run_FragGeneScan.pl error - Hmmsearch failed about metabinner HOT 2 OPEN

Hi,

It seems that no relevant genes have been identified. MetaBinner typically runs on sequences longer than 1000bp. If you wish to run it on sequences longer than 200bp, you can try adding the parameter '-l 200'. However, it's not guaranteed that you will obtain suitable results.

MetaBinner can potentially be installed and run properly in a conda environment with versions of Python other than 3.7.6.

Best,
Ziye

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Dear Ziye Wang,
Thank you for your immediate response. After looking further into the matter I realized that the problem was FragGeneScan not being able to produce the last total "out" file when being used with the "1> and 2>" output redirections. When being used without the latter redirections I believe that the "out" file is normally generated, even when multiple threads are used. Please do correct me if I am mistaken on the latter observation. I found out that this problem is probably based on my system having an older version of GLIBC (glibc/libc6). Unfortunately, I can not update its version. Would it be possible to add an option at MetaBinner (and ideally at COMEBin too) so that the redirections may not occur or that FragGeneScanRs may be used instead of FragGeneScan? I have checked that the total "out" file is generated when FragGeneScanRs is used with redirections. I believe that any of these options would be really helpful.

Edit:
I have tried removing only the "1> ..." redirection in MetaBinner from the FragGeneScan command ("fragCmd") from the files "split_hbins.py" and "component_binning.py" and similarly in COMEBin from the file "utils.py". I have seen that in both cases the output is generated as expected. It would be very helpful for me if you could confirm that these modifications, in MetaBinner and COMEBIn, do not alter the job of another process of the general pipeline which maybe I have not taken into account.

Sincerely,
Georgios Filis

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