Quick start tool installation failing

[LoransM]

Hello,

I have used git clone https://github.com/biocompibens/ALFA to install the program, but when trying to test the tool installation according to the quick start guide, I get following error:

rna2@d33502:~/ALFA/Quick_start$ python alfa.py -a quick_start.gtf --chr_len quick_start.chr_len.txt -g quick_start --bam quick_start.bam quick_start File "alfa.py", line 171 print("Warning: chromosome '" + chrom + "' of the chromosome lengths file does not match any chromosome name in the GTF file provided and was ignored.", file=sys.stderr) ^ SyntaxError: invalid syntax

Can anyone please assist me? Thanks

[mbahin]

Hi,

The first thing that comes to my mind is that maybe you're trying to run ALFA with some version of Python 2 though it has to run with Python 3. Let me know if it was the source of the problem.

Cheers, Mathieu

[LoransM]

Hi Mathieu, Now I get following issue when running with Python3:

python3 alfa.py -a quick_start.gtf --chr_len quick_start.chr_len.txt -g quick_start --bam quick_start.bam quick_start Traceback (most recent call last): File “alfa.py”, line 14, in import pysam ModuleNotFoundError: No module named ‘pysam’

Although pysam is installed and up to date.

Marie Lorans PhD fellow Aarhus University Institute of Molecular Biology and Genetics C.F. Møllers Alle 3 8000 Aarhus Denmark Ph: +4531717672

From: mbahin notifications@github.com Reply to: biocompibens/ALFA reply@reply.github.com Date: Monday, 27 July 2020 at 14.08 To: biocompibens/ALFA ALFA@noreply.github.com Cc: Marie Lorans marie.lorans@mbg.au.dk, Author author@noreply.github.com Subject: Re: [biocompibens/ALFA] Quick start tool installation failing (#5)

Hi,

The first thing that comes to my mind is that maybe you're trying to run ALFA with some version of Python 2 though it has to run with Python 3. Let me know if it was the source of the problem.

Cheers, Mathieu

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/biocompibens/ALFA/issues/5#issuecomment-664357034, or unsubscribehttps://github.com/notifications/unsubscribe-auth/APJ2IL5NCO2RAHFGDEFDTQTR5VU2TANCNFSM4PIVJTWQ.

[mbahin]

Hi Mary,

From the message you get, I strongly doubt that the pysam lib is installed. Maybe it's installed but not for the Python you're calling with ALFA. You could try to run the same Python (typing "python3" in a terminal probably) and do "import pysam" to check.

Cheers, Mathieu

[LoransM]

That worked! Thanks so much!

Marie Lorans PhD fellow Aarhus University Institute of Molecular Biology and Genetics C.F. Møllers Alle 3 8000 Aarhus Denmark Ph: +4531717672

From: mbahin notifications@github.com Reply to: biocompibens/ALFA reply@reply.github.com Date: Tuesday, 4 August 2020 at 13.56 To: biocompibens/ALFA ALFA@noreply.github.com Cc: Marie Lorans marie.lorans@mbg.au.dk, Author author@noreply.github.com Subject: Re: [biocompibens/ALFA] Quick start tool installation failing (#5)

Hi Mary,

From the message you get, I strongly doubt that the pysam lib is installed. Maybe it's installed but not for the Python you're calling with ALFA. You could try to run the same Python (typing "python3" in a terminal probably) and do "import pysam" to check.

Cheers, Mathieu

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/biocompibens/ALFA/issues/5#issuecomment-668551561, or unsubscribehttps://github.com/notifications/unsubscribe-auth/APJ2IL3GPCHQYIIQJWCX52DR67ZPBANCNFSM4PIVJTWQ.