Running entire pipeline: [Errno 2] No such file or directory

[ArnavBharti]

Error: (The pipeline gives OK output until the following error)

Running isONcorrect

python3.11: can't open file '/home/arnav/bitspilani/2-2/StudyOrientedProject/isONform/run_isoncorrect': [Errno 2] No such file or directory
Command exited with non-zero status 2
    Command being timed: "python3.11 run_isoncorrect --t 8 --fastq_folder /home/arnav/.../2-2/StudyOrientedProject/Outputs/P.VivaxSal1/clustering/fastq_files --outfolder /home/arnav/.../2-2/StudyOrientedProject/Outputs/P.VivaxSal1/correction/"
    User time (seconds): 0.01
    System time (seconds): 0.00
    Percent of CPU this job got: 79%
    Elapsed (wall clock) time (h:mm:ss or m:ss): 0:00.02
    Average shared text size (kbytes): 0
    Average unshared data size (kbytes): 0
    Average stack size (kbytes): 0
    Average total size (kbytes): 0
    Maximum resident set size (kbytes): 9728
    Average resident set size (kbytes): 0
    Major (requiring I/O) page faults: 1
    Minor (reclaiming a frame) page faults: 1117
    Voluntary context switches: 31
    Involuntary context switches: 1
    Swaps: 0
    File system inputs: 1032
    File system outputs: 0
    Socket messages sent: 0
    Socket messages received: 0
    Signals delivered: 0
    Page size (bytes): 4096
    Exit status: 2

Command:

./isON_pipeline.sh --raw_reads /home/arnav/.../2-2/StudyOrientedProject/Outputs/P.VivaxSal1/compiled_fastq.fastq  --outfolder /home/arnav/.../2-2/StudyOrientedProject/Outputs/P.VivaxSal1  --num_cores 8 --iso_abundance 5 --mode ont_no_pychopper

[aljpetri]

Hello, thank you for reporting the problem. From what I can see it seems that isONcorrect has not been installed properly. I have now added a test whether the tools are properly installed to the pipeline script so that it does not fail during the run. Please let me know if the error persists and if you encounter any other problems with running the pipeline. Best, Alex