Unable to setup MiCoP

[thierroll]

Hi, I am unable to install MiCoP as I get the following error message: " awk: can't open file ./cookie". This seems to link to a file on a Google Drive according to the script. Has the file maybe moved or is differently named?

Many thanks, Thierry

[nlapier2]

Hi Thierry, sorry for the delay. I haven't been able to replicate this error. Can you tell me exactly what lines you ran to get this error? Did you download the repository and then immediately run the setup, or did you try running the setup or something else beforehand?

[thierroll]

Hi Nathan,

Thanks for getting back to me. In the meantime I figured out the problem. Within the institution network I am not allowed to access google drive.

I have used a workaround and copied the repository to the computer (in /MiCoP/data ), so that all the files (fungi-refseq.fna. and viral-refseqg.fna.) are there.

However if I run the script run-bwa.py script as follows

“python run-bwa.py reads.fq --fungi”

I get the error message: “Eror: must specify either –virus or –fungi”, which I did.

Could you help me out with this?

Many thanks,

Thierry Rolling

From: nlapier2 notifications@github.com Sent: Dienstag, 2. Juli 2019 17:12 To: smangul1/MiCoP MiCoP@noreply.github.com Cc: Thierry Rolling t.rolling@uke.de; Author author@noreply.github.com Subject: Re: [smangul1/MiCoP] Unable to setup MiCoP (#3)

Hi Thierry, sorry for the delay. I haven't been able to replicate this error. Can you tell me exactly what lines you ran to get this error? Did you download the repository and then immediately run the setup, or did you try running the setup or something else beforehand?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/smangul1/MiCoP/issues/3?email_source=notifications&email_token=AMG43NPDD7GZMLRJCZK4HFTP5PABDA5CNFSM4HYYCNT2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODZCR44Y#issuecomment-507846259 , or mute the thread https://github.com/notifications/unsubscribe-auth/AMG43NJN7LQAIPCZJGVJNV3P5PABDANCNFSM4HYYCNTQ .

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[nlapier2]

Hi Thierry,

I haven't been able to replicate this error. Another issue mentioned that there are problems with certain versions of python. Can you report your version via "python --version"? Also, is that the exact line you ran? If not can you paste it here please? (You can redact the reads file name if you want)

Best, Nathan

[thierroll]

Hi Nathan,

My Python version is: 3.7.3

The lines I ran are:

cd micop

python run-bwa.py 34D_clean.fastq --fungi

[I copied the fastq file into the micop working directory for this one]

I get the following error message:

File “run-bwa.py”, line 23

Print ‘Error: must specify either --virus or --fungi.’

SyntaxError: Missing parentheses in call to ‘print’. Did you mean print(‘Error: must specify either --virus or --fungi.’)?

I wonder whether this is due to the fact that I manually copied the indices into the data folder?

What files should be in the data folder [filenames]?

Many thanks

Thierry

From: nlapier2 notifications@github.com Sent: Mittwoch, 3. Juli 2019 14:52 To: smangul1/MiCoP MiCoP@noreply.github.com Cc: Thierry Rolling t.rolling@uke.de; Author author@noreply.github.com Subject: Re: [smangul1/MiCoP] Unable to setup MiCoP (#3)

Hi Thierry,

I haven't been able to replicate this error. Another issue mentioned that there are problems with certain versions of python. Can you report your version via "python --version"? Also, is that the exact line you ran? If not can you paste it here please? (You can redact the reads file name if you want)

Best, Nathan

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/smangul1/MiCoP/issues/3?email_source=notifications&email_token=AMG43NOCW3KFQZMGLX6FXYDP5TYMNA5CNFSM4HYYCNT2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODZFL33A#issuecomment-508214764 , or mute the thread https://github.com/notifications/unsubscribe-auth/AMG43NOUIDZMLT4H7FYFHKLP5TYMNANCNFSM4HYYCNTQ .

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Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg | www.uke.de Vorstandsmitglieder: Prof. Dr. Burkhard Göke (Vorsitzender), Prof. Dr. Dr. Uwe Koch-Gromus, Joachim Prölß, Marya Verdel

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SAVE PAPER - THINK BEFORE PRINTING

[nlapier2]

The error above is due to python 3 having different print syntax. Try running it with python 2 and see if it works. I will work on making this compatible with more versions of python soon. For now, the safest bet is python 2.7.

[thierroll]

Hello Nathan,

I am truly sorry, but I still cannot get the code to work even after installing python 2.7

Please find the error code below:

(base) MSKI2219:micop rollingt$ python run-bwa.py 34D_clean.fastq --fungi

Traceback (most recent call last):

File "run-bwa.py", line 41, in

main()

File "run-bwa.py", line 37, in main

subprocess.call(shlex.split(cmd), stdout=outfile)

File "/Users/rollingt/miniconda3/lib/python2.7/subprocess.py", line 172, in call

return Popen(*popenargs, **kwargs).wait()

File "/Users/rollingt/miniconda3/lib/python2.7/subprocess.py", line 394, in init

errread, errwrite)

File "/Users/rollingt/miniconda3/lib/python2.7/subprocess.py", line 1047, in _execute_child

raise child_exception

OSError: [Errno 8] Exec format error

Many thanks again, Thierry

From: nlapier2 notifications@github.com Sent: Mittwoch, 3. Juli 2019 16:05 To: smangul1/MiCoP MiCoP@noreply.github.com Cc: Thierry Rolling t.rolling@uke.de; Author author@noreply.github.com Subject: Re: [smangul1/MiCoP] Unable to setup MiCoP (#3)

The error above is due to python 3 having different print syntax. Try running it with python 2 and see if it works. I will work on making this compatible with more versions of python soon. For now, the safest bet is python 2.7.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/smangul1/MiCoP/issues/3?email_source=notifications&email_token=AMG43NPZATRYUBUIYQ73LVDP5UBATA5CNFSM4HYYCNT2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODZFRHRY#issuecomment-508236743 , or mute the thread https://github.com/notifications/unsubscribe-auth/AMG43NL3JZPI64VCVPQ2WJDP5UBATANCNFSM4HYYCNTQ .

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Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg | www.uke.de Vorstandsmitglieder: Prof. Dr. Burkhard Göke (Vorsitzender), Prof. Dr. Dr. Uwe Koch-Gromus, Joachim Prölß, Marya Verdel

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SAVE PAPER - THINK BEFORE PRINTING

[bautist2]

Hi there,

I'm having the exact same problem. I also have python 2.7.

Traceback (most recent call last): File "run-bwa.py", line 41, in main() File "run-bwa.py", line 37, in main subprocess.call(shlex.split(cmd), stdout=outfile) File "/Users/mbautista/miniconda2/lib/python2.7/subprocess.py", line 172, in call return Popen(*popenargs, **kwargs).wait() File "/Users/mbautista/miniconda2/lib/python2.7/subprocess.py", line 394, in init errread, errwrite) File "/Users/mbautista/miniconda2/lib/python2.7/subprocess.py", line 1047, in _execute_child raise child_exception OSError: [Errno 8] Exec format error

Thanks!

Maria

[nlapier2]

I am still unable to replicate this error. I've read that this can pop up if the file is not executable. Can you try checking the permissions of MiCoP/bwa.kit/bwa and making sure that you can execute the file?

(If you don't know how to do this, let me know what the output of "ls -lh MiCoP/bwa.kit/bwa" is.)

[nlapier2]

I've also pushed some changes that make the scripts compatible with both python 2 and python 3, and changed the subprocess execution call format in a way that may address the issue, so it's worth trying again. However, I suspect that this may be a permissions issue. Let me know what you find.

Best, Nathan