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 [email protected] 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

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