could not convert string to float: FIRM56_P641593085

[chengdai]

Hello,

I was running MicrobeCensus on my pair end reads and it threw the error:

could not convert string to float: FIRM56_P641593085 Traceback (most recent call last): File "/home/USR/miniconda2/bin/run_microbe_census.py", line 62, in est_ags, args = microbe_census.run_pipeline(args) TypeError: 'NoneType' object is not iterable

Is there any way of fixing this? Thanks!

[snayfach]

Could you send me the a sample of reads from the FASTQ files that are causing the issue?

[snayfach]

Did you install the program from github or using pip? The github version is more up to date. If installing from github, which version? If you send me a sample of the data that is causing the issue I can investigate further

On Wed, May 30, 2018 at 11:02 AM, Erick Cardenas notifications@github.com wrote:

I am having the same problem, do you have an update on this issue?

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/snayfach/MicrobeCensus/issues/18#issuecomment-393260166, or mute the thread https://github.com/notifications/unsubscribe-auth/ACAbrb_LUA1kVTYEvQGCTGnwhmP9nSVjks5t3t7SgaJpZM4TCOA3 .

[carden24]

I did not notice that I had installed the pip version too (1.0.7). I uninstalled it, remove an older version, recloned the github repo and now seems to be working. On a completely unrelated question, I have unpaired and paired reads and I have been passing the three files (separated by commas). Do you think this could bias the results?. my unpaired reads are a mix of extended read, and orphan paired reads. Thanks for the quick reply.

[snayfach]

No, I think that should be fine to run the tool using a mix of paired and unpaired reads

On Wed, May 30, 2018 at 1:09 PM, Erick Cardenas notifications@github.com wrote:

I did not notice that I had installed the pip version too (1.0.7). I uninstalled it, remove an older version, recloned the github repo and now seems to be working. On a completely unrelated question, I have unpaired and paired reads and I have been passing the three files (separated by commas). Do you think this could bias the results?. my unpaired reads are a mix of extended read, and orphan paired reads. Thanks for the quick reply.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/snayfach/MicrobeCensus/issues/18#issuecomment-393300880, or mute the thread https://github.com/notifications/unsubscribe-auth/ACAbrVNKkImEQR54ZbZEPvJbKxlsNMB_ks5t3vxigaJpZM4TCOA3 .