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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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job execution failed --one of the commands exited with non-zero exit code #65

Closed lgallegovillar closed 2 years ago

lgallegovillar commented 2 years ago

Hi @hyunhwan-jeong ,

I got the following error after running SalmonTE with a new reference index, hope you can help me with this.

thanks, Lorena

System: 5.13.0-28-generic x86_64 bits: 64 compiler: N/A CPU: AMD Ryzen 7 4800U Snakemake version: 6.15.5

lorena@Churribuntu:~/SalmonTE$ python3 SalmonTE.py quant --reference=hs_index --outpath=output_JMML_nindex/ example/CTRL_1_R1.fastq example/CTRL_1_R2.fastq
2022-02-14 07:40:37,228 Starting quantification mode 2022-02-14 07:40:37,228 Collecting FASTQ files... 2022-02-14 07:40:37,230 The input dataset is considered as a paired-ends dataset. 2022-02-14 07:40:37,230 Collected 1 FASTQ files. 2022-02-14 07:40:37,231 Quantification has been finished. 2022-02-14 07:40:37,231 Running Salmon using Snakemake 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 1 1 1 total 4 1 1

2022-02-14 07:40:37,782 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 1 1 1 total 4 1 1

/usr/bin/bash: line 1: 141180 Killed salmon/linux/bin/salmon quant -q -i reference/hs_index -l A -1 /tmp/tmpmp16eaic/CTRL_1_R1.fastq -2 /tmp/tmpmp16eaic/CTRL_1_R2.fastq -o output_JMML_nindex/CTRL_1 -p 4 2> /dev/null [Mon Feb 14 13:40:15 2022] 2022-02-14 13:40:15,892 [Mon Feb 14 13:40:15 2022] Error in rule run_salmon_fq: jobid: 2 output: output_JMML_nindex/CTRL_1 shell: salmon/linux/bin/salmon quant -q -i reference/hs_index -l A -1 /tmp/tmpmp16eaic/CTRL_1_R1.fastq -2 /tmp/tmpmp16eaic/CTRL_1_R2.fastq -o output_JMML_nindex/CTRL_1 -p 4 2>/dev/null (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

2022-02-14 13:40:17,127 Error in rule run_salmon_fq: jobid: 2 output: output_JMML_nindex/CTRL_1 shell: salmon/linux/bin/salmon quant -q -i reference/hs_index -l A -1 /tmp/tmpmp16eaic/CTRL_1_R1.fastq -2 /tmp/tmpmp16eaic/CTRL_1_R2.fastq -o output_JMML_nindex/CTRL_1 -p 4 2>/dev/null (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Exiting because a job execution failed. Look above for error message 2022-02-14 13:40:21,174 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: 'output_JMML_nindex/EXPR.csv'

Thanks, Lorena

hyunhwan-jeong commented 2 years ago

@lgallegovillar, are you still facing the issue? If so, could you share an error message when you put the following command line ./salmon/linux/bin/salmon quant -q -i reference/hs_index -l A -1 /tmp/tmpmp16eaic/CTRL_1_R1.fastq -2 /tmp/tmpmp16eaic/CTRL_1_R2.fastq -o output_JMML_nindex/CTRL_1 -p 4 2> /dev/null at the SalmonTE folder?

hyunhwan-jeong commented 2 years ago

Close due to no response