problem to run salmon on macOS arm64 Big_Sur

[lgallegovillar]

Hello,

After running: SalmonTE.py quant --reference=hs example I am getting the following error (please see below). I am using SalmonTE on macOS (arm64_Big_Sur). I saw issue #37. I followed the instructions from README.md. and installed tbb through homebrew. Currently, I am using the snakemake version 6.7.0 and Salmon v0.8.2.

thanks, Lorena

2021-08-25 15:52:52,817 Starting quantification mode 2021-08-25 15:52:52,817 Collecting FASTQ files... 2021-08-25 15:52:52,818 The input dataset is considered as a single-end dataset. 2021-08-25 15:52:52,818 Collected 2 FASTQ files. 2021-08-25 15:52:52,818 Quantification has been finished. 2021-08-25 15:52:52,818 Running Salmon using Snakemake 2021-08-25 15:52:52,944 Lock 140588788803376 acquired on /var/folders/1v/j5yglhtx7wxb6mzlnhz8rsrm0000gn/T/tmpy27i0sodsnakemake-runtime-source-cache/ce70dff53366415fa127fb82e3ac21007323cb2ff0002fe413995a30454d9384.lock 2021-08-25 15:52:52,945 Lock 140588788803376 released on /var/folders/1v/j5yglhtx7wxb6mzlnhz8rsrm0000gn/T/tmpy27i0sodsnakemake-runtime-source-cache/ce70dff53366415fa127fb82e3ac21007323cb2ff0002fe413995a30454d9384.lock /Users/lorena/SalmonTE/snakemake/Snakefile.single:102: 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 2 1 1 total 5 1 1

2021-08-25 15:52:52,978 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 2 1 1 total 5 1 1

/bin/bash: line 1: 23941 Abort trap: 6 salmon/darwin/bin/salmon quant -i reference/hs -l A -r /var/folders/1v/j5yglhtx7wxb6mzlnhz8rsrm0000gn/T/tmpupmtpyhn/CTRL_1_R1.fastq -o /Users/lorena/SalmonTE/SalmonTE_output/CTRL_1_R1 -p 4 2> /dev/null [Wed Aug 25 15:52:53 2021] 2021-08-25 15:52:53,117 [Wed Aug 25 15:52:53 2021] Error in rule run_salmon_fq: 2021-08-25 15:52:53,117 Error in rule run_salmon_fq: jobid: 2 2021-08-25 15:52:53,117 jobid: 2 output: /Users/lorena/SalmonTE/SalmonTE_output/CTRL_1_R1 2021-08-25 15:52:53,117 output: /Users/lorena/SalmonTE/SalmonTE_output/CTRL_1_R1 shell: salmon/darwin/bin/salmon quant -i reference/hs -l A -r /var/folders/1v/j5yglhtx7wxb6mzlnhz8rsrm0000gn/T/tmpupmtpyhn/CTRL_1_R1.fastq -o /Users/lorena/SalmonTE/SalmonTE_output/CTRL_1_R1 -p 4 2>/dev/null (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!) 2021-08-25 15:52:53,118 shell: salmon/darwin/bin/salmon quant -i reference/hs -l A -r /var/folders/1v/j5yglhtx7wxb6mzlnhz8rsrm0000gn/T/tmpupmtpyhn/CTRL_1_R1.fastq -o /Users/lorena/SalmonTE/SalmonTE_output/CTRL_1_R1 -p 4 2>/dev/null (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

2021-08-25 15:52:53,118 Exiting because a job execution failed. Look above for error message 2021-08-25 15:52:53,118 Exiting because a job execution failed. Look above for error message 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: '/Users/lorena/SalmonTE/SalmonTE_output/EXPR.csv'

[hyunhwan-jeong]

Hi @lgallegovillar,

I am not sure SalmonTE could work on arm64 system, could you try this and see what happens? https://github.com/LiuzLab/SalmonTE/issues/55#issuecomment-885276579

Thank you,

Hyun-Hwan Jeong

[lgallegovillar]

Hi Hyun-Hwan Jeong,

unfortunately, I got the same error. If you have any other suggestions please let me know. I am looking forward to testing SalmonTE on my data.

Thank you, Lorena