segatalab / preprocessing Goto Github PK

For installation of the preprocessing I tried the code:

conda install preprocessing -c fasnicar

It returns:

Channels:

• fasnicar
• conda-forge
  Platform: osx-arm64
  Collecting package metadata (repodata.json): -
  done
  Solving environment: failed

LibMambaUnsatisfiableError: Encountered problems while solving:

• nothing provides bowtie2 >=2.0.0 needed by preprocessing-0.2.4-py_0

Could not solve for environment specs
The following package could not be installed
└─ preprocessing is not installable because it requires
└─ bowtie2 >=2.0.0 , which does not exist (perhaps a missing channel).

I installed bowtie2 with the most recent version, and that part works. I am not sure how to solve this problem.

Hi!

I want to make sure I'm running the pipeline correctly. I ran an initial test with two paired-end files in the directory /home/Raw_data:
410M SRR224_R1.fastq.gz  
384M SRR224_R2.fastq.gz

I ran the command:
parallel -j $NCPU 'preprocess.new.py -i /home/Raw_data -s SRR224 -f R1 -r R2 -x /home/GRCh38/index_GRCh38'

But I got:
nohup: ignoring input

Then I ran the command:
preprocess.new.py -i /home/Raw_data -s SRR224 -f R1 -r R2 -x /home/GRCh38/index_GRCh38

It seemed to run, but the output was the following:
1.8G Aug  5 19:20 Raw_data.R1_trimmed.fq
6.0G Aug  5 19:22 Raw_data.data.R2_trimmed.fq

The output of R2_trimmed.fq is very large. It should be similar to that of R1_trimmed.fq. Please clarify how to run the pipeline with preprocess.new.py. The GitHub only has example with preprocess.sh, but with that script I got several errors.