For the past few days I have been trying to use Cufflinks for my RNA seq analysis but I have been repeatedly getting this error:
slurmstepd: error: couldn’t chdir to `/srv/pulsar/main/venv/lib/python3.6/site-packages’: No such file or directory: going to /tmp instead
This started happening a few days ago and up until then I had no issues running the tool at all. My inputs are BAM file obtained from HISAT2 alignment and gtf file for mm10 reference annotation. I noticed that the assembled transcripts gtf file still outputted from Cufflinks despite the error, so I tried inputting these assembled transcripts into Cuffmerge (along with some successfully obtained assembled transcript gtf’s before this error started recurring), but Cuffmerge also resulted in an error:
[Fri Aug 28 23:06:48 2020] Preparing output location output/
Traceback (most recent call last):
File “/cvmfs/main.galaxyproject.org/deps/_conda/envs/__cufflinks@2.2.1/bin/cuffmerge”, line 580, in
sys.exit(main())
File “/cvmfs/main.galaxyproject.org/deps/_conda/envs/__cufflinks@2.2.1/bin/cuffmerge”, line 538, in main
gtf_input_files = test_input_files(transfrag_list_file)
File “/cvmfs/main.galaxyproject.org/deps/_conda/envs/__cufflinks@2.2.1/bin/cuffmerge”, line 268, in test_input_files
g = open(line,“r”)
IOError: [Errno 2] No such file or directory: ‘input_1 input_2 input_3 input_4 input_5’
I have been able to successfully use this tool without any problems up until now. Any solutions would be appreciated; I’m still relatively new to Galaxy.
