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hyunhwan-jeong / SalmonTE

SalmonTE is an ultra-Fast and Scalable Quantification Pipeline of Transpose Element (TE) Abundances
GNU General Public License v3.0
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OSError: [Errno 8] Exec format error_ arm64_using a VM #60

Closed lgallegovillar closed 3 years ago

lgallegovillar commented 3 years ago

Hello Hyun-Hwan Jeong,

I am trying to run SalmonTE on arm64 system (M1 Apple using a VM) and I get the following Errors:

base) parallels@ubuntu-linux-20-04-desktop:~/SalmonTE$ python3 SalmonTE.py quant --reference=hs example 2021-09-20 18:04:21,274 Starting quantification mode 2021-09-20 18:04:21,274 Collecting FASTQ files... 2021-09-20 18:04:21,274 SalmonTE assumes that 'example' is a directory, and SalmonTE will search any FASTQ file in the directory. 2021-09-20 18:04:21,280 The input dataset is considered as a paired-ends dataset. 2021-09-20 18:04:21,280 Collected 4 FASTQ files. 2021-09-20 18:04:21,280 Quantification has been finished. 2021-09-20 18:04:21,280 Running Salmon using Snakemake 2021-09-20 18:04:21,394 Lock 281472830404064 acquired on /tmp/tmpfdzpcto1snakemake-runtime-source-cache/83e66b0398248c995f7650fca9486c37bf9ac41f5b80c89cfa9ab2f138cf3479.lock 2021-09-20 18:04:21,394 Lock 281472830404064 released on /tmp/tmpfdzpcto1snakemake-runtime-source-cache/83e66b0398248c995f7650fca9486c37bf9ac41f5b80c89cfa9ab2f138cf3479.lock /home/parallels/SalmonTE/snakemake/Snakefile.paired:103: SyntaxWarning: "is" with a literal. Did you mean "=="? Job stats: job count min threads max threads

all 1 1 1 collect_abundance 1 1 1 collect_mappability 1 1 1 run_salmon_fq 4 1 1 total 7 1 1

2021-09-20 18:04:21,420 Job stats: job count min threads max threads

all 1 1 1 collect_abundance 1 1 1 collect_mappability 1 1 1 run_salmon_fq 4 1 1 total 7 1 1

Traceback (most recent call last): File "/home/parallels/.local/lib/python3.8/site-packages/snakemake/init.py", line 699, in snakemake success = workflow.execute( File "/home/parallels/.local/lib/python3.8/site-packages/snakemake/workflow.py", line 1060, in execute success = self.scheduler.schedule() File "/home/parallels/.local/lib/python3.8/site-packages/snakemake/scheduler.py", line 492, in schedule run = self.job_selector(needrun) File "/home/parallels/.local/lib/python3.8/site-packages/snakemake/scheduler.py", line 764, in job_selector_ilp self._solve_ilp(prob) File "/home/parallels/.local/lib/python3.8/site-packages/snakemake/scheduler.py", line 813, in _solve_ilp prob.solve(solver) File "/home/parallels/.local/lib/python3.8/site-packages/pulp/pulp.py", line 1880, in solve status = solver.actualSolve(self, kwargs) File "/home/parallels/.local/lib/python3.8/site-packages/pulp/apis/coin_api.py", line 134, in actualSolve return self.solve_CBC(lp, kwargs) File "/home/parallels/.local/lib/python3.8/site-packages/pulp/apis/coin_api.py", line 193, in solve_CBC cbc = subprocess.Popen(args, stdout=pipe, stderr=pipe, stdin=devnull) File "/home/parallels/miniconda3/lib/python3.8/subprocess.py", line 858, in init self._execute_child(args, executable, preexec_fn, close_fds, File "/home/parallels/miniconda3/lib/python3.8/subprocess.py", line 1706, in _execute_child raise child_exception_type(errno_num, err_msg, err_filename) OSError: [Errno 8] Exec format error: '/home/parallels/.local/lib/python3.8/site-packages/pulp/apis/../solverdir/cbc/linux/64/cbc' Traceback (most recent call last): File "SalmonTE.py", line 292, in run(args) File "SalmonTE.py", line 243, in run run_salmon(param) File "SalmonTE.py", line 156, in run_salmon with open(os.path.join(param["--outpath"], "EXPR.csv" ), "r") as inp: FileNotFoundError: [Errno 2] No such file or directory: '/home/parallels/SalmonTE/SalmonTE_output/EXPR.csv'

Hope you can help me with this. Thanks, Lorena

hyunhwan-jeong commented 3 years ago

Duplicate of #57, I will figure it out soon.