error with run test

[Xing-2024]

Hi, It seems I met a error using the following command: Command: ./run_tests Comes out with two errors:

ERROR: test (tests.cd44_example.test.Cd44ExampleTest)

Traceback (most recent call last): File "/data/test/test_data_espresso_sirv/espresso/tests/cd44_example/test.py", line 53, in test self._create_bed_from_gtf() File "/data/test/test_data_espresso_sirv/espresso/tests/cd44_example/test.py", line 98, in _create_bed_from_gtf tests.base_test.run_command_with_output_and_log( File "/data/test/test_data_espresso_sirv/espresso/tests/base_test.py", line 31, in run_command_with_output_and_log process = subprocess.run(command, File "/usr/local/Anaconda/envs/py3.9/lib/python3.9/subprocess.py", line 528, in run raise CalledProcessError(retcode, process.args, subprocess.CalledProcessError: Command '['paftools.js', 'gff2bed', '/data/test/test_data_espresso_sirv/espresso/tests/cd44_example/data/test_data_espresso_cd44/cd44.gtf']' returned non-zero exit status 126.

====================================================================== ERROR: test (tests.sirv_example.test.SirvExampleTest)

Traceback (most recent call last): File "/data/test/test_data_espresso_sirv/espresso/tests/sirv_example/test.py", line 38, in test self._run_visualization() File "/data/test/test_data_espresso_sirv/espresso/tests/sirv_example/test.py", line 178, in _run_visualization tests.base_test.run_command_with_log(command, vis_log) File "/data/test/test_data_espresso_sirv/espresso/tests/base_test.py", line 20, in run_command_with_log process = subprocess.run(command, File "/usr/local/Anaconda/envs/py3.9/lib/python3.9/subprocess.py", line 528, in run raise CalledProcessError(retcode, process.args, subprocess.CalledProcessError: Command '['/usr/local/bin/python', '/data/test/test_data_espresso_sirv/espresso/visualization/visualize.py', '--genome-fasta', '/data/test/test_data_espresso_sirv/espresso/tests/sirv_example/data/test_data_espresso_sirv/SIRV2.fasta', '--updated-gtf', '/data/test/test_data_espresso_sirv/espresso/tests/sirv_example/out/samples_N2_R0_updated.gtf', '--abundance-esp', '/data/test/test_data_espresso_sirv/espresso/tests/sirv_example/out/samples_N2_R0_abundance.esp', '--target-gene', 'SIRV2', '--minimum-count', '1', '--descriptive-name', 'SIRV', '--output-dir', '/data/test/test_data_espresso_sirv/espresso/tests/sirv_example/out/visualization']' returned non-zero exit status 1.

Anyone has any suggestions?

Thank you.

[EricKutschera]

Is there anything written to these files: tests/cd44_example/logs/create_bed_from_gtf.log tests/cd44_example/data/test_data_espresso_cd44/cd44.gtf.bed tests/sirv_example/logs/visualization.log

For the cd44 test maybe paftools.js wasn't found on your $PATH. Similarly for the sirv test maybe one of the programs needed for the visualization (like bedGraphToBigWig) wasn't found

[Xing-2024]

Hi, here is the writtings :

Is there anything written to these files: tests/cd44_example/logs/create_bed_from_gtf.log

log: /usr/bin/env: ‘k8’: Permission denied

tests/cd44_example/data/test_data_espresso_cd44/cd44.gtf.bed

Nothing here

tests/sirv_example/logs/visualization.log

For the cd44 test maybe paftools.js wasn't found on your $PATH. Similarly for the sirv test maybe one of the programs needed for the visualization (like bedGraphToBigWig) wasn't found

thank you.

[EricKutschera]

/usr/bin/env: 'k8': Permission denied is saying that it found k8 (which is used by paftools.js), but the permissions on the file didn't allow you to run it

Similarly PermissionError: [Errno 13] Permission denied: 'faToTwoBit' is saying that it found faToTwoBit (which is used by the visualization script), but you didn't have sufficient permissions on the file

You could try running which k8 and which faToTwoBit to see the paths to those files. Then when you know the path you can run ls -l on those files to see what the permissions are. Maybe those files are owned by another user, or they aren't set as executable

[kwonej0617]

Hi @EricKutschera

I was trying to make a visualization using espresso output using the following code.

python3 espresso_code/visualization/visualize.py --genome-fasta reference/hg38.fa --updated-gtf espresso_data/HEK293T-all/HEK293T-all_N2_R0_updated.gtf --abundance-esp espresso_data/HEK293T-all/HEK293T-all_N2_R0_abundance.esp --target-gene ENSG00000146540.15 --minimum-count 1 --descriptive-name ENSG00000146540.15 --output-dir espresso_data/HEK293T-all/

However, I got the error message. Could you please explain me what this error is about and how to solve it?

Traceback (most recent call last):
  File "espresso_code/visualization/visualize.py", line 186, in <module>
    main()
  File "espresso_code/visualization/visualize.py", line 177, in main
    chrom_sizes = run_fasta_to_chrom_sizes(args.genome_fasta, args.output_dir)
  File "espresso_code/visualization/visualize.py", line 121, in run_fasta_to_chrom_sizes
    subprocess.run(fa_to_two_bit_cmd, check=True)
  File "/usr/lib64/python3.6/subprocess.py", line 423, in run
    with Popen(*popenargs, **kwargs) as process:
  File "/usr/lib64/python3.6/subprocess.py", line 729, in __init__
    restore_signals, start_new_session)
  File "/usr/lib64/python3.6/subprocess.py", line 1364, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'faToTwoBit': 'faToTwoBit'

Thank you!

[EricKutschera]

The visualization code tries to run this command: https://github.com/Xinglab/espresso/blob/v1.4.0/visualization/visualize.py#L119

The error is saying that it can't find the executable file faToTwoBit which is a dependency: https://github.com/Xinglab/espresso/tree/v1.4.0?tab=readme-ov-file#dependencies

You could download it from: http://hgdownload.soe.ucsc.edu/admin/exe/ or it's available from conda: https://github.com/Xinglab/espresso/blob/v1.4.0/snakemake/conda_requirements.txt#L12

If you want to visualize ESPRESSO output you could also try: https://github.com/Xinglab/rMATS-long?tab=readme-ov-file#visualize-isoforms-and-abundance