speedseq waits indefinitely? about speedseq HOT 10 CLOSED

Is your speedseq.config file pointing to the correct paths for the executables?

from speedseq.

I wasn't able to build everything (gemini and lumpy), so maybe this is the
problem?

On Fri, Mar 14, 2014 at 10:28 AM, Colby Chiang [email protected]:

Is your speedseq.config file pointing to the correct paths for the
executables?

Reply to this email directly or view it on GitHubhttps://github.com//issues/8#issuecomment-37652426
.

from speedseq.

No, that shouldn't cause problems because the aln module doesn't look for lumpy or gemini
I produce a bam file when I run the following:

bwa index chr20_bit.fa

speedseq aln -o sample005 -R "@RG\tID:sample005\tSM:sample005" chr20_bit.fa sample005.fa_1.fastq sample005.fa_2.fastq

What's the output of that command for you?

from speedseq.

% speedseq aln -o sample005 -R "@rg\tID:sample005\tSM:sample005"
chr20_bit.fa sample005.fa_1.fastq sample005.fa_2.fastq
Sourcing executables from /share/home/erik/bin/speedseq.config ...
which: no lumpy in
(/share/home/erik/bin/:/share/local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/bin/X11:/share/software/Aspera/aspera/connect/bin)
Aligning...

Nothing happens.

Any way to debug it?

On Fri, Mar 14, 2014 at 10:49 AM, Colby Chiang [email protected]:

No, that shouldn't cause problems because the aln module doesn't look for
lumpy or gemini
I produce a bam file when I run the following:

bwa index chr20_bit.fa

speedseq aln -o sample005 -R "@rg\tID:sample005\tSM:sample005" chr20_bit.fa sample005.fa_1.fastq sample005.fa_2.fastq

What's the output of that command for you?

Reply to this email directly or view it on GitHubhttps://github.com//issues/8#issuecomment-37654703
.

from speedseq.

Sorry, I meant is there a debugging flag I could set?

On Fri, Mar 14, 2014 at 10:54 AM, Erik Garrison [email protected]:

% speedseq aln -o sample005 -R "@rg\tID:sample005\tSM:sample005"
chr20_bit.fa sample005.fa_1.fastq sample005.fa_2.fastq
Sourcing executables from /share/home/erik/bin/speedseq.config ...
which: no lumpy in
(/share/home/erik/bin/:/share/local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/bin/X11:/share/software/Aspera/aspera/connect/bin)
Aligning...

Nothing happens.

Any way to debug it?

On Fri, Mar 14, 2014 at 10:49 AM, Colby Chiang [email protected]:

No, that shouldn't cause problems because the aln module doesn't look for
lumpy or gemini
I produce a bam file when I run the following:

bwa index chr20_bit.fa

speedseq aln -o sample005 -R "@rg\tID:sample005\tSM:sample005" chr20_bit.fa sample005.fa_1.fastq sample005.fa_2.fastq

What's the output of that command for you?

Reply to this email directly or view it on GitHubhttps://github.com//issues/8#issuecomment-37654703
.

from speedseq.

Just added verbosity. Try pulling the latest version and running it with the -v flag and let me know what output you get.

speedseq aln -v -o sample005 -R "@RG\tID:sample005\tSM:sample005" chr20_bit.fa sample005.fa_1.fastq sample005.fa_2.fastq

from speedseq.

Here's my result:

% speedseq aln -v -o sample005 -R "@rg\tID:sample005\tSM:sample005"
chr20_bit.fa sample005.fa_1.fastq sample005.fa_2.fastq
Sourcing executables from /share/home/erik/bin/speedseq.config ...
which: no lumpy in
(/share/home/erik/bin/:/share/local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/bin/X11:/share/software/Aspera/aspera/connect/bin)
Aligning...

    mkdir -p ./temp/full ./temp/spl ./temp/disc
    mkfifo ./temp/spl_pipe ./temp/disc_pipe

    /share/home/erik/bin/bwa mem -t 1 -M -R '@RG    ID:sample005

SM:sample005' chr20_bit.fa sample005.fa_1.fastq sample005.fa_2.fastq |
/share/home/erik/bin/samblaster -e -c 2 -m 20 -s
./temp/spl_pipe -d ./temp/disc_pipe |
/share/home/erik/bin/sambamba_v0.4.4 view -S -f bam -l 0
/dev/stdin |
/share/home/erik/bin/sambamba_v0.4.4 sort -t 1 -m 8G
--tmpdir=./temp/full -o sample005.bam /dev/stdin

    /share/home/erik/bin/sambamba_v0.4.4 view -S -f bam -l 0

./temp/spl_pipe |
/share/home/erik/bin/sambamba_v0.4.4 sort -t 4 -m 8G
--tmpdir=./temp/spl -o sample005.splitters.bam /dev/stdin
/share/home/erik/bin/sambamba_v0.4.4 view -S -f bam
./temp/disc_pipe |
/share/home/erik/bin/sambamba_v0.4.4 sort -t 4 -m 8G
--tmpdir=./temp/disc -o sample005.discordants.bam /dev/stdin

Looks like sambamba is hanging?

On Fri, Mar 14, 2014 at 3:41 PM, Colby Chiang [email protected]:

Just added verbosity. Try pulling the latest version and running it with
the -v flag and let me know what output you get.

speedseq aln -v -o sample005 -R "@rg\tID:sample005\tSM:sample005" chr20_bit.fa sample005.fa_1.fastq sample005.fa_2.fastq

Reply to this email directly or view it on GitHubhttps://github.com//issues/8#issuecomment-37687407
.

from speedseq.

In sambamba versions prior to 0.4.6-beta, the sort function would core dump on empty bam input (i.e. just a sam header with no reads). This occurs with your test alignment, which doesn't have any splitters or discordants.

Try downloading sambamba 0.4.6-beta (https://github.com/lomereiter/sambamba/releases/tag/v0.4.6-beta), and then edit the speedseq.config file to use that instead of sambamba 0.4.4

from speedseq.

I've downloaded 0.4.6 beta but the problem persists. I'm going to try
building from source.

On Mon, Mar 17, 2014 at 12:39 PM, Colby Chiang [email protected]:

In sambamba versions prior to 0.4.6-beta, the sort function would core
dump on empty bam input (i.e. just a sam header with no reads). This occurs
with your test alignment, which doesn't have any splitters or discordants.

Try downloading sambamba 0.4.6-beta (
https://github.com/lomereiter/sambamba/releases/tag/v0.4.6-beta), and
then edit the speedseq.config file to use that instead of sambamba 0.4.4

Reply to this email directly or view it on GitHubhttps://github.com//issues/8#issuecomment-37838253
.

from speedseq.

going to close this because the code and installation has changed substantially since then

from speedseq.