Read Subsampling tool error

[sadikmu]

Hello,
Could you please help me out?

I am getting the following error message after running Read Sampling Tool and tried with different options (-T lr, -Tlr 0.2, -T l, -T r, with and with out scraps.txt) but the error messages throwing are the same.

subreads.txt and scrabs.txt files generated using

find $(pwd) -name "*subreads.bam" > subreads.txt
find $(pwd) -name "*scraps.bam" > scraps.txt

SequelTools.sh run as

SequelTools.sh -t S -u subreads.txt -c scraps.txt -T lr

Error message:

Beginning read subsampling function by chosen criteria:
longest subreads and random subsampling
Running in NO_SCRAPS mode
view: invalid option -- '-'
view: invalid option -- 'O'
[main_samview] fail to open "1" for reading.
`ERROR: BAM to SAM data conversion failed!``

[aseetharam]

Hi Sadik,
Thanks for trying SequelTools!
I don't see anything wrong with the command you ran, so I'm suspecitng something off with the scraps.txt/subreads.txt files. Can you paste the contents for those files?

Thanks,

[sadikmu]

Hi Arun,

scraps.txt/subreads.txt are captured fofn and here is the content

/home/raw_data/file.scraps.bam
/home/raw_data/file.subreads.bam

Best

[DavidEHufnagel]

Hello Sadik, could you please copy and paste the contents of those files in this email chain. I do not have access to those files where they're located now and I suspect my colleague Arun does not either. Best, David

…

On Fri, Mar 27, 2020 at 6:40 PM Sadik Muzemil ***@***.***> wrote: Hi Arun, scraps.txt/subreads.txt are captured fofn and here is the content /home/raw_data/file.scraps.bam /home/raw_data/file.subreads.bam Best — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#5 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABQPE3K6D4PXHUTNPHSMZ23RJU2QFANCNFSM4LVF35AA> .