Python exception error with running example data

[danieljrichard]

Hello, I was trying to run this software with just the basic data included in /example However, I'm getting the following rather opaque error message - might anyone have any suggestions on how to fix this?

python3 /extra/APPENDICULAR_HEIGHT_PAPER_2021/VARIANT_CALL/fastqtl/python/run_FastQTL_threaded.py genotypes.vcf.gz phenotypes.bed.gz TEST_EXAMPLE --covariates covariates.txt.gz --window 1e6 --ma_sample_threshold 10 --maf_threshold 0.01 --chunks 100 --threads 1 -o test [Mar 05 19:50:26] Running FastQTL on 1 threads. Processing chunk 1 Processing chunk 2 Processing chunk 3 Processing chunk 4 Processing chunk 5 Processing chunk 6 Processing chunk 7 Processing chunk 8 Processing chunk 9 Processing chunk 10 Processing chunk 11 Processing chunk 12 Processing chunk 13 Processing chunk 14 Processing chunk 15 Processing chunk 16 Processing chunk 17 Processing chunk 18 Processing chunk 19 Processing chunk 20 Processing chunk 21 Processing chunk 22 Processing chunk 23 Processing chunk 24 Processing chunk 25 Processing chunk 26 Processing chunk 27 Processing chunk 28 Processing chunk 29 Processing chunk 30 Processing chunk 31 Processing chunk 32 Processing chunk 33 Processing chunk 34 Processing chunk 35 Processing chunk 36 Processing chunk 37 Processing chunk 38 Processing chunk 39 Processing chunk 40 Processing chunk 41 Processing chunk 42 Processing chunk 43 Processing chunk 44 Processing chunk 45 Processing chunk 46 Processing chunk 47 Processing chunk 48 Processing chunk 49 Processing chunk 50 Processing chunk 51 Processing chunk 52 Processing chunk 53 Processing chunk 54 Processing chunk 55 Processing chunk 56 Processing chunk 57 Processing chunk 58 Processing chunk 59 Processing chunk 60 Processing chunk 61 Processing chunk 62 Processing chunk 63 Processing chunk 64 Processing chunk 65 Processing chunk 66 Processing chunk 67 Processing chunk 68 Processing chunk 69 Processing chunk 70 Processing chunk 71 Processing chunk 72 Processing chunk 73 Processing chunk 74 Processing chunk 75 Processing chunk 76 Processing chunk 77 Processing chunk 78 Processing chunk 79 Processing chunk 80 Processing chunk 81 Processing chunk 82 Processing chunk 83 Processing chunk 84 Processing chunk 85 Processing chunk 86 Processing chunk 87 Processing chunk 88 Processing chunk 89 Processing chunk 90 Processing chunk 91 Processing chunk 92 Processing chunk 93 Processing chunk 94 Processing chunk 95 Processing chunk 96 Processing chunk 97 Processing chunk 98 Processing chunk 99 Processing chunk 100 multiprocessing.pool.RemoteTraceback: """ Traceback (most recent call last): File "/usr/lib/python3.10/multiprocessing/pool.py", line 125, in worker result = (True, func(*args, **kwds)) File "/usr/lib/python3.10/multiprocessing/pool.py", line 48, in mapstar return list(map(*args)) File "/extra/APPENDICULAR_HEIGHT_PAPER_2021/VARIANT_CALL/fastqtl/python/run_FastQTL_threaded.py", line 54, in perm_worker s = subprocess.check_call(cmd, shell=True, executable='/bin/bash', stdout=subprocess.DEVNULL, stderr=subprocess.DEVNULL) File "/usr/lib/python3.10/subprocess.py", line 369, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command '/extra/APPENDICULAR_HEIGHT_PAPER_2021/VARIANT_CALL/fastqtl/bin/fastQTL --vcf genotypes.vcf.gz --bed phenotypes.bed.gz --window 1e6 --maf-threshold 0.01 --ma-sample-threshold 10 --interaction-maf-threshold 0 --cov covariates.txt.gz --chunk 1 100 --out TEST_EXAMPLE_chunk001.txt.gz --log TEST_EXAMPLE_chunk001.log' returned non-zero exit status 127. """

The above exception was the direct cause of the following exception:

Traceback (most recent call last): File "/extra/APPENDICULAR_HEIGHT_PAPER_2021/VARIANT_CALL/fastqtl/python/run_FastQTL_threaded.py", line 95, in assert res.get()[0]==0 File "/usr/lib/python3.10/multiprocessing/pool.py", line 774, in get raise self._value subprocess.CalledProcessError: Command '/extra/APPENDICULAR_HEIGHT_PAPER_2021/VARIANT_CALL/fastqtl/bin/fastQTL --vcf genotypes.vcf.gz --bed phenotypes.bed.gz --window 1e6 --maf-threshold 0.01 --ma-sample-threshold 10 --interaction-maf-threshold 0 --cov covariates.txt.gz --chunk 1 100 --out TEST_EXAMPLE_chunk001.txt.gz --log TEST_EXAMPLE_chunk001.log' returned non-zero exit status 127.