tempdir error

[jrcunning]

Hi,

I am trying to run psytrans and am getting an error immediately about a temporary directory not existing. Here is a traceback of the error - any help would be much appreciated!

Rosss-MacBook-Pro-2:Poc-gen jrcunning$ /anaconda/bin/python2.7 ~/psytrans/psytrans.py -v \

-A adi_v1.0.scaffold.fa \ -B symbB.v1.0.genome.fa \ -t tempdir \ -o psytrans_output \ weedy_coral_01Feb2017_zhEnG.fasta Traceback (most recent call last): File "/Users/jrcunning/psytrans/psytrans.py", line 1235, in main() File "/Users/jrcunning/psytrans/psytrans.py", line 1145, in main options = PsyTransOptions(args) File "/Users/jrcunning/psytrans/psytrans.py", line 105, in init self.createTempDir() File "/Users/jrcunning/psytrans/psytrans.py", line 110, in createTempDir dir=self.args.tempDir) File "/anaconda/lib/python2.7/tempfile.py", line 333, in mkdtemp _os.mkdir(file, 0700) OSError: [Errno 2] No such file or directory: 'tempdir/psytrans_Z3sIob_temp'

[MichaelAngelou]

Hello. Good day @jrcunning

I am Michael from the University of the Philippines - Diliman. I am interested in separating host and symbiont sequences on my transcriptome data using psytrans.

I downloaded the psytrans script in https://github.com/sylvainforet/psytrans, and run the command below. However, I keep getting similar error that you posted. Were you able to find a work around on this? Thank you very much.

(base) mac@Mikebook psytrans-master % python psytrans.py -A mollusc.pep.fa -B symbiont.pep.fa -t /Users/mac/Desktop/GCAdultranscriptome/psytrans-master/tmp trinity-cdhit90.filter300.Isopct.nozero.fa

Traceback (most recent call last): File "psytrans.py", line 1235, in main() File "psytrans.py", line 1145, in main options = PsyTransOptions(args) File "psytrans.py", line 105, in init self.createTempDir() File "psytrans.py", line 110, in createTempDir dir=self.args.tempDir) File "/Users/mac/miniconda3/lib/python3.7/tempfile.py", line 366, in mkdtemp _os.mkdir(file, 0o700) FileNotFoundError: [Errno 2] No such file or directory: '/Users/mac/Desktop/GCAdultranscriptome/psytrans-master/tmp/psytrans_hvv7sm11_temp'

[jrcunning]

I ended up not using psytrans and used custom blast databases to separate sequences... see: https://github.com/jrcunning/pdam-genome/blob/master/data/Makefile

[MichaelAngelou]

Hello Dr @jrcunning. Thank you for email and for the link. Will try this method.

[echille]

Hello, I am also getting the errors mentioned above immediately after psytrans begins to run:

Traceback (most recent call last):
  File "psytrans.py", line 1235, in <module>
    main()
  File "psytrans.py", line 1145, in main
    options = PsyTransOptions(args)
  File "psytrans.py", line 105, in __init__
    self.createTempDir()
  File "psytrans.py", line 110, in createTempDir
    dir=self.args.tempDir)
  File "/usr/lib64/python2.7/tempfile.py", line 329, in mkdtemp
    _os.mkdir(file, 0700)
OSError: [Errno 2] No such file or directory: 'tempDir/psytrans_SBmB_b_temp'

My usage is as follows:

python psytrans.py -A Mcap.protein.fa -B SymbC1.Gene_Models.PEP.fasta -p 20 -t tempDir Mcap_holobiont.fasta

Any help would be appreciated. Thanks!

[MichaelAngelou]

Hello The command below works for me, atleast on our hpc.

mkdir tempDir chmod 775 tempDir Then, run psytrans command

On Fri, Apr 2, 2021 at 9:08 AM Erin Chille @.***> wrote:

Hello, I am also getting the errors mentioned above immediately after psytrans begins to run:

Traceback (most recent call last): File "psytrans.py", line 1235, in main() File "psytrans.py", line 1145, in main options = PsyTransOptions(args) File "psytrans.py", line 105, in init self.createTempDir() File "psytrans.py", line 110, in createTempDir dir=self.args.tempDir) File "/usr/lib64/python2.7/tempfile.py", line 329, in mkdtemp _os.mkdir(file, 0700) OSError: [Errno 2] No such file or directory: 'tempDir/psytrans_SBmB_b_temp'

My usage is as follows:

python psytrans.py -A Mcap.protein.fa -B SymbC1.Gene_Models.PEP.fasta -p 20 -t tempDir Mcap_holobiont.fasta

Any help would be appreciated. Thanks!

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/jueshengong/psytrans/issues/2#issuecomment-812261977, or unsubscribe https://github.com/notifications/unsubscribe-auth/AIOMUUSHDDPLTN4WZ7VQOYLTGUKJBANCNFSM4DBVHTYQ .

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ᜋᜌ᜔ᜃᜒᜎ᜔ ᜀᜅ᜔ᜑᜒᜎᜓ ᜈᜇ Michael Angelou L. Nada

Graduate student Marine Molecular Biology Laboratory Marine Science Institute University of the Philippines-Diliman

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[echille]

Hello The command below works for me, atleast on our hpc. mkdir tempDir chmod 775 tempDir Then, run psytrans command On Fri, Apr 2, 2021 at 9:08 AM Erin Chille @.**> wrote: Hello, I am also getting the errors mentioned above immediately after psytrans begins to run: Traceback (most recent call last): File "psytrans.py", line 1235, in main() File "psytrans.py", line 1145, in main options = PsyTransOptions(args) File "psytrans.py", line 105, in init self.createTempDir() File "psytrans.py", line 110, in createTempDir dir=self.args.tempDir) File "/usr/lib64/python2.7/tempfile.py", line 329, in mkdtemp _os.mkdir(file, 0700) OSError: [Errno 2] No such file or directory: 'tempDir/psytrans_SBmB_b_temp' My usage is as follows: python psytrans.py -A Mcap.protein.fa -B SymbC1.Gene_Models.PEP.fasta -p 20 -t tempDir Mcap_holobiont.fasta Any help would be appreciated. Thanks! — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#2 (comment)>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AIOMUUSHDDPLTN4WZ7VQOYLTGUKJBANCNFSM4DBVHTYQ . -- ------------------------------------------------------ ᜋᜌ᜔ᜃᜒᜎ᜔ ᜀᜅ᜔ᜑᜒᜎᜓ ᜈᜇ Michael Angelou L. Nada Graduate student Marine Molecular Biology Laboratory Marine Science Institute University of the Philippines-Diliman ------------------------------------------------------*

Thank you, that did it!