ncRNA research and explore recent technological advancements that improve the study of ncRNAs.
Nobel Prize for MicroRNA Discovery
This week,...-
Channel: Articles
10-07-2024, 08:07 AM -
ad_right_rmr
Collapse
News
Collapse
Topics | Statistics | Last Post | ||
---|---|---|---|---|
Started by seqadmin, 11-01-2024, 06:09 AM
|
0 responses
18 views
0 likes
|
Last Post
by seqadmin
11-01-2024, 06:09 AM
|
||
New Model Aims to Explain Polygenic Diseases by Connecting Genomic Mutations and Regulatory Networks
by seqadmin
Started by seqadmin, 10-30-2024, 05:31 AM
|
0 responses
18 views
0 likes
|
Last Post
by seqadmin
10-30-2024, 05:31 AM
|
||
Started by seqadmin, 10-24-2024, 06:58 AM
|
0 responses
24 views
0 likes
|
Last Post
by seqadmin
10-24-2024, 06:58 AM
|
||
New AI Model Designs Synthetic DNA Switches for Targeted Gene Expression in Specific Cell Types
by seqadmin
Started by seqadmin, 10-23-2024, 08:43 AM
|
0 responses
53 views
0 likes
|
Last Post
by seqadmin
10-23-2024, 08:43 AM
|
Leave a comment: