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smangul1 / rop

The Read Origin Protocol (ROP) is a computational protocol that aims to discover the source of all reads, including those originating from repeat sequences, recombinant B and T cell receptors, and microbial communities.
https://github.com/smangul1/rop/wiki
GNU General Public License v3.0
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rop error message #139

Closed fadista closed 6 years ago

fadista commented 6 years ago

Hi,

I have the following error when running the latest version of rop: Traceback (most recent call last): File "/home/projects/ssi_gen1/data/pregnancy/unmapped/rop/rop.py", line 197, in <module> nReads["NCL"] = step_4(unmapped_file, cmd) File "/home/projects/ssi_gen1/data/pregnancy/unmapped/rop/rop_functions.py", line 344, in step_4 if subprocess.Popen([cmd], shell=True).wait(): raise SubprocessError() rop_functions.SubprocessError

Do you know what might be wrong? Thanks.

smangul1 commented 6 years ago

Can you please send the command you are running

Serghei

kahsieh commented 6 years ago

Hi @fadista,

Please check that you are using the latest version and running rop.sh, not rop.py (additional details available in README.md).

fadista commented 6 years ago

The command was python /home/projects/ssi_gen1/data/pregnancy/unmapped/rop/rop.py --f /home/projects/ssi_gen1/data/pregnancy/unmapped/batch1/PINE_DEN15_01_GAGATTCC_ACGTCCTGUnmapped.out.mate1.fastq /home/projects/ssi_gen1/data/pregnancy/unmapped/batch1/PINE_DEN15_01_GAGATTCC_ACGTCCTGUnmapped.out.mate1

kahsieh commented 6 years ago

Hi @fadista,

I can see that you're running rop.py, which doesn't exist in the latest version of ROP. Again, please check that you are using the latest version.

fadista commented 6 years ago

Hi @kahsieh Thanks, I am now running rop.sh on the newest version. Can I ask why circrna, metaphlan, and bacteria are not available in the current release? Thanks.

kahsieh commented 6 years ago

Hi @fadista,

Those three steps have been disabled due to database problems. @smangul1 will rebuild the circrna and bacteria databases, while the metaphlan issue will have to be addressed upstream.

smangul1 commented 6 years ago

Hi @fadista,

We are planning to have the circrna and bacteria steps ready in the next release.

Thanks, Serghei

fadista commented 6 years ago

Thanks. Do you know more or less when would the next release be out?

smangul1 commented 6 years ago

we plan a new release in 2 weeks!

Serghei

fadista commented 6 years ago

Thanks. Can you notify me when it becomes available? Thanks

João